From b2e7be55427d0bc063373d45e505d0c6b5509ed2 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 28 Oct 2024 14:56:37 +0000
Subject: [PATCH 01/42] Fran's draft

---
 modules.json                                  |  5 ++
 .../fastqscreen/fastqscreen/environment.yml   |  9 ++
 .../nf-core/fastqscreen/fastqscreen/main.nf   | 54 ++++++++++++
 .../nf-core/fastqscreen/fastqscreen/meta.yml  | 44 ++++++++++
 .../fastqscreen/tests/main.nf.test            | 87 +++++++++++++++++++
 .../fastqscreen/tests/main.nf.test.snap       | 81 +++++++++++++++++
 .../fastqscreen/fastqscreen/tests/tags.yml    |  2 +
 nextflow.config                               |  1 +
 nextflow_schema.json                          |  5 ++
 workflows/seqinspector.nf                     | 12 +++
 10 files changed, 300 insertions(+)
 create mode 100644 modules/nf-core/fastqscreen/fastqscreen/environment.yml
 create mode 100644 modules/nf-core/fastqscreen/fastqscreen/main.nf
 create mode 100644 modules/nf-core/fastqscreen/fastqscreen/meta.yml
 create mode 100644 modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
 create mode 100644 modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml

diff --git a/modules.json b/modules.json
index 8e632d5..cb726e0 100644
--- a/modules.json
+++ b/modules.json
@@ -10,6 +10,11 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "fastqscreen/fastqscreen": {
+                        "branch": "master",
+                        "git_sha": "e1316cdcbef318b9cdfd35586423f8337c3d45f0",
+                        "installed_by": ["modules"]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
diff --git a/modules/nf-core/fastqscreen/fastqscreen/environment.yml b/modules/nf-core/fastqscreen/fastqscreen/environment.yml
new file mode 100644
index 0000000..5097f09
--- /dev/null
+++ b/modules/nf-core/fastqscreen/fastqscreen/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "fastqscreen_fastqscreen"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::fastq-screen=0.15.3"
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
new file mode 100644
index 0000000..8686f20
--- /dev/null
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -0,0 +1,54 @@
+process FASTQSCREEN_FASTQSCREEN {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0':
+        'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
+
+    input:
+    tuple val(meta), path(reads)  // .fastq files
+    path database
+
+    output:
+    tuple val(meta), path("*.txt") , emit: txt
+    tuple val(meta), path("*.png") , emit: png
+    tuple val(meta), path("*.html"), emit: html
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ""
+
+    """
+    fastq_screen --threads ${task.cpus} \\
+        --aligner bowtie2 \\
+        --conf ${database}/fastq_screen.conf \\
+        $reads \\
+        $args \\
+        --outdir .
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch test_1_screen.html
+    touch test_1_screen.png
+    touch test_1_screen.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
+    END_VERSIONS
+    """
+
+}
diff --git a/modules/nf-core/fastqscreen/fastqscreen/meta.yml b/modules/nf-core/fastqscreen/fastqscreen/meta.yml
new file mode 100644
index 0000000..623dacf
--- /dev/null
+++ b/modules/nf-core/fastqscreen/fastqscreen/meta.yml
@@ -0,0 +1,44 @@
+name: fastqscreen_fastqscreen
+description: Align reads to multiple reference genomes using fastq-screen
+keywords:
+  - align
+  - map
+  - fasta
+  - fastq
+  - genome
+  - reference
+tools:
+  - "fastqscreen":
+      description: "FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect."
+      homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/"
+      documentation: "https://stevenwingett.github.io/FastQ-Screen/"
+      tool_dev_url: "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.zip"
+      doi: "10.5281/zenodo.5838377"
+      licence: ["GPL-3.0-or-later"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+  - database:
+      type: directory
+      description: fastq screen database folder containing config file and index folders
+      pattern: "FastQ_Screen_Genomes"
+output:
+  - fastq_screen:
+      type: directory
+      description: Output fastq_screen file containing alignment statistics
+      pattern: "*.{_fq_screen}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@snesic"
+  - "@JPejovicApis"
diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
new file mode 100644
index 0000000..6d858a4
--- /dev/null
+++ b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
@@ -0,0 +1,87 @@
+nextflow_process {
+
+    name "Test Process FASTQSCREEN_FASTQSCREEN"
+    script "../main.nf"
+    process "FASTQSCREEN_FASTQSCREEN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bowtie2/build"
+    tag "fastqscreen"
+    tag "fastqscreen/buildfromindex"
+    tag "fastqscreen/fastqscreen"
+
+    setup {
+
+        run("BOWTIE2_BUILD") {
+            script "../../../bowtie2/build/main.nf"
+            process {
+                """
+                input[0] =  Channel.from([
+                                    [[id: "sarscov2"], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)],
+                                    [[id: "human"]   , file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)]
+                            ])
+                """
+            }
+        }
+
+        run("FASTQSCREEN_BUILDFROMINDEX") {
+            script "../../../fastqscreen/buildfromindex/main.nf"
+            process {
+                """
+                input[0] = BOWTIE2_BUILD.out.index.map{meta, index -> meta.id}.collect()
+                input[1] = BOWTIE2_BUILD.out.index.map{meta, index -> index}.collect()
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - human") {
+
+        when {
+            process {
+                """
+                input[0] =  [[ id:'test', single_end:true ],
+                             [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+                            ]
+                input[1] = FASTQSCREEN_BUILDFROMINDEX.out.database
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.version).match("version") },
+                { assert file(process.out.txt.get(0).get(1)).exists() },
+                { assert file(process.out.png.get(0).get(1)).exists() },
+                { assert file(process.out.html.get(0).get(1)).exists() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - human - stub") {
+
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] =  [[ id:'test', single_end:true ],
+                             [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+                            ]
+                input[1] = FASTQSCREEN_BUILDFROMINDEX.out.database
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap
new file mode 100644
index 0000000..b245019
--- /dev/null
+++ b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap
@@ -0,0 +1,81 @@
+{
+    "version": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-30T14:22:56.541922683"
+    },
+    "sarscov2 - human - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_1_screen.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_1_screen.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_1_screen.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,8ac0239b5103352958d9a9e562b23103"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_1_screen.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "png": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_1_screen.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_1_screen.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8ac0239b5103352958d9a9e562b23103"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-30T14:23:12.70922619"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml b/modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml
new file mode 100644
index 0000000..b03bfb4
--- /dev/null
+++ b/modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml
@@ -0,0 +1,2 @@
+fastqscreen/fastqscreen:
+  - "modules/nf-core/fastqscreen/fastqscreen/**"
diff --git a/nextflow.config b/nextflow.config
index 50c1ecb..210f03e 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -17,6 +17,7 @@ params {
     genome                     = null
     fasta                      = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
+    config_fastq_screen        = "${projectDir}/modules/nf-core/fastqscreen/references"
     igenomes_ignore            = false
 
     // MultiQC options
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 88fd607..f18a5f1 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -65,6 +65,11 @@
                     "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
                     "fa_icon": "far fa-file-code"
                 },
+                "config_fastq_screen": {
+                    "type": "string",
+                    "description": "path to directory with fastq_screen config (fastq_screen.conf)",
+                    "fa_icon": "fas fa-braille"
+                },
                 "igenomes_ignore": {
                     "type": "boolean",
                     "description": "Do not load the iGenomes reference config.",
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index ea62811..6ec9ca9 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -4,6 +4,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 include { FASTQC                        } from '../modules/nf-core/fastqc/main'
+include { FASTQSCREEN_FASTQSCREEN       } from '../modules/nf-core/fastqscreen/fastqscreen/main'
 
 include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc/main'
@@ -39,6 +40,17 @@ workflow SEQINSPECTOR {
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
+    //
+    // MODULE: Run FastQ Screen
+    //
+
+    FASTQSCREEN_FASTQSCREEN (
+        ch_samplesheet,
+        Channel.fromPath(params.config_fastq_screen)
+    )
+    ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
+    ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())
+
     //
     // Collate and save software versions
     //

From d833d913c5f0da94eeee1c9eaf44fd14c5fdb2fa Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 28 Oct 2024 15:02:08 +0000
Subject: [PATCH 02/42] nf-core modules update --> fastqscreen

---
 modules.json                                  |  2 +-
 .../fastqscreen/fastqscreen/environment.yml   |  3 +-
 .../nf-core/fastqscreen/fastqscreen/main.nf   | 10 +--
 .../nf-core/fastqscreen/fastqscreen/meta.yml  | 78 +++++++++++++------
 .../fastqscreen/tests/main.nf.test            | 32 +++++++-
 .../fastqscreen/tests/main.nf.test.snap       | 65 ++++++++++++++--
 .../fastqscreen/tests/nextflow.config         |  5 ++
 7 files changed, 157 insertions(+), 38 deletions(-)
 create mode 100644 modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config

diff --git a/modules.json b/modules.json
index cb726e0..f8b4855 100644
--- a/modules.json
+++ b/modules.json
@@ -12,7 +12,7 @@
                     },
                     "fastqscreen/fastqscreen": {
                         "branch": "master",
-                        "git_sha": "e1316cdcbef318b9cdfd35586423f8337c3d45f0",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
diff --git a/modules/nf-core/fastqscreen/fastqscreen/environment.yml b/modules/nf-core/fastqscreen/fastqscreen/environment.yml
index 5097f09..c63c61e 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/environment.yml
+++ b/modules/nf-core/fastqscreen/fastqscreen/environment.yml
@@ -1,9 +1,8 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "fastqscreen_fastqscreen"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "bioconda::fastq-screen=0.15.3"
+  - bioconda::perl-gdgraph=1.54
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 8686f20..88c4e5c 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -12,10 +12,11 @@ process FASTQSCREEN_FASTQSCREEN {
     path database
 
     output:
-    tuple val(meta), path("*.txt") , emit: txt
-    tuple val(meta), path("*.png") , emit: png
-    tuple val(meta), path("*.html"), emit: html
-    path "versions.yml"            , emit: versions
+    tuple val(meta), path("*.txt")     , emit: txt
+    tuple val(meta), path("*.png")     , emit: png  , optional: true
+    tuple val(meta), path("*.html")    , emit: html
+    tuple val(meta), path("*.fastq.gz"), emit: fastq, optional: true
+    path "versions.yml"                , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -30,7 +31,6 @@ process FASTQSCREEN_FASTQSCREEN {
         --conf ${database}/fastq_screen.conf \\
         $reads \\
         $args \\
-        --outdir .
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/fastqscreen/fastqscreen/meta.yml b/modules/nf-core/fastqscreen/fastqscreen/meta.yml
index 623dacf..39c86b4 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/meta.yml
+++ b/modules/nf-core/fastqscreen/fastqscreen/meta.yml
@@ -9,36 +9,70 @@ keywords:
   - reference
 tools:
   - "fastqscreen":
-      description: "FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect."
+      description: "FastQ Screen allows you to screen a library of sequences in FastQ
+        format against a set of sequence databases so you can see if the composition
+        of the library matches with what you expect."
       homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/"
       documentation: "https://stevenwingett.github.io/FastQ-Screen/"
       tool_dev_url: "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.zip"
       doi: "10.5281/zenodo.5838377"
       licence: ["GPL-3.0-or-later"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
-  - database:
-      type: directory
-      description: fastq screen database folder containing config file and index folders
-      pattern: "FastQ_Screen_Genomes"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+          respectively.
+  - - database:
+        type: directory
+        description: fastq screen database folder containing config file and index folders
+        pattern: "FastQ_Screen_Genomes"
 output:
-  - fastq_screen:
-      type: directory
-      description: Output fastq_screen file containing alignment statistics
-      pattern: "*.{_fq_screen}"
+  - txt:
+      - meta:
+          type: map
+          description: Groovy Map containing sample information
+      - "*.txt":
+          type: file
+          description: TXT file containing alignment statistics
+          pattern: "*.txt"
+  - png:
+      - meta:
+          type: map
+          description: Groovy Map containing sample information
+      - "*.png":
+          type: file
+          description: PNG file with graphical representation of alignments
+          pattern: "*.png"
+  - html:
+      - meta:
+          type: map
+          description: Groovy Map containing sample information
+      - "*.html":
+          type: file
+          description: HTML file containing mapping results as a table and graphical representation
+          pattern: "*.html"
+  - fastq:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.fastq.gz":
+          type: file
+          description: FastQ file containing reads that did not align to any database (optional)
+          pattern: "*.fastq.gz"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@snesic"
   - "@JPejovicApis"
diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
index 6d858a4..71230a2 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
+++ b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
@@ -10,6 +10,8 @@ nextflow_process {
     tag "fastqscreen"
     tag "fastqscreen/buildfromindex"
     tag "fastqscreen/fastqscreen"
+    tag "buildfromindex"
+    tag "modules_fastqscreen"
 
     setup {
 
@@ -52,7 +54,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.version).match("version") },
+                { assert snapshot(process.out.version).match() },
                 { assert file(process.out.txt.get(0).get(1)).exists() },
                 { assert file(process.out.png.get(0).get(1)).exists() },
                 { assert file(process.out.html.get(0).get(1)).exists() }
@@ -61,6 +63,34 @@ nextflow_process {
 
     }
 
+    test("sarscov2 - human - tags") {
+        config './nextflow.config'
+        when {
+            process {
+                """
+                input[0] =  [[ id:'test', single_end:false ],
+                             [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
+                            ]
+                input[1] = FASTQSCREEN_BUILDFROMINDEX.out.database
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.version,
+                    process.out.txt,
+                    process.out.fastq,
+                    path(process.out.html.get(0).get(1)).readLines()[0..10],
+                    path(process.out.png.get(0).get(1)).exists()
+                    ).match() }
+            )
+        }
+
+    }
+
     test("sarscov2 - human - stub") {
 
         options "-stub"
diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap
index b245019..2afffde 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap
+++ b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap
@@ -1,11 +1,56 @@
 {
-    "version": {
+    "sarscov2 - human": {
         "content": null,
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-04-30T14:22:56.541922683"
+        "timestamp": "2024-08-31T05:42:29.972454812"
+    },
+    "sarscov2 - human - tags": {
+        "content": [
+            null,
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_1_screen.txt:md5,b0b0ea58bc26ebaa4d573a85e7898f25"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test_1.tagged.fastq.gz:md5,f742b162c43ce28f80b89608d5c47f3d",
+                        "test_1.tagged_filter.fastq.gz:md5,28527a76bb0bb3fce0ee76afe01e90aa"
+                    ]
+                ]
+            ],
+            [
+                "<!DOCTYPE html>",
+                "<html>",
+                "",
+                "",
+                "<!-- Style, and Plotly code -->",
+                "<head>",
+                "\t<meta http-equiv=\"content-type\" content=\"text/html; charset=UTF-8\">",
+                "\t<title>FastQ Screen Processing Report - test_1.fastq.gz</title>",
+                "\t<style type=\"text/css\">",
+                "\t\tbody {",
+                "\t\t\tfont-family: Arial, sans-serif;"
+            ],
+            true
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-31T06:23:02.73675229"
     },
     "sarscov2 - human - stub": {
         "content": [
@@ -38,7 +83,13 @@
                     ]
                 ],
                 "3": [
+                    
+                ],
+                "4": [
                     "versions.yml:md5,8ac0239b5103352958d9a9e562b23103"
+                ],
+                "fastq": [
+                    
                 ],
                 "html": [
                     [
@@ -73,9 +124,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-04-30T14:23:12.70922619"
+        "timestamp": "2024-08-31T05:45:54.845041829"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config b/modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config
new file mode 100644
index 0000000..ccf580b
--- /dev/null
+++ b/modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: FASTQSCREEN_FASTQSCREEN {
+        ext.args = "--tag --filter 10"
+    }
+}

From 285a4b396885f85bb4f966d9220e3c884616a379 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 28 Oct 2024 15:15:37 +0000
Subject: [PATCH 03/42] add fastq_screen.conf

---
 conf/fastq_screen.conf | 64 ++++++++++++++++++++++++++++++++++++++++++
 nextflow.config        |  2 +-
 2 files changed, 65 insertions(+), 1 deletion(-)
 create mode 100644 conf/fastq_screen.conf

diff --git a/conf/fastq_screen.conf b/conf/fastq_screen.conf
new file mode 100644
index 0000000..aaa1964
--- /dev/null
+++ b/conf/fastq_screen.conf
@@ -0,0 +1,64 @@
+# This is a configuration file for fastq_screen
+
+###########
+## Bowtie #
+###########
+## If the bowtie binary is not in your PATH then you can
+## set this value to tell the program where to find it.
+## Uncomment the line below and set the appropriate location
+##
+
+#BOWTIE2 /sw/data/uppnex/reference/sw/mf/bioinfo-tools/pipelines/bowtie2/2.1.0/bowtie2
+
+############
+## Threads #
+############
+## Bowtie can be made to run across multiple CPU cores to
+## speed up your searches. Set this value to the number
+## of cores you want to use for your searches.
+
+#THREADS                16
+
+##############
+## Databases #
+##############
+## This section allows you to configure multiple databases
+## to search against in your screen.  For each database
+## you need to provide a database name (which can't contain
+## spaces) and the location of the bowtie indices which
+## you created for that database.
+##
+## The default entries shown below are only suggested examples
+## you can add as many DATABASE sections as you like, and you
+## can comment out or remove as many of the existing entries
+## as you like.
+##
+## Either the original bowtie or bowtie 2 may be used for the
+## mapping. Specify the aligner to use with the command line
+## flag --aligner with arguments 'bowtie' (default) or
+## 'bowtie2'.
+##
+## The configuration file may list paths to both bowtie and
+## bowtie2 indices, which are specified with either 'BOWTIE'
+## or 'BOWTIE2' after the path (leaving unspecified will
+## default to bowtie). While the configuration file may list
+## paths to both bowtie and bowtie2 indices, only one aligner
+## will be used for the mapping, as specified by the --aligner
+## flag.
+##
+## For example:
+## DATABASE     Human_Bowtie    /data/public/Genomes/Human_Bowtie/GRCh37/Homo_sapiens.GRCh37 BOWTIE
+## DATABASE     Human_Bowtie    /data/public/Genomes/Human_Bowtie/GRCh37/Homo_sapiens.GRCh37
+## DATABASE     Human_Bowtie2   /data/public/Genomes/Human_Bowtie2/GRCh37/Homo_sapiens.GRCh37 BOWTIE2
+
+## E. coli (igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1)
+DATABASE    Ecoli   ../../../modules/nf-core/fastqscreen/references/genome_ecoli/genome BOWTIE2
+
+## M. tuberculosis (igenomes/Mycobacterium_tuberculosis_H37RV/Ensembl/H37Rv.EB1)
+DATABASE    Tuberculosis   ../../../modules/nf-core/fastqscreen/references/genome_tuberculosis/genome BOWTIE2
+
+## PhiX (/igenomes/PhiX/Illumina/RTA)
+DATABASE    PhiX   ../../../modules/nf-core/fastqscreen/references/genome_phix/genome BOWTIE2
+
+##S. cerevisiae (igenomes/Saccharomyces_cerevisiae/Ensembl/EF4)
+DATABASE    Scerevisiae   ../../../modules/nf-core/fastqscreen/references/genome_cerevisiae/genome BOWTIE2
diff --git a/nextflow.config b/nextflow.config
index 210f03e..1600a70 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -17,7 +17,7 @@ params {
     genome                     = null
     fasta                      = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
-    config_fastq_screen        = "${projectDir}/modules/nf-core/fastqscreen/references"
+    config_fastq_screen        = "${projectDir}/conf"
     igenomes_ignore            = false
 
     // MultiQC options

From a0815635ea42aca9b42488ad5163ba96f9c75267 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 09:57:43 +0100
Subject: [PATCH 04/42] hack out some ideas

---
 workflows/seqinspector.nf | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 6ec9ca9..a0e9d90 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -44,6 +44,14 @@ workflow SEQINSPECTOR {
     // MODULE: Run FastQ Screen
     //
 
+    Channel.fromPath(params.config_fastq_screen)
+        .splitText()
+    .filter // TODO anything that doesn't have "database"
+        .collect()
+
+    file(list_of_configs)
+    // TODO write configs to text file?
+
     FASTQSCREEN_FASTQSCREEN (
         ch_samplesheet,
         Channel.fromPath(params.config_fastq_screen)

From 7a4dccd0bf9b5abe66e66af52e8c196b8e8d232d Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 10:33:48 +0100
Subject: [PATCH 05/42] test: Update path for database

---
 conf/fastq_screen.conf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/fastq_screen.conf b/conf/fastq_screen.conf
index aaa1964..f170f28 100644
--- a/conf/fastq_screen.conf
+++ b/conf/fastq_screen.conf
@@ -52,10 +52,10 @@
 ## DATABASE     Human_Bowtie2   /data/public/Genomes/Human_Bowtie2/GRCh37/Homo_sapiens.GRCh37 BOWTIE2
 
 ## E. coli (igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1)
-DATABASE    Ecoli   ../../../modules/nf-core/fastqscreen/references/genome_ecoli/genome BOWTIE2
+DATABASE    Ecoli   ./database/EB1 BOWTIE2
 
 ## M. tuberculosis (igenomes/Mycobacterium_tuberculosis_H37RV/Ensembl/H37Rv.EB1)
-DATABASE    Tuberculosis   ../../../modules/nf-core/fastqscreen/references/genome_tuberculosis/genome BOWTIE2
+DATABASE    Tuberculosis   ./references/genome_tuberculosis/genome BOWTIE2
 
 ## PhiX (/igenomes/PhiX/Illumina/RTA)
 DATABASE    PhiX   ../../../modules/nf-core/fastqscreen/references/genome_phix/genome BOWTIE2

From f0b23a78de7ac4df475a28c0af2aad8030ef67c4 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 11:14:00 +0100
Subject: [PATCH 06/42] Hack ideas

---
 workflows/seqinspector.nf | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index a0e9d90..20bec7a 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -46,15 +46,23 @@ workflow SEQINSPECTOR {
 
     Channel.fromPath(params.config_fastq_screen)
         .splitText()
-    .filter // TODO anything that doesn't have "database"
+        .filter(!it.contains('database')) // TODO anything that doesn't have "database"
         .collect()
+        .view()
 
-    file(list_of_configs)
-    // TODO write configs to text file?
+    if(params.database_tar.endsWith('.tar.gz')) {
+        UNTAR (
+            params.database_tar,
+        )
+        ch_database = UNTAR.out.untar
+    } else {
+        ch_database = params.database_tar
+    }
 
     FASTQSCREEN_FASTQSCREEN (
         ch_samplesheet,
-        Channel.fromPath(params.config_fastq_screen)
+        Channel.fromPath(params.config_fastq_screen),
+        ch_database,
     )
     ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
     ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())

From 3ea8d8b73e97f8e38ee5ae500ef8cc3c2f53567d Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 11:36:11 +0100
Subject: [PATCH 07/42] Initial datasheet example

---
 assets/databasesheet.csv | 9 +++++++++
 1 file changed, 9 insertions(+)
 create mode 100644 assets/databasesheet.csv

diff --git a/assets/databasesheet.csv b/assets/databasesheet.csv
new file mode 100644
index 0000000..9923e8d
--- /dev/null
+++ b/assets/databasesheet.csv
@@ -0,0 +1,9 @@
+name,index,aligner
+Ecoli,./database/EB1,BOWTIE2
+Ecoli,s3://ngi-igenomes/database/EB1,BOWTIE2
+## M. tuberculosis (igenomes/Mycobacterium_tuberculosis_H37RV/Ensembl/H37Rv.EB1)
+Tuberculosis,./references/genome_tuberculosis/genome,BOWTIE2
+## PhiX (/igenomes/PhiX/Illumina/RTA)
+PhiX,../../../modules/nf-core/fastqscreen/references/genome_phix/genome,BOWTIE2
+##S. cerevisiae (igenomes/Saccharomyces_cerevisiae/Ensembl/EF4)
+Scerevisiae,../../../modules/nf-core/fastqscreen/references/genome_cerevisiae/genome,BOWTIE2

From fea850fff822a6baa47d6ad62137c6d28ccd769e Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 11:44:19 +0100
Subject: [PATCH 08/42] refactor: Rework fastqscreen with new ideas

---
 assets/databasesheet.csv                      |  9 +----
 assets/schema_database.json                   | 32 +++++++++++++++
 conf/test.config                              |  1 +
 main.nf                                       |  7 +++-
 modules.json                                  |  3 +-
 .../fastqscreen/fastqscreen-fastqscreen.diff  | 40 +++++++++++++++++++
 .../nf-core/fastqscreen/fastqscreen/main.nf   | 13 +++---
 workflows/seqinspector.nf                     | 23 ++++-------
 8 files changed, 96 insertions(+), 32 deletions(-)
 create mode 100644 assets/schema_database.json
 create mode 100644 modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff

diff --git a/assets/databasesheet.csv b/assets/databasesheet.csv
index 9923e8d..f300a04 100644
--- a/assets/databasesheet.csv
+++ b/assets/databasesheet.csv
@@ -1,9 +1,2 @@
 name,index,aligner
-Ecoli,./database/EB1,BOWTIE2
-Ecoli,s3://ngi-igenomes/database/EB1,BOWTIE2
-## M. tuberculosis (igenomes/Mycobacterium_tuberculosis_H37RV/Ensembl/H37Rv.EB1)
-Tuberculosis,./references/genome_tuberculosis/genome,BOWTIE2
-## PhiX (/igenomes/PhiX/Illumina/RTA)
-PhiX,../../../modules/nf-core/fastqscreen/references/genome_phix/genome,BOWTIE2
-##S. cerevisiae (igenomes/Saccharomyces_cerevisiae/Ensembl/EF4)
-Scerevisiae,../../../modules/nf-core/fastqscreen/references/genome_cerevisiae/genome,BOWTIE2
+PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,BOWTIE2
diff --git a/assets/schema_database.json b/assets/schema_database.json
new file mode 100644
index 0000000..df54284
--- /dev/null
+++ b/assets/schema_database.json
@@ -0,0 +1,32 @@
+{
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/seqinspector/master/assets/schema_database.json",
+    "title": "nf-core/seqinspector pipeline - params.databasesheet schema",
+    "description": "Schema for the file provided with params.databasesheet",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "name": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "The database name for fastq screen",
+                "meta": ["database_name"]
+            },
+            "index": {
+                "type": "string",
+                "format": "file-path",
+                "exists": true,
+                "pattern": "^\\S+$",
+                "errorMessage": "Path to the aligner index"
+            },
+            "aligner": {
+                "type": "string",
+                "enum": ["BOWTIE", "BOWTIE2", "BWA", "MINIMAP2"],
+                "errorMessage": "Specify the aligner to use for the mapping. Valid arguments are 'bowtie', bowtie2' (default), 'bwa' or 'minimap2'.",
+                "meta": ["database_notes"]
+            }
+        },
+        "required": ["name", "index", "aligner"]
+    }
+}
diff --git a/conf/test.config b/conf/test.config
index 76a7ad0..c032431 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -26,6 +26,7 @@ params {
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
+    database_sheet = "${projectDir}/assets/databasesheet.csv"
 
     // Genome references
     genome = 'R64-1-1'
diff --git a/main.nf b/main.nf
index 85027a4..79e8a33 100644
--- a/main.nf
+++ b/main.nf
@@ -44,6 +44,7 @@ workflow NFCORE_SEQINSPECTOR {
 
     take:
     samplesheet // channel: samplesheet read in from --input
+    database_sheet
 
     main:
 
@@ -51,7 +52,8 @@ workflow NFCORE_SEQINSPECTOR {
     // WORKFLOW: Run pipeline
     //
     SEQINSPECTOR (
-        samplesheet
+        samplesheet,
+        database_sheet,
     )
     emit:
     global_report   = SEQINSPECTOR.out.global_report    // channel: /path/to/multiqc_report.html
@@ -83,7 +85,8 @@ workflow {
     // WORKFLOW: Run main workflow
     //
     NFCORE_SEQINSPECTOR (
-        PIPELINE_INITIALISATION.out.samplesheet
+        PIPELINE_INITIALISATION.out.samplesheet,
+        params.database_sheet,
     )
     //
     // SUBWORKFLOW: Run completion tasks
diff --git a/modules.json b/modules.json
index f8b4855..cb48bc3 100644
--- a/modules.json
+++ b/modules.json
@@ -13,7 +13,8 @@
                     "fastqscreen/fastqscreen": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff"
                     },
                     "multiqc": {
                         "branch": "master",
diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
new file mode 100644
index 0000000..e8ff52e
--- /dev/null
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -0,0 +1,40 @@
+Changes in module 'nf-core/fastqscreen/fastqscreen'
+'modules/nf-core/fastqscreen/fastqscreen/environment.yml' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
+Changes in 'fastqscreen/fastqscreen/main.nf':
+--- modules/nf-core/fastqscreen/fastqscreen/main.nf
++++ modules/nf-core/fastqscreen/fastqscreen/main.nf
+@@ -9,7 +9,7 @@
+ 
+     input:
+     tuple val(meta), path(reads)  // .fastq files
+-    path database
++    tuple val(meta), path(database) // [[database_name,  database_notes], database_path]
+ 
+     output:
+     tuple val(meta), path("*.txt")     , emit: txt
+@@ -24,11 +24,14 @@
+     script:
+     def prefix = task.ext.prefix ?: "${meta.id}"
+     def args = task.ext.args ?: ""
++    // 'Database name','Genome path and basename','Notes'
++    """
++    fastq_screen --add_genome \\
++        '$meta.database_name','$database_path','$meta.database_notes'
+ 
+-    """
+-    fastq_screen --threads ${task.cpus} \\
+-        --aligner bowtie2 \\
+-        --conf ${database}/fastq_screen.conf \\
++    fastq_screen
++        --conf fastq_screen.conf \\
++        --threads ${task.cpus} \\
+         $reads \\
+         $args \\
+ 
+
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
+************************************************************
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 88c4e5c..0106e6e 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -9,7 +9,7 @@ process FASTQSCREEN_FASTQSCREEN {
 
     input:
     tuple val(meta), path(reads)  // .fastq files
-    path database
+    tuple val(meta), path(database) // [[database_name,  database_notes], database_path]
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt
@@ -24,11 +24,14 @@ process FASTQSCREEN_FASTQSCREEN {
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def args = task.ext.args ?: ""
-
+    // 'Database name','Genome path and basename','Notes'
     """
-    fastq_screen --threads ${task.cpus} \\
-        --aligner bowtie2 \\
-        --conf ${database}/fastq_screen.conf \\
+    fastq_screen --add_genome \\
+        '$meta.database_name','$database_path','$meta.database_notes'
+
+    fastq_screen
+        --conf fastq_screen.conf \\
+        --threads ${task.cpus} \\
         $reads \\
         $args \\
 
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 20bec7a..d283c2a 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -1,3 +1,5 @@
+include { samplesheetToList } from 'plugin/nf-schema'
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS
@@ -24,6 +26,8 @@ workflow SEQINSPECTOR {
 
     take:
     ch_samplesheet // channel: samplesheet read in from --input
+    ch_databasesheet // channel: database sheet read in from --database_sheet
+
     main:
 
     ch_versions            = Channel.empty()
@@ -43,26 +47,13 @@ workflow SEQINSPECTOR {
     //
     // MODULE: Run FastQ Screen
     //
-
-    Channel.fromPath(params.config_fastq_screen)
-        .splitText()
-        .filter(!it.contains('database')) // TODO anything that doesn't have "database"
-        .collect()
+    ch_databases = Channel
+        .fromList(samplesheetToList(ch_databasesheet, "${projectDir}/assets/schema_database.json"))
         .view()
 
-    if(params.database_tar.endsWith('.tar.gz')) {
-        UNTAR (
-            params.database_tar,
-        )
-        ch_database = UNTAR.out.untar
-    } else {
-        ch_database = params.database_tar
-    }
-
     FASTQSCREEN_FASTQSCREEN (
         ch_samplesheet,
-        Channel.fromPath(params.config_fastq_screen),
-        ch_database,
+        ch_databases,
     )
     ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
     ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())

From 600c2fb4d8e6150fe6111f55f5f9321d9fde4f26 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 12:20:59 +0100
Subject: [PATCH 09/42] chore: Bump fastq-screen

---
 modules/nf-core/fastqscreen/fastqscreen/environment.yml | 8 +++++++-
 modules/nf-core/fastqscreen/fastqscreen/main.nf         | 4 ++--
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/environment.yml b/modules/nf-core/fastqscreen/fastqscreen/environment.yml
index c63c61e..7d4c892 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/environment.yml
+++ b/modules/nf-core/fastqscreen/fastqscreen/environment.yml
@@ -4,5 +4,11 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::fastq-screen=0.15.3"
+  - bioconda::fastq-screen=0.16.0
   - bioconda::perl-gdgraph=1.54
+  # - gzip
+  # - SAMtools
+  # - bowtie
+  # - bowtie2
+  # - bwa
+  # - bismark
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 0106e6e..c792707 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -4,8 +4,8 @@ process FASTQSCREEN_FASTQSCREEN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0':
-        'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data' :
+        'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
 
     input:
     tuple val(meta), path(reads)  // .fastq files

From 89e67fa7534c2654e4a43e81953e1ba611c17df9 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 13:00:00 +0100
Subject: [PATCH 10/42] fix: Give up on fastq_screen writing it's own config

---
 modules/nf-core/fastqscreen/fastqscreen/main.nf | 12 +++++++-----
 workflows/seqinspector.nf                       |  1 -
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index c792707..771c6ac 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -1,5 +1,5 @@
 process FASTQSCREEN_FASTQSCREEN {
-    tag "$meta.id"
+    tag "$meta.id | $meta2.database_name"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
@@ -9,7 +9,7 @@ process FASTQSCREEN_FASTQSCREEN {
 
     input:
     tuple val(meta), path(reads)  // .fastq files
-    tuple val(meta), path(database) // [[database_name,  database_notes], database_path]
+    tuple val(meta2), path(database) // [[database_name,  database_notes], database_path]
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt
@@ -26,12 +26,14 @@ process FASTQSCREEN_FASTQSCREEN {
     def args = task.ext.args ?: ""
     // 'Database name','Genome path and basename','Notes'
     """
-    fastq_screen --add_genome \\
-        '$meta.database_name','$database_path','$meta.database_notes'
+    echo "Writing config"
+    echo "DATABASE    ${meta2.database_name}    ./${database}/genome    ${meta2.database_notes}" > fastq_screen.conf
+    echo "Wrote config"
 
-    fastq_screen
+    fastq_screen \\
         --conf fastq_screen.conf \\
         --threads ${task.cpus} \\
+        --aligner ${meta2.database_notes.toLowerCase()} \\
         $reads \\
         $args \\
 
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index d283c2a..ad6dc2c 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -49,7 +49,6 @@ workflow SEQINSPECTOR {
     //
     ch_databases = Channel
         .fromList(samplesheetToList(ch_databasesheet, "${projectDir}/assets/schema_database.json"))
-        .view()
 
     FASTQSCREEN_FASTQSCREEN (
         ch_samplesheet,

From a6565f78155c4fae14031af4a9d2a6afe72b111b Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 13:05:42 +0100
Subject: [PATCH 11/42] test: Update databases

---
 assets/databasesheet.csv                        | 2 ++
 modules/nf-core/fastqscreen/fastqscreen/main.nf | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/assets/databasesheet.csv b/assets/databasesheet.csv
index f300a04..150f831 100644
--- a/assets/databasesheet.csv
+++ b/assets/databasesheet.csv
@@ -1,2 +1,4 @@
 name,index,aligner
+Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/,BOWTIE2
 PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,BOWTIE2
+Scerevisiae,s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/NCBI/build3.1/Sequence/Bowtie2Index/,BOWTIE2
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 771c6ac..eab5afb 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -35,7 +35,7 @@ process FASTQSCREEN_FASTQSCREEN {
         --threads ${task.cpus} \\
         --aligner ${meta2.database_notes.toLowerCase()} \\
         $reads \\
-        $args \\
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From 4af6dd4bf344612bc92ffa7ae34a8952740ed46e Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 14:32:09 +0100
Subject: [PATCH 12/42] fix: Run every sample and every DB

---
 modules/nf-core/fastqscreen/fastqscreen/main.nf | 4 ++--
 workflows/seqinspector.nf                       | 3 +--
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index eab5afb..5037db6 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -8,8 +8,8 @@ process FASTQSCREEN_FASTQSCREEN {
         'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
 
     input:
-    tuple val(meta), path(reads)  // .fastq files
-    tuple val(meta2), path(database) // [[database_name,  database_notes], database_path]
+    // NOTE for meta 2 and database [[database_name,  database_notes], database_path]
+    tuple val(meta), path(reads), val(meta2), path(database)
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index ad6dc2c..75ea2d6 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -51,8 +51,7 @@ workflow SEQINSPECTOR {
         .fromList(samplesheetToList(ch_databasesheet, "${projectDir}/assets/schema_database.json"))
 
     FASTQSCREEN_FASTQSCREEN (
-        ch_samplesheet,
-        ch_databases,
+        ch_samplesheet.combine(ch_databases)
     )
     ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
     ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())

From 46805e871bcd352f949d49df7f8eeaab1475d291 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 13:00:00 +0100
Subject: [PATCH 13/42] fix: Give up on fastq_screen writing it's own config

---
 .../fastqscreen/fastqscreen-fastqscreen.diff  | 51 +++++++++++++++----
 .../nf-core/fastqscreen/fastqscreen/main.nf   | 14 ++---
 workflows/seqinspector.nf                     |  1 -
 3 files changed, 50 insertions(+), 16 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
index e8ff52e..e2f8a54 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -1,37 +1,70 @@
 Changes in module 'nf-core/fastqscreen/fastqscreen'
-'modules/nf-core/fastqscreen/fastqscreen/environment.yml' is unchanged
+Changes in 'fastqscreen/fastqscreen/environment.yml':
+--- modules/nf-core/fastqscreen/fastqscreen/environment.yml
++++ modules/nf-core/fastqscreen/fastqscreen/environment.yml
+@@ -4,5 +4,11 @@
+   - conda-forge
+   - bioconda
+ dependencies:
+-  - "bioconda::fastq-screen=0.15.3"
++  - bioconda::fastq-screen=0.16.0
+   - bioconda::perl-gdgraph=1.54
++  # - gzip
++  # - SAMtools
++  # - bowtie
++  # - bowtie2
++  # - bwa
++  # - bismark
+
 'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
 Changes in 'fastqscreen/fastqscreen/main.nf':
 --- modules/nf-core/fastqscreen/fastqscreen/main.nf
 +++ modules/nf-core/fastqscreen/fastqscreen/main.nf
-@@ -9,7 +9,7 @@
+@@ -1,15 +1,15 @@
+ process FASTQSCREEN_FASTQSCREEN {
+-    tag "$meta.id"
++    tag "$meta.id | $meta2.database_name"
+     label 'process_medium'
+ 
+     conda "${moduleDir}/environment.yml"
+     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+-        'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0':
+-        'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
++        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data' :
++        'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
  
      input:
-     tuple val(meta), path(reads)  // .fastq files
+-    tuple val(meta), path(reads)  // .fastq files
 -    path database
-+    tuple val(meta), path(database) // [[database_name,  database_notes], database_path]
++    // NOTE for meta 2 and database [[database_name,  database_notes], database_path]
++    tuple val(meta), path(reads), val(meta2), path(database)
  
      output:
      tuple val(meta), path("*.txt")     , emit: txt
-@@ -24,11 +24,14 @@
+@@ -24,13 +24,18 @@
      script:
      def prefix = task.ext.prefix ?: "${meta.id}"
      def args = task.ext.args ?: ""
 +    // 'Database name','Genome path and basename','Notes'
 +    """
-+    fastq_screen --add_genome \\
-+        '$meta.database_name','$database_path','$meta.database_notes'
++    echo "Writing config"
++    echo "DATABASE    ${meta2.database_name}    ./${database}/genome    ${meta2.database_notes}" > fastq_screen.conf
++    echo "Wrote config"
  
 -    """
 -    fastq_screen --threads ${task.cpus} \\
 -        --aligner bowtie2 \\
 -        --conf ${database}/fastq_screen.conf \\
-+    fastq_screen
++    fastq_screen \\
 +        --conf fastq_screen.conf \\
 +        --threads ${task.cpus} \\
++        --aligner ${meta2.database_notes.toLowerCase()} \\
          $reads \\
-         $args \\
+-        $args \\
++        $args
  
+     cat <<-END_VERSIONS > versions.yml
+     "${task.process}":
 
 'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' is unchanged
 'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index c792707..eab5afb 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -1,5 +1,5 @@
 process FASTQSCREEN_FASTQSCREEN {
-    tag "$meta.id"
+    tag "$meta.id | $meta2.database_name"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
@@ -9,7 +9,7 @@ process FASTQSCREEN_FASTQSCREEN {
 
     input:
     tuple val(meta), path(reads)  // .fastq files
-    tuple val(meta), path(database) // [[database_name,  database_notes], database_path]
+    tuple val(meta2), path(database) // [[database_name,  database_notes], database_path]
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt
@@ -26,14 +26,16 @@ process FASTQSCREEN_FASTQSCREEN {
     def args = task.ext.args ?: ""
     // 'Database name','Genome path and basename','Notes'
     """
-    fastq_screen --add_genome \\
-        '$meta.database_name','$database_path','$meta.database_notes'
+    echo "Writing config"
+    echo "DATABASE    ${meta2.database_name}    ./${database}/genome    ${meta2.database_notes}" > fastq_screen.conf
+    echo "Wrote config"
 
-    fastq_screen
+    fastq_screen \\
         --conf fastq_screen.conf \\
         --threads ${task.cpus} \\
+        --aligner ${meta2.database_notes.toLowerCase()} \\
         $reads \\
-        $args \\
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index d283c2a..ad6dc2c 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -49,7 +49,6 @@ workflow SEQINSPECTOR {
     //
     ch_databases = Channel
         .fromList(samplesheetToList(ch_databasesheet, "${projectDir}/assets/schema_database.json"))
-        .view()
 
     FASTQSCREEN_FASTQSCREEN (
         ch_samplesheet,

From 4001a50caae62121dc8778cc88dc7a596d8a2242 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 13:05:42 +0100
Subject: [PATCH 14/42] test: Update databases

---
 assets/databasesheet.csv | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/assets/databasesheet.csv b/assets/databasesheet.csv
index f300a04..150f831 100644
--- a/assets/databasesheet.csv
+++ b/assets/databasesheet.csv
@@ -1,2 +1,4 @@
 name,index,aligner
+Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/,BOWTIE2
 PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,BOWTIE2
+Scerevisiae,s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/NCBI/build3.1/Sequence/Bowtie2Index/,BOWTIE2

From 7ebb6c144666ae62c2071a3e4c56ef7a4f70004b Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 14:32:09 +0100
Subject: [PATCH 15/42] fix: Run every sample and every DB

---
 modules/nf-core/fastqscreen/fastqscreen/main.nf | 4 ++--
 workflows/seqinspector.nf                       | 3 +--
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index eab5afb..5037db6 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -8,8 +8,8 @@ process FASTQSCREEN_FASTQSCREEN {
         'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
 
     input:
-    tuple val(meta), path(reads)  // .fastq files
-    tuple val(meta2), path(database) // [[database_name,  database_notes], database_path]
+    // NOTE for meta 2 and database [[database_name,  database_notes], database_path]
+    tuple val(meta), path(reads), val(meta2), path(database)
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index ad6dc2c..75ea2d6 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -51,8 +51,7 @@ workflow SEQINSPECTOR {
         .fromList(samplesheetToList(ch_databasesheet, "${projectDir}/assets/schema_database.json"))
 
     FASTQSCREEN_FASTQSCREEN (
-        ch_samplesheet,
-        ch_databases,
+        ch_samplesheet.combine(ch_databases)
     )
     ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
     ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())

From e56018190e120c3d39acc3c255ee5039b3db0f6e Mon Sep 17 00:00:00 2001
From: FranBonath <franziska.bonath@scilifelab.se>
Date: Wed, 30 Oct 2024 12:02:01 +0100
Subject: [PATCH 16/42] adding fastqscreen database parameter, updating docs

---
 CHANGELOG.md                |  1 +
 CITATIONS.md                |  4 ++++
 assets/schema_database.json |  4 ++--
 docs/output.md              | 17 +++++++++++++++++
 main.nf                     |  2 +-
 nextflow.config             |  3 +++
 nextflow_schema.json        |  9 ++++++++-
 workflows/seqinspector.nf   |  4 ++--
 8 files changed, 38 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b0b12de..e396512 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
 - [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
 - [#49](https://github.com/nf-core/seqinspector/pull/49) Merge with template 3.0.2.
+- [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing
 
 ### `Fixed`
 
diff --git a/CITATIONS.md b/CITATIONS.md
index ecbfb16..9cbd9f8 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -14,6 +14,10 @@
 
 > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
+- [Fastqscreen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)
+
+> Wingett SW and Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control [version 2; referees: 4 approved]. F1000Research 2018, 7:1338 (https://doi.org/10.12688/f1000research.15931.2)
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
diff --git a/assets/schema_database.json b/assets/schema_database.json
index df54284..e735ea4 100644
--- a/assets/schema_database.json
+++ b/assets/schema_database.json
@@ -1,8 +1,8 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/seqinspector/master/assets/schema_database.json",
-    "title": "nf-core/seqinspector pipeline - params.databasesheet schema",
-    "description": "Schema for the file provided with params.databasesheet",
+    "title": "nf-core/seqinspector pipeline - params.fastqscreen_databasesheet schema",
+    "description": "Schema for the file provided with params.fastq_screen_databasesheet",
     "type": "array",
     "items": {
         "type": "object",
diff --git a/docs/output.md b/docs/output.md
index e14c3ad..337037d 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -11,6 +11,7 @@ The directories listed below will be created in the results directory after the
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
 - [FastQC](#fastqc) - Raw read QC
+- [Fastqscreen](#fastqscreen) - mapping against a set of references for basic contamination QC
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
@@ -27,6 +28,22 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
+### FASTQSCREEN
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `fastqc/`
+  - `*_screen.html`: Interactive graphical fastqscreen report which summaries the mapping of your sequences against each of your libraries.
+  - `*_screen.pdf`: Static graphical fastqscreen report which summaries the mapping of your sequences against each of your libraries.
+  - `*_screen.txt` : text based fastqscreen report which summaries the mapping of your sequences against each of your libraries.
+
+</details>
+
+[Fastqscreen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) allows you to set up a standard set of libraries against which all of your sequences can be searched. Your search libraries might contain the genomes of all of the organisms you work on, along with PhiX, Vectors or other contaminants commonly seen in sequencing experiments.
+
+It requires the supply of referenced (databases) in a config file. In order to parallelize the mapping of the different samples, in seqinspector, this a fastqscreen config file is generated for every sample/reference combination.
+
 ### MultiQC
 
 nf-core/seqinspector will generate the following MultiQC reports:
diff --git a/main.nf b/main.nf
index 79e8a33..cd4af96 100644
--- a/main.nf
+++ b/main.nf
@@ -86,7 +86,7 @@ workflow {
     //
     NFCORE_SEQINSPECTOR (
         PIPELINE_INITIALISATION.out.samplesheet,
-        params.database_sheet,
+        params.fastqscreen_database_sheet,
     )
     //
     // SUBWORKFLOW: Run completion tasks
diff --git a/nextflow.config b/nextflow.config
index 1600a70..42372b9 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -20,6 +20,9 @@ params {
     config_fastq_screen        = "${projectDir}/conf"
     igenomes_ignore            = false
 
+    // Fastqscreen options
+    fastqscreen_database_sheet = './assets/databasesheet.csv'
+
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index f18a5f1..8331a2e 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -68,7 +68,8 @@
                 "config_fastq_screen": {
                     "type": "string",
                     "description": "path to directory with fastq_screen config (fastq_screen.conf)",
-                    "fa_icon": "fas fa-braille"
+                    "fa_icon": "fas fa-braille",
+                    "default": "/Users/franziska.franziska/workspace/seqinspector/conf"
                 },
                 "igenomes_ignore": {
                     "type": "boolean",
@@ -84,6 +85,12 @@
                     "fa_icon": "fas fa-ban",
                     "hidden": true,
                     "default": "s3://ngi-igenomes/igenomes/"
+                },
+                "fastqscreen_database_sheet": {
+                    "type": "string",
+                    "default": "./assets/databasesheet.csv",
+                    "fa_icon": "fas fa-search",
+                    "description": "list of reference genomes (databases) to be mapped against in fastqscreen"
                 }
             }
         },
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 75ea2d6..535448d 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -26,7 +26,7 @@ workflow SEQINSPECTOR {
 
     take:
     ch_samplesheet // channel: samplesheet read in from --input
-    ch_databasesheet // channel: database sheet read in from --database_sheet
+    ch_fastqscreen_databasesheet // channel: database sheet read in from --fastqscreen_database_sheet
 
     main:
 
@@ -48,7 +48,7 @@ workflow SEQINSPECTOR {
     // MODULE: Run FastQ Screen
     //
     ch_databases = Channel
-        .fromList(samplesheetToList(ch_databasesheet, "${projectDir}/assets/schema_database.json"))
+        .fromList(samplesheetToList(ch_fastqscreen_databasesheet, "${projectDir}/assets/schema_database.json"))
 
     FASTQSCREEN_FASTQSCREEN (
         ch_samplesheet.combine(ch_databases)

From effa9c9d1b886f1b3e79e2ad8cff4c79b8ce4f16 Mon Sep 17 00:00:00 2001
From: Franziska Bonath <41994400+FranBonath@users.noreply.github.com>
Date: Thu, 7 Nov 2024 10:43:32 +0100
Subject: [PATCH 17/42] remove absolute path of fastqscreen config

---
 nextflow_schema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 8331a2e..ba1304e 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -69,7 +69,7 @@
                     "type": "string",
                     "description": "path to directory with fastq_screen config (fastq_screen.conf)",
                     "fa_icon": "fas fa-braille",
-                    "default": "/Users/franziska.franziska/workspace/seqinspector/conf"
+                    "default": "./conf"
                 },
                 "igenomes_ignore": {
                     "type": "boolean",

From a2f2dfc50c4952ea5a67b4399f751203a7db12dc Mon Sep 17 00:00:00 2001
From: Franziska Bonath <41994400+FranBonath@users.noreply.github.com>
Date: Thu, 7 Nov 2024 10:47:53 +0100
Subject: [PATCH 18/42] remove "projectDir" from path for fastqscreen config in
 nextflow.config

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 42372b9..791764c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -17,7 +17,7 @@ params {
     genome                     = null
     fasta                      = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
-    config_fastq_screen        = "${projectDir}/conf"
+    config_fastq_screen        = "./conf"
     igenomes_ignore            = false
 
     // Fastqscreen options

From 2c4432061c578b90b42db70b253fb115e3114437 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 12:03:05 +0000
Subject: [PATCH 19/42] remove conf/fastq_screen.conf and it's references, as
 the file is built by the process on the fly

---
 conf/fastq_screen.conf | 64 ------------------------------------------
 nextflow.config        |  1 -
 nextflow_schema.json   |  6 ----
 3 files changed, 71 deletions(-)
 delete mode 100644 conf/fastq_screen.conf

diff --git a/conf/fastq_screen.conf b/conf/fastq_screen.conf
deleted file mode 100644
index f170f28..0000000
--- a/conf/fastq_screen.conf
+++ /dev/null
@@ -1,64 +0,0 @@
-# This is a configuration file for fastq_screen
-
-###########
-## Bowtie #
-###########
-## If the bowtie binary is not in your PATH then you can
-## set this value to tell the program where to find it.
-## Uncomment the line below and set the appropriate location
-##
-
-#BOWTIE2 /sw/data/uppnex/reference/sw/mf/bioinfo-tools/pipelines/bowtie2/2.1.0/bowtie2
-
-############
-## Threads #
-############
-## Bowtie can be made to run across multiple CPU cores to
-## speed up your searches. Set this value to the number
-## of cores you want to use for your searches.
-
-#THREADS                16
-
-##############
-## Databases #
-##############
-## This section allows you to configure multiple databases
-## to search against in your screen.  For each database
-## you need to provide a database name (which can't contain
-## spaces) and the location of the bowtie indices which
-## you created for that database.
-##
-## The default entries shown below are only suggested examples
-## you can add as many DATABASE sections as you like, and you
-## can comment out or remove as many of the existing entries
-## as you like.
-##
-## Either the original bowtie or bowtie 2 may be used for the
-## mapping. Specify the aligner to use with the command line
-## flag --aligner with arguments 'bowtie' (default) or
-## 'bowtie2'.
-##
-## The configuration file may list paths to both bowtie and
-## bowtie2 indices, which are specified with either 'BOWTIE'
-## or 'BOWTIE2' after the path (leaving unspecified will
-## default to bowtie). While the configuration file may list
-## paths to both bowtie and bowtie2 indices, only one aligner
-## will be used for the mapping, as specified by the --aligner
-## flag.
-##
-## For example:
-## DATABASE     Human_Bowtie    /data/public/Genomes/Human_Bowtie/GRCh37/Homo_sapiens.GRCh37 BOWTIE
-## DATABASE     Human_Bowtie    /data/public/Genomes/Human_Bowtie/GRCh37/Homo_sapiens.GRCh37
-## DATABASE     Human_Bowtie2   /data/public/Genomes/Human_Bowtie2/GRCh37/Homo_sapiens.GRCh37 BOWTIE2
-
-## E. coli (igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1)
-DATABASE    Ecoli   ./database/EB1 BOWTIE2
-
-## M. tuberculosis (igenomes/Mycobacterium_tuberculosis_H37RV/Ensembl/H37Rv.EB1)
-DATABASE    Tuberculosis   ./references/genome_tuberculosis/genome BOWTIE2
-
-## PhiX (/igenomes/PhiX/Illumina/RTA)
-DATABASE    PhiX   ../../../modules/nf-core/fastqscreen/references/genome_phix/genome BOWTIE2
-
-##S. cerevisiae (igenomes/Saccharomyces_cerevisiae/Ensembl/EF4)
-DATABASE    Scerevisiae   ../../../modules/nf-core/fastqscreen/references/genome_cerevisiae/genome BOWTIE2
diff --git a/nextflow.config b/nextflow.config
index 0c7668c..9b9a8bd 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -17,7 +17,6 @@ params {
     genome                     = null
     fasta                      = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
-    config_fastq_screen        = "./conf"
     igenomes_ignore            = false
 
     // Fastqscreen options
diff --git a/nextflow_schema.json b/nextflow_schema.json
index b464e2a..b320d2b 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -72,12 +72,6 @@
                     "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
                     "fa_icon": "far fa-file-code"
                 },
-                "config_fastq_screen": {
-                    "type": "string",
-                    "description": "path to directory with fastq_screen config (fastq_screen.conf)",
-                    "fa_icon": "fas fa-braille",
-                    "default": "./conf"
-                },
                 "igenomes_ignore": {
                     "type": "boolean",
                     "description": "Do not load the iGenomes reference config.",

From fedeab2f55efaa5fc01687e398d6f43f84818977 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 12:03:40 +0000
Subject: [PATCH 20/42] remove diff dump, I don't see why it should be here

---
 .../fastqscreen/fastqscreen-fastqscreen.diff  | 73 -------------------
 1 file changed, 73 deletions(-)
 delete mode 100644 modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff

diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
deleted file mode 100644
index e2f8a54..0000000
--- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
+++ /dev/null
@@ -1,73 +0,0 @@
-Changes in module 'nf-core/fastqscreen/fastqscreen'
-Changes in 'fastqscreen/fastqscreen/environment.yml':
---- modules/nf-core/fastqscreen/fastqscreen/environment.yml
-+++ modules/nf-core/fastqscreen/fastqscreen/environment.yml
-@@ -4,5 +4,11 @@
-   - conda-forge
-   - bioconda
- dependencies:
--  - "bioconda::fastq-screen=0.15.3"
-+  - bioconda::fastq-screen=0.16.0
-   - bioconda::perl-gdgraph=1.54
-+  # - gzip
-+  # - SAMtools
-+  # - bowtie
-+  # - bowtie2
-+  # - bwa
-+  # - bismark
-
-'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
-Changes in 'fastqscreen/fastqscreen/main.nf':
---- modules/nf-core/fastqscreen/fastqscreen/main.nf
-+++ modules/nf-core/fastqscreen/fastqscreen/main.nf
-@@ -1,15 +1,15 @@
- process FASTQSCREEN_FASTQSCREEN {
--    tag "$meta.id"
-+    tag "$meta.id | $meta2.database_name"
-     label 'process_medium'
- 
-     conda "${moduleDir}/environment.yml"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
--        'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0':
--        'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
-+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data' :
-+        'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
- 
-     input:
--    tuple val(meta), path(reads)  // .fastq files
--    path database
-+    // NOTE for meta 2 and database [[database_name,  database_notes], database_path]
-+    tuple val(meta), path(reads), val(meta2), path(database)
- 
-     output:
-     tuple val(meta), path("*.txt")     , emit: txt
-@@ -24,13 +24,18 @@
-     script:
-     def prefix = task.ext.prefix ?: "${meta.id}"
-     def args = task.ext.args ?: ""
-+    // 'Database name','Genome path and basename','Notes'
-+    """
-+    echo "Writing config"
-+    echo "DATABASE    ${meta2.database_name}    ./${database}/genome    ${meta2.database_notes}" > fastq_screen.conf
-+    echo "Wrote config"
- 
--    """
--    fastq_screen --threads ${task.cpus} \\
--        --aligner bowtie2 \\
--        --conf ${database}/fastq_screen.conf \\
-+    fastq_screen \\
-+        --conf fastq_screen.conf \\
-+        --threads ${task.cpus} \\
-+        --aligner ${meta2.database_notes.toLowerCase()} \\
-         $reads \\
--        $args \\
-+        $args
- 
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
-
-'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
-************************************************************

From 588ad1d41dfd8d42d09b05123c805605d6dd9521 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 12:05:16 +0000
Subject: [PATCH 21/42] spacing

---
 workflows/seqinspector.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 54974dc..fe8e99d 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -27,7 +27,7 @@ include { methodsDescriptionText        } from '../subworkflows/local/utils_nfco
 workflow SEQINSPECTOR {
 
     take:
-    ch_samplesheet // channel: samplesheet read in from --input
+    ch_samplesheet               // channel: samplesheet read in from --input
     ch_fastqscreen_databasesheet // channel: database sheet read in from --fastqscreen_database_sheet
 
     main:

From 2001ccdda102520266db3c991ed0b5d247bce0f6 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 12:21:06 +0000
Subject: [PATCH 22/42] Revert remove diff dump, now I see why it should be
 here :)

---
 .../fastqscreen/fastqscreen-fastqscreen.diff  | 73 +++++++++++++++++++
 1 file changed, 73 insertions(+)
 create mode 100644 modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff

diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
new file mode 100644
index 0000000..e2f8a54
--- /dev/null
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -0,0 +1,73 @@
+Changes in module 'nf-core/fastqscreen/fastqscreen'
+Changes in 'fastqscreen/fastqscreen/environment.yml':
+--- modules/nf-core/fastqscreen/fastqscreen/environment.yml
++++ modules/nf-core/fastqscreen/fastqscreen/environment.yml
+@@ -4,5 +4,11 @@
+   - conda-forge
+   - bioconda
+ dependencies:
+-  - "bioconda::fastq-screen=0.15.3"
++  - bioconda::fastq-screen=0.16.0
+   - bioconda::perl-gdgraph=1.54
++  # - gzip
++  # - SAMtools
++  # - bowtie
++  # - bowtie2
++  # - bwa
++  # - bismark
+
+'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
+Changes in 'fastqscreen/fastqscreen/main.nf':
+--- modules/nf-core/fastqscreen/fastqscreen/main.nf
++++ modules/nf-core/fastqscreen/fastqscreen/main.nf
+@@ -1,15 +1,15 @@
+ process FASTQSCREEN_FASTQSCREEN {
+-    tag "$meta.id"
++    tag "$meta.id | $meta2.database_name"
+     label 'process_medium'
+ 
+     conda "${moduleDir}/environment.yml"
+     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+-        'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0':
+-        'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
++        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data' :
++        'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
+ 
+     input:
+-    tuple val(meta), path(reads)  // .fastq files
+-    path database
++    // NOTE for meta 2 and database [[database_name,  database_notes], database_path]
++    tuple val(meta), path(reads), val(meta2), path(database)
+ 
+     output:
+     tuple val(meta), path("*.txt")     , emit: txt
+@@ -24,13 +24,18 @@
+     script:
+     def prefix = task.ext.prefix ?: "${meta.id}"
+     def args = task.ext.args ?: ""
++    // 'Database name','Genome path and basename','Notes'
++    """
++    echo "Writing config"
++    echo "DATABASE    ${meta2.database_name}    ./${database}/genome    ${meta2.database_notes}" > fastq_screen.conf
++    echo "Wrote config"
+ 
+-    """
+-    fastq_screen --threads ${task.cpus} \\
+-        --aligner bowtie2 \\
+-        --conf ${database}/fastq_screen.conf \\
++    fastq_screen \\
++        --conf fastq_screen.conf \\
++        --threads ${task.cpus} \\
++        --aligner ${meta2.database_notes.toLowerCase()} \\
+         $reads \\
+-        $args \\
++        $args
+ 
+     cat <<-END_VERSIONS > versions.yml
+     "${task.process}":
+
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
+************************************************************

From 5bb8dfdead84a2a7f471b40ae1a2a8dd17dc039a Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 12:31:04 +0000
Subject: [PATCH 23/42] fix faulty params var name in test config

---
 conf/test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/test.config b/conf/test.config
index c032431..1a6f84b 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -26,7 +26,7 @@ params {
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
-    database_sheet = "${projectDir}/assets/databasesheet.csv"
+    fastqscreen_database_sheet = "${projectDir}/assets/databasesheet.csv"
 
     // Genome references
     genome = 'R64-1-1'

From 3baa7fc7d1ff871bc71612c28c0a30a2f140a004 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 12:37:41 +0000
Subject: [PATCH 24/42] update snapshots for new multiqc citations

---
 tests/MiSeq.main.nf.test.snap                 |  8 ++++----
 tests/NovaSeq6000.main.nf.test.snap           | 16 ++++++++--------
 tests/NovaSeq6000.main_subsample.nf.test.snap | 16 ++++++++--------
 tests/PromethION.main.nf.test.snap            |  8 ++++----
 4 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index de0afa2..1dc646e 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -1,14 +1,14 @@
 {
     "MiSeq data test": {
         "content": [
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
             "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf"
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-30T09:08:29.692511055"
+        "timestamp": "2024-11-07T12:32:20.523618752"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 62ccd4a..823926f 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -1,26 +1,26 @@
 {
     "NovaSeq6000 data test": {
         "content": [
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
             "multiqc_general_stats.txt:md5,25abe0f6a35eb4a3b056fc3cf5c13732",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
             "multiqc_general_stats.txt:md5,90ee35137492b80aab36ef67f72d8921",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
             "multiqc_general_stats.txt:md5,d62a2fc39e674d98783d408791803148",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
             "multiqc_general_stats.txt:md5,2f09b8f199ac40cf67ba50843cebd29c",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
             "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a"
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-30T09:09:57.158871165"
+        "timestamp": "2024-11-07T12:33:47.150820885"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index 651973b..024fa66 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -1,26 +1,26 @@
 {
     "NovaSeq6000 data test sample size": {
         "content": [
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
             "multiqc_general_stats.txt:md5,ad1ec9c64cbdb1131a26aeb6de51e31c",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
             "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
             "multiqc_general_stats.txt:md5,834e1868b887171cfda72029bbbe2d3f",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
             "multiqc_general_stats.txt:md5,274a001b007521970f14d68bd176e5be",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
             "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012"
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-30T09:37:46.182191597"
+        "timestamp": "2024-11-07T12:35:00.745830145"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index dfa4eb6..24a7766 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -1,14 +1,14 @@
 {
     "PromethION data test": {
         "content": [
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
             "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32"
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-30T09:12:03.048502046"
+        "timestamp": "2024-11-07T12:35:46.010641114"
     }
 }
\ No newline at end of file

From 843e2c62a6a1429797c80b72b73e4075400138bb Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 12:53:19 +0000
Subject: [PATCH 25/42] module tests of fastqscreen are dependent on
 non-installed modules, so try to limit the scope of nf-test to the tests/ dir

---
 .github/workflows/nf-test.yml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index b0d7b8e..3a2abcb 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -5,9 +5,7 @@ on: [push, pull_request]
 jobs:
   test:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        shard: [1, 2, 3, 4]
+
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -28,5 +26,5 @@ jobs:
           wget -qO- https://get.nf-test.com | bash
           sudo mv nf-test /usr/local/bin/
 
-      - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
-        run: nf-test test --ci --shard ${{ matrix.shard }}/${{ strategy.job-total }} .
+      - name: Run Tests
+        run: nf-test test --ci tests

From 66d08ad14e2d5f8d4eb085fb0300727eda6c7d94 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 13:34:52 +0000
Subject: [PATCH 26/42] Append changelog entry

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 299e030..01d9401 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,7 +15,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#50](https://github.com/nf-core/seqinspector/pull/50) Add an optional subsampling step.
 - [#51](https://github.com/nf-core/seqinspector/pull/51) Add nf-test to CI.
 - [#63](https://github.com/nf-core/seqinspector/pull/63) Contribution guidelines added about displaying results for new tools
-- [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing
+- [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI.
 
 ### `Fixed`
 

From 9567f475929d83b6b6d8b1fe4b02309d973c300f Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 13:38:26 +0000
Subject: [PATCH 27/42] Check for fastQ Screen files in multiqc report in
 pipeline tests and update snapshots accordingly

---
 tests/MiSeq.main.nf.test                      | 1 +
 tests/MiSeq.main.nf.test.snap                 | 5 +++--
 tests/NovaSeq6000.main.nf.test                | 7 ++++++-
 tests/NovaSeq6000.main.nf.test.snap           | 9 +++++++--
 tests/NovaSeq6000.main_subsample.nf.test      | 5 +++++
 tests/NovaSeq6000.main_subsample.nf.test.snap | 9 +++++++--
 tests/PromethION.main.nf.test                 | 1 +
 tests/PromethION.main.nf.test.snap            | 5 +++--
 8 files changed, 33 insertions(+), 9 deletions(-)

diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index 246a05a..a1badfa 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -21,6 +21,7 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt"),
                     ).match()
                 }
             )
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 1dc646e..0e8fec2 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -3,12 +3,13 @@
         "content": [
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
-            "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf"
+            "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf",
+            "multiqc_fastq_screen.txt:md5,88473b5190a4ff3bbe5a1b5b92da2601"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-07T12:32:20.523618752"
+        "timestamp": "2024-11-07T13:33:59.180570696"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
index e24637c..06a5cb1 100644
--- a/tests/NovaSeq6000.main.nf.test
+++ b/tests/NovaSeq6000.main.nf.test
@@ -21,23 +21,28 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt"),
 
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt"),
 
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt"),
 
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt"),
 
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt"),
-                    ).match()
+                                        path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt"),
+                                        ).match()
                 },
             )
         }
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 823926f..c22361f 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -4,23 +4,28 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
             "multiqc_general_stats.txt:md5,25abe0f6a35eb4a3b056fc3cf5c13732",
+            "multiqc_fastq_screen.txt:md5,836b01175da79f0de458df899b9751e1",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
             "multiqc_general_stats.txt:md5,90ee35137492b80aab36ef67f72d8921",
+            "multiqc_fastq_screen.txt:md5,fd72aaf00fd4fac3da4ef222608e0c32",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
             "multiqc_general_stats.txt:md5,d62a2fc39e674d98783d408791803148",
+            "multiqc_fastq_screen.txt:md5,301fe12a6c6ccd09904c4f759008d416",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
             "multiqc_general_stats.txt:md5,2f09b8f199ac40cf67ba50843cebd29c",
+            "multiqc_fastq_screen.txt:md5,045f5b7623f6abb99b7075734fdb0cf4",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
-            "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a"
+            "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a",
+            "multiqc_fastq_screen.txt:md5,ee786f054e356ee005ca33c7558866dc"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-07T12:33:47.150820885"
+        "timestamp": "2024-11-07T13:35:28.998292704"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test b/tests/NovaSeq6000.main_subsample.nf.test
index fe2b068..d006de3 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test
+++ b/tests/NovaSeq6000.main_subsample.nf.test
@@ -21,22 +21,27 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt"),
 
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt"),
 
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt"),
 
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt"),
 
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt"),
                     ).match()
                 },
             )
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index 024fa66..b3407e2 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -4,23 +4,28 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
             "multiqc_general_stats.txt:md5,ad1ec9c64cbdb1131a26aeb6de51e31c",
+            "multiqc_fastq_screen.txt:md5,2730834c61a9e1349b357ef6a729ddd9",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
             "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60",
+            "multiqc_fastq_screen.txt:md5,a2b7469ab6b81d2872214eeba32933f5",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
             "multiqc_general_stats.txt:md5,834e1868b887171cfda72029bbbe2d3f",
+            "multiqc_fastq_screen.txt:md5,956cb8876c334293186ea213c4c39c6e",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
             "multiqc_general_stats.txt:md5,274a001b007521970f14d68bd176e5be",
+            "multiqc_fastq_screen.txt:md5,81cedab716aa382d7b4db2e42b681cb2",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
-            "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012"
+            "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012",
+            "multiqc_fastq_screen.txt:md5,8bbb1968587dbf3139bac07991a225cb"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-07T12:35:00.745830145"
+        "timestamp": "2024-11-07T13:36:43.785887669"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.main.nf.test
index ad6fe6d..126a58c 100644
--- a/tests/PromethION.main.nf.test
+++ b/tests/PromethION.main.nf.test
@@ -21,6 +21,7 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt"),
                     ).match()
                 },
             )
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 24a7766..17178fd 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -3,12 +3,13 @@
         "content": [
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
-            "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32"
+            "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32",
+            "multiqc_fastq_screen.txt:md5,37efa56cefb899abf506cf7a7fba0d54"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-07T12:35:46.010641114"
+        "timestamp": "2024-11-07T13:37:39.008847194"
     }
 }
\ No newline at end of file

From 5248fad891a8687679f8147eaf4041b3d6416109 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 13:54:40 +0000
Subject: [PATCH 28/42] fix indent

---
 tests/NovaSeq6000.main.nf.test | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
index 06a5cb1..e70a191 100644
--- a/tests/NovaSeq6000.main.nf.test
+++ b/tests/NovaSeq6000.main.nf.test
@@ -41,8 +41,8 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt"),
-                                        path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt"),
-                                        ).match()
+                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt"),
+                    ).match()
                 },
             )
         }

From e2a290c25d09b9d4d3871a4cdf57d5fb6385a9e5 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Thu, 14 Nov 2024 11:14:57 -0600
Subject: [PATCH 29/42] fix: Rename fastqscreen files so they're unique

---
 .../fastqscreen/fastqscreen-fastqscreen.diff       |  6 +++++-
 modules/nf-core/fastqscreen/fastqscreen/main.nf    |  4 ++++
 tests/MiSeq.main.nf.test.snap                      |  6 +++---
 tests/NovaSeq6000.main.nf.test.snap                | 14 +++++++-------
 tests/NovaSeq6000.main_subsample.nf.test.snap      | 14 +++++++-------
 tests/PromethION.main.nf.test.snap                 |  6 +++---
 6 files changed, 29 insertions(+), 21 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
index e2f8a54..ad5b6fe 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -41,7 +41,7 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
  
      output:
      tuple val(meta), path("*.txt")     , emit: txt
-@@ -24,13 +24,18 @@
+@@ -24,13 +24,22 @@
      script:
      def prefix = task.ext.prefix ?: "${meta.id}"
      def args = task.ext.args ?: ""
@@ -62,6 +62,10 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
          $reads \\
 -        $args \\
 +        $args
++
++    mv *_screen.txt ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.txt
++    mv *_screen.html ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.html
++    mv *_screen.png ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.png
  
      cat <<-END_VERSIONS > versions.yml
      "${task.process}":
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 5037db6..c0f98b9 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -37,6 +37,10 @@ process FASTQSCREEN_FASTQSCREEN {
         $reads \\
         $args
 
+    mv *_screen.txt ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.txt
+    mv *_screen.html ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.html
+    mv *_screen.png ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.png
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 0e8fec2..9207f88 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -4,12 +4,12 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
             "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf",
-            "multiqc_fastq_screen.txt:md5,88473b5190a4ff3bbe5a1b5b92da2601"
+            "multiqc_fastq_screen.txt:md5,435d8c1ac6e237448c9ce38e853ac82e"
         ],
         "meta": {
-            "nf-test": "0.9.0",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-07T13:33:59.180570696"
+        "timestamp": "2024-11-14T11:21:34.348023"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index c22361f..8b0f136 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -4,28 +4,28 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
             "multiqc_general_stats.txt:md5,25abe0f6a35eb4a3b056fc3cf5c13732",
-            "multiqc_fastq_screen.txt:md5,836b01175da79f0de458df899b9751e1",
+            "multiqc_fastq_screen.txt:md5,c7b24e20fd157128924384e52eb3405d",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
             "multiqc_general_stats.txt:md5,90ee35137492b80aab36ef67f72d8921",
-            "multiqc_fastq_screen.txt:md5,fd72aaf00fd4fac3da4ef222608e0c32",
+            "multiqc_fastq_screen.txt:md5,a1e15006994d06a47634ccf07a08df0f",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
             "multiqc_general_stats.txt:md5,d62a2fc39e674d98783d408791803148",
-            "multiqc_fastq_screen.txt:md5,301fe12a6c6ccd09904c4f759008d416",
+            "multiqc_fastq_screen.txt:md5,d4f1cc5396c4f719b1fcaab2470e7d7c",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
             "multiqc_general_stats.txt:md5,2f09b8f199ac40cf67ba50843cebd29c",
-            "multiqc_fastq_screen.txt:md5,045f5b7623f6abb99b7075734fdb0cf4",
+            "multiqc_fastq_screen.txt:md5,02246ddb4bf5373b157b45eab698cdc8",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
             "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a",
-            "multiqc_fastq_screen.txt:md5,ee786f054e356ee005ca33c7558866dc"
+            "multiqc_fastq_screen.txt:md5,483995ed26ba25b3217650840b2d82fa"
         ],
         "meta": {
-            "nf-test": "0.9.0",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-07T13:35:28.998292704"
+        "timestamp": "2024-11-14T11:22:20.902938"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index b3407e2..da7ba9a 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -4,28 +4,28 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
             "multiqc_general_stats.txt:md5,ad1ec9c64cbdb1131a26aeb6de51e31c",
-            "multiqc_fastq_screen.txt:md5,2730834c61a9e1349b357ef6a729ddd9",
+            "multiqc_fastq_screen.txt:md5,c7b24e20fd157128924384e52eb3405d",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
             "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60",
-            "multiqc_fastq_screen.txt:md5,a2b7469ab6b81d2872214eeba32933f5",
+            "multiqc_fastq_screen.txt:md5,a1e15006994d06a47634ccf07a08df0f",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
             "multiqc_general_stats.txt:md5,834e1868b887171cfda72029bbbe2d3f",
-            "multiqc_fastq_screen.txt:md5,956cb8876c334293186ea213c4c39c6e",
+            "multiqc_fastq_screen.txt:md5,d4f1cc5396c4f719b1fcaab2470e7d7c",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
             "multiqc_general_stats.txt:md5,274a001b007521970f14d68bd176e5be",
-            "multiqc_fastq_screen.txt:md5,81cedab716aa382d7b4db2e42b681cb2",
+            "multiqc_fastq_screen.txt:md5,02246ddb4bf5373b157b45eab698cdc8",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
             "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012",
-            "multiqc_fastq_screen.txt:md5,8bbb1968587dbf3139bac07991a225cb"
+            "multiqc_fastq_screen.txt:md5,483995ed26ba25b3217650840b2d82fa"
         ],
         "meta": {
-            "nf-test": "0.9.0",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-07T13:36:43.785887669"
+        "timestamp": "2024-11-14T11:23:19.55095"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 17178fd..74c12f5 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -4,12 +4,12 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
             "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32",
-            "multiqc_fastq_screen.txt:md5,37efa56cefb899abf506cf7a7fba0d54"
+            "multiqc_fastq_screen.txt:md5,2931dcec302d74c378b69a0831363224"
         ],
         "meta": {
-            "nf-test": "0.9.0",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-07T13:37:39.008847194"
+        "timestamp": "2024-11-14T11:23:42.382002"
     }
 }
\ No newline at end of file

From 46d1bfd93a2a622c091bfea1ea908c360919ebbf Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Thu, 14 Nov 2024 12:05:44 -0600
Subject: [PATCH 30/42] fix: collectFile fastqscreen rough draft

---
 workflows/seqinspector.nf | 24 +++++++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 307b163..d999682 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -83,7 +83,29 @@ workflow SEQINSPECTOR {
     FASTQSCREEN_FASTQSCREEN (
         ch_samplesheet.combine(ch_databases)
     )
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
+    // Group by sample
+    FASTQSCREEN_FASTQSCREEN.out.txt
+        .groupTuple(by: [0])
+        .collectFile(
+            keepHeader: true,
+            skip: 1,
+            newLine: false,
+            storeDir: "${params.outdir}/fastqscreen/",
+        )
+        { meta, file ->
+            filename = "${meta.id}_screen.txt"
+            [filename, file.text]
+        }
+        // TODO Add % Not hit
+        .map { path ->
+            meta = [
+                id:path.getSimpleName(),
+            ]
+            [meta, file(path)]
+        }
+        .set { ch_fastqscreen_clean }
+
+    ch_multiqc_files = ch_multiqc_files.mix(ch_fastqscreen_clean)
     ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())
 
     //

From b8c363c9fed1b28cf14738eb0ad675f8d63383d1 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Thu, 14 Nov 2024 12:10:07 -0600
Subject: [PATCH 31/42] chore: Lock down arity in fastqscreen

---
 .../fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff        | 2 +-
 modules/nf-core/fastqscreen/fastqscreen/main.nf                 | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
index ad5b6fe..df84f5a 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -37,7 +37,7 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
 -    tuple val(meta), path(reads)  // .fastq files
 -    path database
 +    // NOTE for meta 2 and database [[database_name,  database_notes], database_path]
-+    tuple val(meta), path(reads), val(meta2), path(database)
++    tuple val(meta), path(reads, arity: '1..2'), val(meta2), path(database, arity: '1')
  
      output:
      tuple val(meta), path("*.txt")     , emit: txt
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index c0f98b9..fff1414 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -9,7 +9,7 @@ process FASTQSCREEN_FASTQSCREEN {
 
     input:
     // NOTE for meta 2 and database [[database_name,  database_notes], database_path]
-    tuple val(meta), path(reads), val(meta2), path(database)
+    tuple val(meta), path(reads, arity: '1..2'), val(meta2), path(database, arity: '1')
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt

From d021ed012a20107c97103d029159c49e7d5548dc Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Thu, 14 Nov 2024 13:16:41 -0600
Subject: [PATCH 32/42] feat: Getting close to making the config on the head
 node

---
 .../nf-core/fastqscreen/fastqscreen/main.nf   | 20 +++++-----
 workflows/seqinspector.nf                     | 37 +++++++------------
 2 files changed, 23 insertions(+), 34 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index fff1414..4f2bdf9 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -1,5 +1,5 @@
 process FASTQSCREEN_FASTQSCREEN {
-    tag "$meta.id | $meta2.database_name"
+    tag "$meta.id"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
@@ -8,8 +8,10 @@ process FASTQSCREEN_FASTQSCREEN {
         'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
 
     input:
-    // NOTE for meta 2 and database [[database_name,  database_notes], database_path]
-    tuple val(meta), path(reads, arity: '1..2'), val(meta2), path(database, arity: '1')
+    tuple val(meta), path(reads, arity: '1..2')
+    path('fastq_screen.conf', arity: '1')
+    path(database, arity:'1..*', name: '*/*')
+
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt
@@ -25,21 +27,17 @@ process FASTQSCREEN_FASTQSCREEN {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def args = task.ext.args ?: ""
     // 'Database name','Genome path and basename','Notes'
+    // FIXME? --aligner ${meta2.database_notes.toLowerCase()} \\
     """
-    echo "Writing config"
-    echo "DATABASE    ${meta2.database_name}    ./${database}/genome    ${meta2.database_notes}" > fastq_screen.conf
-    echo "Wrote config"
-
     fastq_screen \\
         --conf fastq_screen.conf \\
         --threads ${task.cpus} \\
-        --aligner ${meta2.database_notes.toLowerCase()} \\
         $reads \\
         $args
 
-    mv *_screen.txt ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.txt
-    mv *_screen.html ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.html
-    mv *_screen.png ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.png
+    mv *_screen.txt ${prefix}_screen.txt
+    mv *_screen.html ${prefix}_screen.html
+    mv *_screen.png ${prefix}_screen.png
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index d999682..059bda7 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -79,33 +79,24 @@ workflow SEQINSPECTOR {
     //
     ch_databases = Channel
         .fromList(samplesheetToList(ch_fastqscreen_databasesheet, "${projectDir}/assets/schema_database.json"))
-
-    FASTQSCREEN_FASTQSCREEN (
-        ch_samplesheet.combine(ch_databases)
-    )
-    // Group by sample
-    FASTQSCREEN_FASTQSCREEN.out.txt
-        .groupTuple(by: [0])
+    ch_fastqscreen_config = ch_databases
         .collectFile(
-            keepHeader: true,
-            skip: 1,
-            newLine: false,
+            newLine: true,
+            name: 'fastq_screen.conf',
             storeDir: "${params.outdir}/fastqscreen/",
         )
-        { meta, file ->
-            filename = "${meta.id}_screen.txt"
-            [filename, file.text]
-        }
-        // TODO Add % Not hit
-        .map { path ->
-            meta = [
-                id:path.getSimpleName(),
-            ]
-            [meta, file(path)]
-        }
-        .set { ch_fastqscreen_clean }
+    {
+        meta, db ->
+        "DATABASE    ${meta.database_name}    ./${db}/genome    ${meta.database_notes}"
+    }
+    ch_database_files = ch_databases.collect { meta, db -> db}
 
-    ch_multiqc_files = ch_multiqc_files.mix(ch_fastqscreen_clean)
+    FASTQSCREEN_FASTQSCREEN (
+        ch_samplesheet,
+        ch_fastqscreen_config,
+        ch_database_files,
+    )
+    ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
     ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())
 
     //

From 4b278bf946476a951c40244722266cb4d21d171e Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 11:57:04 +0000
Subject: [PATCH 33/42] make functional :')

---
 assets/databasesheet.csv                      |  6 ++--
 .../nf-core/fastqscreen/fastqscreen/main.nf   | 31 +++++++++----------
 workflows/seqinspector.nf                     | 26 +++++++---------
 3 files changed, 28 insertions(+), 35 deletions(-)

diff --git a/assets/databasesheet.csv b/assets/databasesheet.csv
index 150f831..16d1a3e 100644
--- a/assets/databasesheet.csv
+++ b/assets/databasesheet.csv
@@ -1,4 +1,4 @@
 name,index,aligner
-Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/,BOWTIE2
-PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,BOWTIE2
-Scerevisiae,s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/NCBI/build3.1/Sequence/Bowtie2Index/,BOWTIE2
+Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/,Bowtie2
+PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,Bowtie2
+Scerevisiae,s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/NCBI/build3.1/Sequence/Bowtie2Index/,Bowtie2
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 4f2bdf9..6b0a04d 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -9,9 +9,7 @@ process FASTQSCREEN_FASTQSCREEN {
 
     input:
     tuple val(meta), path(reads, arity: '1..2')
-    path('fastq_screen.conf', arity: '1')
-    path(database, arity:'1..*', name: '*/*')
-
+    tuple val(ref_names), path(ref_paths, name:"ref*"), val(ref_aligners)
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt
@@ -26,9 +24,10 @@ process FASTQSCREEN_FASTQSCREEN {
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def args = task.ext.args ?: ""
-    // 'Database name','Genome path and basename','Notes'
-    // FIXME? --aligner ${meta2.database_notes.toLowerCase()} \\
+    def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_paths[i]}/genome ${ref_aligners[i]}" }.join('\n')
     """
+    echo '${config_content}' > fastq_screen.conf
+
     fastq_screen \\
         --conf fastq_screen.conf \\
         --threads ${task.cpus} \\
@@ -39,23 +38,21 @@ process FASTQSCREEN_FASTQSCREEN {
     mv *_screen.html ${prefix}_screen.html
     mv *_screen.png ${prefix}_screen.png
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
-    END_VERSIONS
+    fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
+    echo "\\\"${task.process}\\\":" > versions.yml
+    echo "    fastqscreen: \$fastq_screen_version" >> versions.yml
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch test_1_screen.html
-    touch test_1_screen.png
-    touch test_1_screen.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
-    END_VERSIONS
+    touch ${prefix}_screen.html
+    touch ${prefix}_screen.png
+    touch ${prefix}_screen.txt
+
+    fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
+    echo "\\\"${task.process}\\\":" > versions.yml
+    echo "    fastqscreen: \$fastq_screen_version" >> versions.yml
     """
 
 }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 059bda7..a66bece 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -77,24 +77,20 @@ workflow SEQINSPECTOR {
     //
     // MODULE: Run FastQ Screen
     //
-    ch_databases = Channel
-        .fromList(samplesheetToList(ch_fastqscreen_databasesheet, "${projectDir}/assets/schema_database.json"))
-    ch_fastqscreen_config = ch_databases
-        .collectFile(
-            newLine: true,
-            name: 'fastq_screen.conf',
-            storeDir: "${params.outdir}/fastqscreen/",
-        )
-    {
-        meta, db ->
-        "DATABASE    ${meta.database_name}    ./${db}/genome    ${meta.database_notes}"
-    }
-    ch_database_files = ch_databases.collect { meta, db -> db}
+
+    // Parse the reference info needed to create a FastQ Screen config file
+    // and transpose it into a tuple containing lists of names, index paths and aligners
+    ch_fastqscreen_refs = Channel
+        .fromPath("${projectDir}/assets/databasesheet.csv")
+        .splitCsv(header: true)
+        .map { row -> tuple(row.name, row.index, row.aligner) }
+        .toList()
+        .transpose()
+        .toList()
 
     FASTQSCREEN_FASTQSCREEN (
         ch_samplesheet,
-        ch_fastqscreen_config,
-        ch_database_files,
+        ch_fastqscreen_refs
     )
     ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
     ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())

From 63ebd6737455d384065092dda52747a08fbc565e Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 13:46:38 +0000
Subject: [PATCH 34/42] make input mounting more flexible by separating mounted
 dir path from basename of reference / index files therein

---
 assets/databasesheet.csv                        | 8 ++++----
 modules/nf-core/fastqscreen/fastqscreen/main.nf | 4 ++--
 workflows/seqinspector.nf                       | 2 +-
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/assets/databasesheet.csv b/assets/databasesheet.csv
index 16d1a3e..31f93a1 100644
--- a/assets/databasesheet.csv
+++ b/assets/databasesheet.csv
@@ -1,4 +1,4 @@
-name,index,aligner
-Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/,Bowtie2
-PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,Bowtie2
-Scerevisiae,s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/NCBI/build3.1/Sequence/Bowtie2Index/,Bowtie2
+name,dir,basename,aligner
+Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/,genome,Bowtie2
+PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,genome,Bowtie2
+Scerevisiae,s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/NCBI/build3.1/Sequence/Bowtie2Index/,genome,Bowtie2
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 6b0a04d..2eba839 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -9,7 +9,7 @@ process FASTQSCREEN_FASTQSCREEN {
 
     input:
     tuple val(meta), path(reads, arity: '1..2')
-    tuple val(ref_names), path(ref_paths, name:"ref*"), val(ref_aligners)
+    tuple val(ref_names), path(ref_dirs, name:"ref*"), val(ref_basenames), val(ref_aligners)
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt
@@ -24,7 +24,7 @@ process FASTQSCREEN_FASTQSCREEN {
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def args = task.ext.args ?: ""
-    def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_paths[i]}/genome ${ref_aligners[i]}" }.join('\n')
+    def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_dirs[i]}/${ref_basenames[i]} ${ref_aligners[i]}" }.join('\n')
     """
     echo '${config_content}' > fastq_screen.conf
 
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index a66bece..8536a87 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -83,7 +83,7 @@ workflow SEQINSPECTOR {
     ch_fastqscreen_refs = Channel
         .fromPath("${projectDir}/assets/databasesheet.csv")
         .splitCsv(header: true)
-        .map { row -> tuple(row.name, row.index, row.aligner) }
+        .map { row -> tuple(row.name, row.dir, row.basename, row.aligner) }
         .toList()
         .transpose()
         .toList()

From 2608088905388fe77c6a4272a1872219f72d5726 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 14:31:55 +0000
Subject: [PATCH 35/42] successfully use schema validation for fastqscreen
 reference .csv

---
 assets/databasesheet.csv    |  6 +++---
 assets/schema_database.json | 19 +++++++++++--------
 workflows/seqinspector.nf   |  8 +++++---
 3 files changed, 19 insertions(+), 14 deletions(-)

diff --git a/assets/databasesheet.csv b/assets/databasesheet.csv
index 31f93a1..59f0cdf 100644
--- a/assets/databasesheet.csv
+++ b/assets/databasesheet.csv
@@ -1,4 +1,4 @@
 name,dir,basename,aligner
-Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/,genome,Bowtie2
-PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,genome,Bowtie2
-Scerevisiae,s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/NCBI/build3.1/Sequence/Bowtie2Index/,genome,Bowtie2
+Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/,genome,bowtie2
+PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,genome,bowtie2
+Scerevisiae,s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/NCBI/build3.1/Sequence/Bowtie2Index/,genome,bowtie2
diff --git a/assets/schema_database.json b/assets/schema_database.json
index e735ea4..4a796bb 100644
--- a/assets/schema_database.json
+++ b/assets/schema_database.json
@@ -10,23 +10,26 @@
             "name": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "The database name for fastq screen",
-                "meta": ["database_name"]
+                "errorMessage": "The reference name as referred to by FastQ Screen."
             },
-            "index": {
+            "dir": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
                 "pattern": "^\\S+$",
-                "errorMessage": "Path to the aligner index"
+                "errorMessage": "Path to the dir containing the aligner reference and index. Can be remote."
+            },
+            "basename": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "The shared basename of the reference and index files contained in the dir."
             },
             "aligner": {
                 "type": "string",
-                "enum": ["BOWTIE", "BOWTIE2", "BWA", "MINIMAP2"],
-                "errorMessage": "Specify the aligner to use for the mapping. Valid arguments are 'bowtie', bowtie2' (default), 'bwa' or 'minimap2'.",
-                "meta": ["database_notes"]
+                "enum": ["bowtie", "bowtie2", "bwa", "minimap2"],
+                "errorMessage": "Specify the aligner to use for the mapping. Valid arguments are 'bowtie', bowtie2' (default), 'bwa' or 'minimap2'."
             }
         },
-        "required": ["name", "index", "aligner"]
+        "required": ["name", "dir", "basename", "aligner"]
     }
 }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 8536a87..0d622cc 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -81,9 +81,11 @@ workflow SEQINSPECTOR {
     // Parse the reference info needed to create a FastQ Screen config file
     // and transpose it into a tuple containing lists of names, index paths and aligners
     ch_fastqscreen_refs = Channel
-        .fromPath("${projectDir}/assets/databasesheet.csv")
-        .splitCsv(header: true)
-        .map { row -> tuple(row.name, row.dir, row.basename, row.aligner) }
+        .fromList(samplesheetToList(
+            "${projectDir}/assets/databasesheet.csv",
+            "${projectDir}/assets/schema_database.json"
+        ))
+        .map { row -> tuple(row[0], row[1], row[2], row[3]) }
         .toList()
         .transpose()
         .toList()

From 4f743e243c571c8d79a2018cf80682a882fea89a Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 14:42:57 +0000
Subject: [PATCH 36/42] remove redundant operator

---
 workflows/seqinspector.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 0d622cc..4c745f7 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -85,7 +85,6 @@ workflow SEQINSPECTOR {
             "${projectDir}/assets/databasesheet.csv",
             "${projectDir}/assets/schema_database.json"
         ))
-        .map { row -> tuple(row[0], row[1], row[2], row[3]) }
         .toList()
         .transpose()
         .toList()

From 5aeb8d18da74781bfd2b97c3727b95e21cd52336 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 14:46:05 +0000
Subject: [PATCH 37/42] update comment

---
 workflows/seqinspector.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 4c745f7..b2b7f67 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -79,7 +79,7 @@ workflow SEQINSPECTOR {
     //
 
     // Parse the reference info needed to create a FastQ Screen config file
-    // and transpose it into a tuple containing lists of names, index paths and aligners
+    // and transpose it into a tuple containing lists for each property
     ch_fastqscreen_refs = Channel
         .fromList(samplesheetToList(
             "${projectDir}/assets/databasesheet.csv",

From a31a392c209fd302f1aee575feebc0751a9649ff Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 14:59:48 +0000
Subject: [PATCH 38/42] switch to cleaner file and variable names, remove
 fastqscreen .csv as main workflow input

---
 ...tabasesheet.csv => example_fastq_screen_references.csv} | 0
 ...a_database.json => schema_fastq_screen_references.json} | 6 +++---
 conf/test.config                                           | 2 +-
 main.nf                                                    | 7 ++-----
 nextflow.config                                            | 2 +-
 nextflow_schema.json                                       | 6 +++---
 workflows/seqinspector.nf                                  | 6 +++---
 7 files changed, 13 insertions(+), 16 deletions(-)
 rename assets/{databasesheet.csv => example_fastq_screen_references.csv} (100%)
 rename assets/{schema_database.json => schema_fastq_screen_references.json} (89%)

diff --git a/assets/databasesheet.csv b/assets/example_fastq_screen_references.csv
similarity index 100%
rename from assets/databasesheet.csv
rename to assets/example_fastq_screen_references.csv
diff --git a/assets/schema_database.json b/assets/schema_fastq_screen_references.json
similarity index 89%
rename from assets/schema_database.json
rename to assets/schema_fastq_screen_references.json
index 4a796bb..9a938d9 100644
--- a/assets/schema_database.json
+++ b/assets/schema_fastq_screen_references.json
@@ -1,8 +1,8 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/seqinspector/master/assets/schema_database.json",
-    "title": "nf-core/seqinspector pipeline - params.fastqscreen_databasesheet schema",
-    "description": "Schema for the file provided with params.fastq_screen_databasesheet",
+    "$id": "https://raw.githubusercontent.com/nf-core/seqinspector/master/assets/schema_fastq_screen_references.json",
+    "title": "nf-core/seqinspector pipeline - params.fastq_screen_references schema",
+    "description": "Schema for the file provided with params.fastq_screen_references",
     "type": "array",
     "items": {
         "type": "object",
diff --git a/conf/test.config b/conf/test.config
index 1a6f84b..0ebc405 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -26,7 +26,7 @@ params {
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
-    fastqscreen_database_sheet = "${projectDir}/assets/databasesheet.csv"
+    fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv"
 
     // Genome references
     genome = 'R64-1-1'
diff --git a/main.nf b/main.nf
index cd4af96..85027a4 100644
--- a/main.nf
+++ b/main.nf
@@ -44,7 +44,6 @@ workflow NFCORE_SEQINSPECTOR {
 
     take:
     samplesheet // channel: samplesheet read in from --input
-    database_sheet
 
     main:
 
@@ -52,8 +51,7 @@ workflow NFCORE_SEQINSPECTOR {
     // WORKFLOW: Run pipeline
     //
     SEQINSPECTOR (
-        samplesheet,
-        database_sheet,
+        samplesheet
     )
     emit:
     global_report   = SEQINSPECTOR.out.global_report    // channel: /path/to/multiqc_report.html
@@ -85,8 +83,7 @@ workflow {
     // WORKFLOW: Run main workflow
     //
     NFCORE_SEQINSPECTOR (
-        PIPELINE_INITIALISATION.out.samplesheet,
-        params.fastqscreen_database_sheet,
+        PIPELINE_INITIALISATION.out.samplesheet
     )
     //
     // SUBWORKFLOW: Run completion tasks
diff --git a/nextflow.config b/nextflow.config
index 9b9a8bd..5b835a8 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -20,7 +20,7 @@ params {
     igenomes_ignore            = false
 
     // Fastqscreen options
-    fastqscreen_database_sheet = './assets/databasesheet.csv'
+    fastq_screen_references    = './assets/example_fastq_screen_references.csv'
 
     // MultiQC options
     multiqc_config             = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index b320d2b..722d80b 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -87,11 +87,11 @@
                     "hidden": true,
                     "default": "s3://ngi-igenomes/igenomes/"
                 },
-                "fastqscreen_database_sheet": {
+                "fastq_screen_references": {
                     "type": "string",
-                    "default": "./assets/databasesheet.csv",
+                    "default": "./assets/example_fastq_screen_references.csv",
                     "fa_icon": "fas fa-search",
-                    "description": "list of reference genomes (databases) to be mapped against in fastqscreen"
+                    "description": "A .csv of reference genomes to be mapped against by FastQ Screen"
                 }
             }
         },
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index b2b7f67..4afff15 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -29,7 +29,6 @@ workflow SEQINSPECTOR {
 
     take:
     ch_samplesheet               // channel: samplesheet read in from --input
-    ch_fastqscreen_databasesheet // channel: database sheet read in from --fastqscreen_database_sheet
 
     main:
 
@@ -80,10 +79,11 @@ workflow SEQINSPECTOR {
 
     // Parse the reference info needed to create a FastQ Screen config file
     // and transpose it into a tuple containing lists for each property
+
     ch_fastqscreen_refs = Channel
         .fromList(samplesheetToList(
-            "${projectDir}/assets/databasesheet.csv",
-            "${projectDir}/assets/schema_database.json"
+            "${projectDir}/assets/example_fastq_screen_references.csv",
+            "${projectDir}/assets/schema_fastq_screen_references.json"
         ))
         .toList()
         .transpose()

From 7396d4ccfd26d573269f32a1592ac20137ccf833 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 15:11:32 +0000
Subject: [PATCH 39/42] update docs

---
 docs/output.md | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/docs/output.md b/docs/output.md
index a2706a8..dc26159 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -56,7 +56,16 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [Fastqscreen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) allows you to set up a standard set of libraries against which all of your sequences can be searched. Your search libraries might contain the genomes of all of the organisms you work on, along with PhiX, Vectors or other contaminants commonly seen in sequencing experiments.
 
-It requires the supply of referenced (databases) in a config file. In order to parallelize the mapping of the different samples, in seqinspector, this a fastqscreen config file is generated for every sample/reference combination.
+It requires a `.csv` detailing:
+
+- the working name of the reference
+- the name of the aligner used to generate its index (which is also the aligner and index used by the tool)
+- the file basename of the reference and its index (e.g. the reference `genoma.fa` and its index `genome.bt2` have the basename `genome`)
+- the path to a dir where the reference and index files both reside.
+
+See `assets/example_fastq_screen_references.csv` for example.
+
+The `.csv` is provided as a pipeline parameter `fastq_screen_references`. The `.csv` is used to construct a `FastQ Screen` configuration file within the context of the process work directory in order to properly mount the references.
 
 ### SeqFu Stats
 

From e3a88624ed49d21a8176079e20b370e9e9207c6a Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 15:20:51 +0000
Subject: [PATCH 40/42] update snapshots

---
 tests/MiSeq.main.nf.test.snap                 |  8 ++++----
 tests/NovaSeq6000.main.nf.test.snap           | 16 ++++++++--------
 tests/NovaSeq6000.main_subsample.nf.test.snap | 16 ++++++++--------
 tests/PromethION.main.nf.test.snap            |  8 ++++----
 4 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 9207f88..af7022d 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -4,12 +4,12 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
             "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf",
-            "multiqc_fastq_screen.txt:md5,435d8c1ac6e237448c9ce38e853ac82e"
+            "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607"
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-14T11:21:34.348023"
+        "timestamp": "2024-12-05T15:15:09.227024034"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 8b0f136..9b3826a 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -4,28 +4,28 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
             "multiqc_general_stats.txt:md5,25abe0f6a35eb4a3b056fc3cf5c13732",
-            "multiqc_fastq_screen.txt:md5,c7b24e20fd157128924384e52eb3405d",
+            "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
             "multiqc_general_stats.txt:md5,90ee35137492b80aab36ef67f72d8921",
-            "multiqc_fastq_screen.txt:md5,a1e15006994d06a47634ccf07a08df0f",
+            "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
             "multiqc_general_stats.txt:md5,d62a2fc39e674d98783d408791803148",
-            "multiqc_fastq_screen.txt:md5,d4f1cc5396c4f719b1fcaab2470e7d7c",
+            "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
             "multiqc_general_stats.txt:md5,2f09b8f199ac40cf67ba50843cebd29c",
-            "multiqc_fastq_screen.txt:md5,02246ddb4bf5373b157b45eab698cdc8",
+            "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
             "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a",
-            "multiqc_fastq_screen.txt:md5,483995ed26ba25b3217650840b2d82fa"
+            "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5"
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-14T11:22:20.902938"
+        "timestamp": "2024-12-05T15:16:34.893751981"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index da7ba9a..3ba5046 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -4,28 +4,28 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
             "multiqc_general_stats.txt:md5,ad1ec9c64cbdb1131a26aeb6de51e31c",
-            "multiqc_fastq_screen.txt:md5,c7b24e20fd157128924384e52eb3405d",
+            "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
             "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60",
-            "multiqc_fastq_screen.txt:md5,a1e15006994d06a47634ccf07a08df0f",
+            "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
             "multiqc_general_stats.txt:md5,834e1868b887171cfda72029bbbe2d3f",
-            "multiqc_fastq_screen.txt:md5,d4f1cc5396c4f719b1fcaab2470e7d7c",
+            "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
             "multiqc_general_stats.txt:md5,274a001b007521970f14d68bd176e5be",
-            "multiqc_fastq_screen.txt:md5,02246ddb4bf5373b157b45eab698cdc8",
+            "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
             "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012",
-            "multiqc_fastq_screen.txt:md5,483995ed26ba25b3217650840b2d82fa"
+            "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5"
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-14T11:23:19.55095"
+        "timestamp": "2024-12-05T15:17:50.525033752"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 74c12f5..7d0a6bf 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -4,12 +4,12 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
             "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32",
-            "multiqc_fastq_screen.txt:md5,2931dcec302d74c378b69a0831363224"
+            "multiqc_fastq_screen.txt:md5,7c5d711e27c53d13c81644a1f2468dba"
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-14T11:23:42.382002"
+        "timestamp": "2024-12-05T15:18:25.176791779"
     }
 }
\ No newline at end of file

From 586ac9bb757ae40020332ed46da21185d4c37af5 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 15:28:25 +0000
Subject: [PATCH 41/42] re-generate module patch

---
 .../fastqscreen/fastqscreen-fastqscreen.diff  | 62 ++++++++++++-------
 1 file changed, 41 insertions(+), 21 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
index df84f5a..2fbd94b 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -16,15 +16,10 @@ Changes in 'fastqscreen/fastqscreen/environment.yml':
 +  # - bwa
 +  # - bismark
 
-'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
 Changes in 'fastqscreen/fastqscreen/main.nf':
 --- modules/nf-core/fastqscreen/fastqscreen/main.nf
 +++ modules/nf-core/fastqscreen/fastqscreen/main.nf
-@@ -1,15 +1,15 @@
- process FASTQSCREEN_FASTQSCREEN {
--    tag "$meta.id"
-+    tag "$meta.id | $meta2.database_name"
-     label 'process_medium'
+@@ -4,12 +4,12 @@
  
      conda "${moduleDir}/environment.yml"
      container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -36,20 +31,18 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
      input:
 -    tuple val(meta), path(reads)  // .fastq files
 -    path database
-+    // NOTE for meta 2 and database [[database_name,  database_notes], database_path]
-+    tuple val(meta), path(reads, arity: '1..2'), val(meta2), path(database, arity: '1')
++    tuple val(meta), path(reads, arity: '1..2')
++    tuple val(ref_names), path(ref_dirs, name:"ref*"), val(ref_basenames), val(ref_aligners)
  
      output:
      tuple val(meta), path("*.txt")     , emit: txt
-@@ -24,13 +24,22 @@
+@@ -24,31 +24,35 @@
      script:
      def prefix = task.ext.prefix ?: "${meta.id}"
      def args = task.ext.args ?: ""
-+    // 'Database name','Genome path and basename','Notes'
++    def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_dirs[i]}/${ref_basenames[i]} ${ref_aligners[i]}" }.join('\n')
 +    """
-+    echo "Writing config"
-+    echo "DATABASE    ${meta2.database_name}    ./${database}/genome    ${meta2.database_notes}" > fastq_screen.conf
-+    echo "Wrote config"
++    echo '${config_content}' > fastq_screen.conf
  
 -    """
 -    fastq_screen --threads ${task.cpus} \\
@@ -58,20 +51,47 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
 +    fastq_screen \\
 +        --conf fastq_screen.conf \\
 +        --threads ${task.cpus} \\
-+        --aligner ${meta2.database_notes.toLowerCase()} \\
          $reads \\
 -        $args \\
 +        $args
+ 
+-    cat <<-END_VERSIONS > versions.yml
+-    "${task.process}":
+-        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
+-    END_VERSIONS
++    mv *_screen.txt ${prefix}_screen.txt
++    mv *_screen.html ${prefix}_screen.html
++    mv *_screen.png ${prefix}_screen.png
 +
-+    mv *_screen.txt ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.txt
-+    mv *_screen.html ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.html
-+    mv *_screen.png ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.png
++    fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
++    echo "\\\"${task.process}\\\":" > versions.yml
++    echo "    fastqscreen: \$fastq_screen_version" >> versions.yml
+     """
+ 
+     stub:
+     def prefix = task.ext.prefix ?: "${meta.id}"
+     """
+-    touch test_1_screen.html
+-    touch test_1_screen.png
+-    touch test_1_screen.txt
++    touch ${prefix}_screen.html
++    touch ${prefix}_screen.png
++    touch ${prefix}_screen.txt
+ 
+-    cat <<-END_VERSIONS > versions.yml
+-    "${task.process}":
+-        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
+-    END_VERSIONS
++    fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
++    echo "\\\"${task.process}\\\":" > versions.yml
++    echo "    fastqscreen: \$fastq_screen_version" >> versions.yml
+     """
  
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
+ }
 
+'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
 'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
 'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
 ************************************************************

From 7b6c18bdc55f74f32edb9397b1a6411b400688b9 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 15:50:17 +0000
Subject: [PATCH 42/42] try gha update

---
 .github/workflows/nf-test.yml | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 3a2abcb..233897e 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -10,14 +10,8 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Set up JDK 11
-        uses: actions/setup-java@v2
-        with:
-          java-version: "11"
-          distribution: "adopt"
-
       - name: Setup Nextflow latest-edge
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "latest-edge"