From b412e6dabc99ea1b1bae07e09a4dbcb6e92e5439 Mon Sep 17 00:00:00 2001
From: Priyanka Surana <ps22@sanger.ac.uk>
Date: Thu, 27 Jan 2022 14:36:18 +0000
Subject: [PATCH 01/19] Busco module commit with nf-core v2.2 c1

---
 modules/busco/main.nf               | 42 +++++++++++++++++++++++
 modules/busco/meta.yml              | 52 +++++++++++++++++++++++++++++
 tests/config/pytest_modules.yml     |  4 +++
 tests/modules/busco/main.nf         | 26 +++++++++++++++
 tests/modules/busco/nextflow.config |  5 +++
 tests/modules/busco/test.yml        | 20 +++++++++++
 6 files changed, 149 insertions(+)
 create mode 100644 modules/busco/main.nf
 create mode 100644 modules/busco/meta.yml
 create mode 100644 tests/modules/busco/main.nf
 create mode 100644 tests/modules/busco/nextflow.config
 create mode 100644 tests/modules/busco/test.yml

diff --git a/modules/busco/main.nf b/modules/busco/main.nf
new file mode 100644
index 00000000000..445f8ed4417
--- /dev/null
+++ b/modules/busco/main.nf
@@ -0,0 +1,42 @@
+process BUSCO {
+    tag "$meta.id"
+    label 'process_medium'
+    
+    conda (params.enable_conda ? "bioconda::busco=5.2.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/busco:5.2.2--pyhdfd78af_0':
+        'quay.io/biocontainers/busco:5.2.2--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+    path(augustus_config)
+    val(lineage)
+
+    output:
+    tuple val(meta), path("${meta.id}/run_*/full_table.tsv"), emit: tsv
+    tuple val(meta), path("${meta.id}/run_*/short_summary.txt"), emit: txt
+    path "versions.yml"           , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if (lineage) args += " --lineage_dataset $lineage"
+    """
+    # Ensure the input is uncompressed
+    gzip -cdf $fasta > __UNCOMPRESSED_FASTA_FILE__
+    # Copy the image's AUGUSTUS config directory if it was not provided to the module
+    [ ! -e augustus_config ] && cp -a /usr/local/config augustus_config
+    AUGUSTUS_CONFIG_PATH=augustus_config \\
+    busco \\
+        $args \\
+        --augustus \\
+        --cpu $task.cpus \\
+        --in __UNCOMPRESSED_FASTA_FILE__ \\
+        --out $meta.id
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        busco: \$( busco --version 2>&1 | sed 's/^BUSCO //' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/busco/meta.yml b/modules/busco/meta.yml
new file mode 100644
index 00000000000..0cd9e40254c
--- /dev/null
+++ b/modules/busco/meta.yml
@@ -0,0 +1,52 @@
+name: busco
+description: Benchmarking Universal Single Copy Orthologs
+keywords:
+  - quality control
+  - genome
+  - transcriptome
+  - proteome
+tools:
+  - busco:
+      description: BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
+      homepage: https://busco.ezlab.org/
+      documentation: https://busco.ezlab.org/busco_userguide.html
+      tool_dev_url: https://gitlab.com/ezlab/busco
+      doi: "10.1007/978-1-4939-9173-0_14"
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: Nucleic or amino acid sequence file in FASTA format
+      pattern: "*.{fasta}"
+  - augustus_config:
+      type: directory
+      description: AUGUSTUS config directory
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - tsv:
+      type: file
+      description: Full summary table
+      pattern: "*.{tsv}"
+  - txt:
+      type: file
+      description: Short summary text
+      pattern: "*.{txt}"
+
+authors:
+  - "@priyanka-surana"
+  - "@charles-plessy"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 2321c918099..920b85bd1a2 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -230,6 +230,10 @@ bowtie2/build:
   - modules/bowtie2/build/**
   - tests/modules/bowtie2/build_test/**
 
+busco:
+  - modules/busco/**
+  - tests/modules/busco/**
+
 bwa/aln:
   - modules/bwa/aln/**
   - tests/modules/bwa/aln/**
diff --git a/tests/modules/busco/main.nf b/tests/modules/busco/main.nf
new file mode 100644
index 00000000000..28a4921c41f
--- /dev/null
+++ b/tests/modules/busco/main.nf
@@ -0,0 +1,26 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BUSCO as BUSCO_BACTE } from '../../../modules/busco/main.nf'
+include { BUSCO as BUSCO_CHR22 } from '../../../modules/busco/main.nf'
+include { UNTAR                } from '../../../modules/untar/main.nf'
+
+// This tests genome decompression, empty input channels and data download
+workflow test_busco_bacteroidales {
+   input = [ [ id:'test' ], file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true) ]    
+   BUSCO_BACTE ( input,
+                 [],
+                 [] )
+}
+
+// This tests uncompressed genome, BUSCO lineage file provided via input channel, and offline mode
+workflow test_busco_chr22 {
+    input = [ [ id:'test' ],  file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
+    lineage_dataset = [ file(params.test_data['homo_sapiens']['genome']['chr22_odb10_tar_gz'], checkIfExists: true) ]
+    UNTAR(lineage_dataset)
+    BUSCO_CHR22 ( input,
+                  [],
+                  UNTAR.out.untar )
+}
+
diff --git a/tests/modules/busco/nextflow.config b/tests/modules/busco/nextflow.config
new file mode 100644
index 00000000000..50f50a7a357
--- /dev/null
+++ b/tests/modules/busco/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
\ No newline at end of file
diff --git a/tests/modules/busco/test.yml b/tests/modules/busco/test.yml
new file mode 100644
index 00000000000..32553d2eb5d
--- /dev/null
+++ b/tests/modules/busco/test.yml
@@ -0,0 +1,20 @@
+- name: busco test_busco_bacteroidales
+  command: nextflow run ./tests/modules/busco -entry test_busco_bacteroidales -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config
+  tags:
+    - busco
+  files:
+    - path: output/busco/test/run_bacteroidales_odb10/full_table.tsv
+      md5sum: 8d7b401d875ecd9291b01bf4485bf080
+    - path: output/busco/test/run_bacteroidales_odb10/short_summary.txt
+      contains: ['Complete BUSCOs (C)']
+
+- name: busco test_busco_chr22
+  command: nextflow run ./tests/modules/busco -entry test_busco_chr22 -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config
+  tags:
+    - busco
+  files:
+    - path: output/busco/test/run_chr22_odb10/full_table.tsv
+      md5sum: 83f20e8996c591338ada73b6ab0eb269
+    - path: output/busco/test/run_chr22_odb10/short_summary.txt
+      contains: ['Complete BUSCOs (C)']
+

From 3e6be5060007d3feb24e3dfb95d602a3fbd3eb58 Mon Sep 17 00:00:00 2001
From: Priyanka Surana <ps22@sanger.ac.uk>
Date: Fri, 25 Feb 2022 13:26:23 +0000
Subject: [PATCH 02/19] Adjusted Augustus Config Path settings. Suggested by
 @mahesh-panchal

---
 modules/busco/main.nf        | 26 +++++++++++++++++++-------
 modules/busco/meta.yml       |  3 +++
 tests/modules/busco/main.nf  | 15 ++-------------
 tests/modules/busco/test.yml | 14 ++------------
 4 files changed, 26 insertions(+), 32 deletions(-)

diff --git a/modules/busco/main.nf b/modules/busco/main.nf
index 445f8ed4417..6e5265384e3 100644
--- a/modules/busco/main.nf
+++ b/modules/busco/main.nf
@@ -9,6 +9,7 @@ process BUSCO {
 
     input:
     tuple val(meta), path(fasta)
+    val(mode)
     path(augustus_config)
     val(lineage)
 
@@ -24,15 +25,26 @@ process BUSCO {
     """
     # Ensure the input is uncompressed
     gzip -cdf $fasta > __UNCOMPRESSED_FASTA_FILE__
+    
+    # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
+    # Check for container variable initialisation script and source it.
+    if [ -f "/usr/local/env-activate.sh" ]; then
+        # . "/usr/local/env-activate.sh"  # Errors out because of various unbound variables
+        export PATH='/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'
+        export CONDA_PREFIX='/usr/local'
+        export CONDA_SHLVL='1'
+        export CONDA_DEFAULT_ENV='/usr/local'
+        export CONDA_PROMPT_MODIFIER=''
+        . "/usr/local/etc/conda/activate.d/activate-r-base.sh"
+        . "/usr/local/etc/conda/activate.d/augustus.sh"
+        . "/usr/local/etc/conda/activate.d/openjdk_activate.sh"
+    fi
+    
     # Copy the image's AUGUSTUS config directory if it was not provided to the module
     [ ! -e augustus_config ] && cp -a /usr/local/config augustus_config
-    AUGUSTUS_CONFIG_PATH=augustus_config \\
-    busco \\
-        $args \\
-        --augustus \\
-        --cpu $task.cpus \\
-        --in __UNCOMPRESSED_FASTA_FILE__ \\
-        --out $meta.id
+    
+    # Busco command
+    AUGUSTUS_CONFIG_PATH=augustus_config busco $args --augustus --mode $mode --cpu $task.cpus --in __UNCOMPRESSED_FASTA_FILE__ --out $meta.id
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/busco/meta.yml b/modules/busco/meta.yml
index 0cd9e40254c..8f41f2f3b63 100644
--- a/modules/busco/meta.yml
+++ b/modules/busco/meta.yml
@@ -24,6 +24,9 @@ input:
       type: file
       description: Nucleic or amino acid sequence file in FASTA format
       pattern: "*.{fasta}"
+  - mode:
+      type: value
+      description: Sets the assessment MODE – genome, proteins, transcriptome
   - augustus_config:
       type: directory
       description: AUGUSTUS config directory
diff --git a/tests/modules/busco/main.nf b/tests/modules/busco/main.nf
index 28a4921c41f..d12abae9c77 100644
--- a/tests/modules/busco/main.nf
+++ b/tests/modules/busco/main.nf
@@ -3,24 +3,13 @@
 nextflow.enable.dsl = 2
 
 include { BUSCO as BUSCO_BACTE } from '../../../modules/busco/main.nf'
-include { BUSCO as BUSCO_CHR22 } from '../../../modules/busco/main.nf'
-include { UNTAR                } from '../../../modules/untar/main.nf'
 
 // This tests genome decompression, empty input channels and data download
-workflow test_busco_bacteroidales {
+workflow test_busco {
    input = [ [ id:'test' ], file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true) ]    
    BUSCO_BACTE ( input,
+                 "genome",
                  [],
                  [] )
 }
 
-// This tests uncompressed genome, BUSCO lineage file provided via input channel, and offline mode
-workflow test_busco_chr22 {
-    input = [ [ id:'test' ],  file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
-    lineage_dataset = [ file(params.test_data['homo_sapiens']['genome']['chr22_odb10_tar_gz'], checkIfExists: true) ]
-    UNTAR(lineage_dataset)
-    BUSCO_CHR22 ( input,
-                  [],
-                  UNTAR.out.untar )
-}
-
diff --git a/tests/modules/busco/test.yml b/tests/modules/busco/test.yml
index 32553d2eb5d..d66bd3050ce 100644
--- a/tests/modules/busco/test.yml
+++ b/tests/modules/busco/test.yml
@@ -1,5 +1,5 @@
-- name: busco test_busco_bacteroidales
-  command: nextflow run ./tests/modules/busco -entry test_busco_bacteroidales -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config
+- name: busco test_busco
+  command: nextflow run ./tests/modules/busco -entry test_busco -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config
   tags:
     - busco
   files:
@@ -8,13 +8,3 @@
     - path: output/busco/test/run_bacteroidales_odb10/short_summary.txt
       contains: ['Complete BUSCOs (C)']
 
-- name: busco test_busco_chr22
-  command: nextflow run ./tests/modules/busco -entry test_busco_chr22 -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config
-  tags:
-    - busco
-  files:
-    - path: output/busco/test/run_chr22_odb10/full_table.tsv
-      md5sum: 83f20e8996c591338ada73b6ab0eb269
-    - path: output/busco/test/run_chr22_odb10/short_summary.txt
-      contains: ['Complete BUSCOs (C)']
-

From 9a72548ee122607e46681f4b0b87296b48580cb3 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Tue, 3 May 2022 08:42:56 +0000
Subject: [PATCH 03/19] Update busco module

---
 modules/busco/main.nf               | 62 +++++++++++++++++++----------
 tests/modules/busco/main.nf         | 20 +++++++---
 tests/modules/busco/nextflow.config |  5 ++-
 tests/modules/busco/test.yml        |  9 ++---
 4 files changed, 60 insertions(+), 36 deletions(-)

diff --git a/modules/busco/main.nf b/modules/busco/main.nf
index 6e5265384e3..e66beeeb01d 100644
--- a/modules/busco/main.nf
+++ b/modules/busco/main.nf
@@ -1,31 +1,31 @@
 process BUSCO {
     tag "$meta.id"
     label 'process_medium'
-    
-    conda (params.enable_conda ? "bioconda::busco=5.2.2" : null)
+
+    conda (params.enable_conda ? "bioconda::busco=5.3.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/busco:5.2.2--pyhdfd78af_0':
-        'quay.io/biocontainers/busco:5.2.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/busco:5.3.2--pyhdfd78af_0':
+        'quay.io/biocontainers/busco:5.3.2--pyhdfd78af_0' }"
 
     input:
-    tuple val(meta), path(fasta)
-    val(mode)
-    path(augustus_config)
-    val(lineage)
+    tuple val(meta), path(fasta)  // Required:    meta map, and fasta sequence file
+    each lineage                  // Required:    lineage to check against
+    path busco_lineages_path      // Recommended: path to busco lineages - downloads if not set
+    path config_file              // Optional:    busco configuration file
 
     output:
-    tuple val(meta), path("${meta.id}/run_*/full_table.tsv"), emit: tsv
-    tuple val(meta), path("${meta.id}/run_*/short_summary.txt"), emit: txt
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*-busco"), emit: busco_dir
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    if (lineage) args += " --lineage_dataset $lineage"
+    def prefix = task.ext.prefix ?: "${meta.id}-${lineage}"
+    def busco_config = config_file ? "--config $config_file" : ''
+    def busco_lineage_dir = busco_lineages_path ? "--download_path ${busco_lineages_path}" : ''
     """
-    # Ensure the input is uncompressed
-    gzip -cdf $fasta > __UNCOMPRESSED_FASTA_FILE__
-    
     # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
     # Check for container variable initialisation script and source it.
     if [ -f "/usr/local/env-activate.sh" ]; then
@@ -39,12 +39,30 @@ process BUSCO {
         . "/usr/local/etc/conda/activate.d/augustus.sh"
         . "/usr/local/etc/conda/activate.d/openjdk_activate.sh"
     fi
-    
-    # Copy the image's AUGUSTUS config directory if it was not provided to the module
-    [ ! -e augustus_config ] && cp -a /usr/local/config augustus_config
-    
-    # Busco command
-    AUGUSTUS_CONFIG_PATH=augustus_config busco $args --augustus --mode $mode --cpu $task.cpus --in __UNCOMPRESSED_FASTA_FILE__ --out $meta.id
+
+    # If the augustus config directory is not writable, then copy to writeable area
+    if [ ! -w "\${AUGUSTUS_CONFIG_PATH}" ]; then
+        # Create writable tmp directory for augustus
+        AUG_CONF_DIR=\$( mktemp -d -p \$PWD )
+        cp -r \$AUGUSTUS_CONFIG_PATH/* \$AUG_CONF_DIR
+        export AUGUSTUS_CONFIG_PATH=\$AUG_CONF_DIR
+        echo "New AUGUSTUS_CONFIG_PATH=\${AUGUSTUS_CONFIG_PATH}"
+    fi
+
+    # Ensure the input is uncompressed
+    gzip -cdf $fasta > ${prefix}_uncompressed.fasta
+
+    busco \\
+        --cpu $task.cpus \\
+        --in ${prefix}_uncompressed.fasta \\
+        --out ${prefix}-busco \\
+        --lineage_dataset $lineage \\
+        $busco_lineage_dir \\
+        $busco_config \\
+        $args
+
+    # clean up
+    rm ${prefix}_uncompressed.fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/tests/modules/busco/main.nf b/tests/modules/busco/main.nf
index d12abae9c77..4985bd18906 100644
--- a/tests/modules/busco/main.nf
+++ b/tests/modules/busco/main.nf
@@ -2,14 +2,22 @@
 
 nextflow.enable.dsl = 2
 
-include { BUSCO as BUSCO_BACTE } from '../../../modules/busco/main.nf'
+include { BUSCO } from '../../../modules/busco/main.nf'
 
 // This tests genome decompression, empty input channels and data download
 workflow test_busco {
-   input = [ [ id:'test' ], file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true) ]    
-   BUSCO_BACTE ( input,
-                 "genome",
-                 [],
-                 [] )
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+    ]
+
+    BUSCO (
+        input,
+        'bacteria_odb10',
+        [], // Download busco lineage
+        [], // No config
+    )
+
 }
 
diff --git a/tests/modules/busco/nextflow.config b/tests/modules/busco/nextflow.config
index 50f50a7a357..feea8d40035 100644
--- a/tests/modules/busco/nextflow.config
+++ b/tests/modules/busco/nextflow.config
@@ -1,5 +1,6 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
+    ext.args = '--mode genome'
+
+}
diff --git a/tests/modules/busco/test.yml b/tests/modules/busco/test.yml
index d66bd3050ce..3e7c1bf647d 100644
--- a/tests/modules/busco/test.yml
+++ b/tests/modules/busco/test.yml
@@ -1,10 +1,7 @@
 - name: busco test_busco
-  command: nextflow run ./tests/modules/busco -entry test_busco -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config
+  command: nextflow run tests/modules/busco -entry test_busco -c tests/config/nextflow.config
   tags:
     - busco
   files:
-    - path: output/busco/test/run_bacteroidales_odb10/full_table.tsv
-      md5sum: 8d7b401d875ecd9291b01bf4485bf080
-    - path: output/busco/test/run_bacteroidales_odb10/short_summary.txt
-      contains: ['Complete BUSCOs (C)']
-
+    - path: output/busco/versions.yml
+      md5sum: 921e2abe85bf73e63a8b494453dc83cf

From 9eff38ff94c2ecf7236b770b005518bacd272983 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Tue, 3 May 2022 09:15:15 +0000
Subject: [PATCH 04/19] Update meta.yml

---
 modules/busco/meta.yml | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/modules/busco/meta.yml b/modules/busco/meta.yml
index 8f41f2f3b63..72ae4c29f84 100644
--- a/modules/busco/meta.yml
+++ b/modules/busco/meta.yml
@@ -22,14 +22,17 @@ input:
         e.g. [ id:'test', single_end:false ]
   - fasta:
       type: file
-      description: Nucleic or amino acid sequence file in FASTA format
-      pattern: "*.{fasta}"
-  - mode:
+      description: Nucleic or amino acid sequence file in FASTA format.
+      pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}"
+  - lineage:
       type: value
-      description: Sets the assessment MODE – genome, proteins, transcriptome
-  - augustus_config:
+      description: The BUSCO lineage to use.
+  - busco_lineages_path:
       type: directory
-      description: AUGUSTUS config directory
+      description: Path to local BUSCO lineages directory.
+  - config_file:
+      type: directory
+      description: Path to BUSCO config file.
 
 output:
   - meta:
@@ -37,19 +40,16 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
+  - busco_dir:
+      type: directory
+      description: BUSCO lineage specific output
+      pattern: "*-busco"
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  - tsv:
-      type: file
-      description: Full summary table
-      pattern: "*.{tsv}"
-  - txt:
-      type: file
-      description: Short summary text
-      pattern: "*.{txt}"
 
 authors:
   - "@priyanka-surana"
   - "@charles-plessy"
+  - "@mahesh-panchal"

From 012f08537880805ad70a006f0076e6f8933b860f Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Tue, 3 May 2022 09:19:39 +0000
Subject: [PATCH 05/19] Prettier

---
 modules/busco/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/busco/meta.yml b/modules/busco/meta.yml
index 72ae4c29f84..b73f498b57e 100644
--- a/modules/busco/meta.yml
+++ b/modules/busco/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: https://busco.ezlab.org/busco_userguide.html
       tool_dev_url: https://gitlab.com/ezlab/busco
       doi: "10.1007/978-1-4939-9173-0_14"
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:

From 57db28386ebd236e4ffd07c47eba21f284cda55c Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Tue, 3 May 2022 13:26:49 +0000
Subject: [PATCH 06/19] Support batch fasta analysis

---
 modules/busco/main.nf       | 24 +++++++++++++++++-------
 tests/modules/busco/main.nf |  6 ++++--
 2 files changed, 21 insertions(+), 9 deletions(-)

diff --git a/modules/busco/main.nf b/modules/busco/main.nf
index e66beeeb01d..4ba4baac1f6 100644
--- a/modules/busco/main.nf
+++ b/modules/busco/main.nf
@@ -8,10 +8,10 @@ process BUSCO {
         'quay.io/biocontainers/busco:5.3.2--pyhdfd78af_0' }"
 
     input:
-    tuple val(meta), path(fasta)  // Required:    meta map, and fasta sequence file
-    each lineage                  // Required:    lineage to check against
-    path busco_lineages_path      // Recommended: path to busco lineages - downloads if not set
-    path config_file              // Optional:    busco configuration file
+    tuple val(meta), path(fasta, stageAs: 'tmp_input/*')  // Required:    meta map, and fasta sequence files
+    each lineage                                          // Required:    lineage to check against
+    path busco_lineages_path                              // Recommended: path to busco lineages - downloads if not set
+    path config_file                                      // Optional:    busco configuration file
 
     output:
     tuple val(meta), path("*-busco"), emit: busco_dir
@@ -50,11 +50,21 @@ process BUSCO {
     fi
 
     # Ensure the input is uncompressed
-    gzip -cdf $fasta > ${prefix}_uncompressed.fasta
+    INPUT_SEQS=input_seqs
+    mkdir "\$INPUT_SEQS"
+    cd "\$INPUT_SEQS"
+    for FASTA in ../tmp_input/*; do
+        if [ "\${FASTA##*.}" == 'gz' ]; then
+            gzip -cdf "\$FASTA" > \$( basename "\$FASTA" .gz )
+        else
+            ln -s "\$FASTA" .
+        fi
+    done
+    cd ..
 
     busco \\
         --cpu $task.cpus \\
-        --in ${prefix}_uncompressed.fasta \\
+        --in "\$INPUT_SEQS" \\
         --out ${prefix}-busco \\
         --lineage_dataset $lineage \\
         $busco_lineage_dir \\
@@ -62,7 +72,7 @@ process BUSCO {
         $args
 
     # clean up
-    rm ${prefix}_uncompressed.fasta
+    rm -rf "\$INPUT_SEQS"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/tests/modules/busco/main.nf b/tests/modules/busco/main.nf
index 4985bd18906..bdd5f40d450 100644
--- a/tests/modules/busco/main.nf
+++ b/tests/modules/busco/main.nf
@@ -9,7 +9,10 @@ workflow test_busco {
 
     input = [
         [ id:'test', single_end:false ], // meta map
-        file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+        [
+            file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true),
+            file( params.test_data['candidatus_portiera_aleyrodidarum']['genome']['genome_fasta'], checkIfExists: true)
+        ]
     ]
 
     BUSCO (
@@ -20,4 +23,3 @@ workflow test_busco {
     )
 
 }
-

From 4be754b0080364ea14470ea152e3d0f3ca38baa8 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <cortexspam-github@yahoo.fr>
Date: Tue, 3 May 2022 14:53:17 +0100
Subject: [PATCH 07/19] It's a file, not a directory

---
 modules/busco/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/busco/meta.yml b/modules/busco/meta.yml
index b73f498b57e..e546c5ae1ba 100644
--- a/modules/busco/meta.yml
+++ b/modules/busco/meta.yml
@@ -31,7 +31,7 @@ input:
       type: directory
       description: Path to local BUSCO lineages directory.
   - config_file:
-      type: directory
+      type: file
       description: Path to BUSCO config file.
 
 output:

From 6351ec745ea35861554a0896470a43d47d1abee4 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <cortexspam-github@yahoo.fr>
Date: Tue, 3 May 2022 14:56:27 +0100
Subject: [PATCH 08/19] Update contributor list

---
 modules/busco/meta.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/busco/meta.yml b/modules/busco/meta.yml
index e546c5ae1ba..1301e091837 100644
--- a/modules/busco/meta.yml
+++ b/modules/busco/meta.yml
@@ -53,3 +53,4 @@ authors:
   - "@priyanka-surana"
   - "@charles-plessy"
   - "@mahesh-panchal"
+  - "@muffato"

From 1c54c0b1ae684dba97345a136b802b5ef8e31e4d Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Tue, 3 May 2022 16:02:11 +0200
Subject: [PATCH 09/19] Apply suggestions from code review

Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr>
---
 modules/busco/main.nf | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

diff --git a/modules/busco/main.nf b/modules/busco/main.nf
index 4ba4baac1f6..c011b05ba0e 100644
--- a/modules/busco/main.nf
+++ b/modules/busco/main.nf
@@ -24,20 +24,14 @@ process BUSCO {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}-${lineage}"
     def busco_config = config_file ? "--config $config_file" : ''
-    def busco_lineage_dir = busco_lineages_path ? "--download_path ${busco_lineages_path}" : ''
+    def busco_lineage_dir = busco_lineages_path ? "--offline --download_path ${busco_lineages_path}" : ''
     """
     # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
     # Check for container variable initialisation script and source it.
     if [ -f "/usr/local/env-activate.sh" ]; then
-        # . "/usr/local/env-activate.sh"  # Errors out because of various unbound variables
-        export PATH='/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'
-        export CONDA_PREFIX='/usr/local'
-        export CONDA_SHLVL='1'
-        export CONDA_DEFAULT_ENV='/usr/local'
-        export CONDA_PROMPT_MODIFIER=''
-        . "/usr/local/etc/conda/activate.d/activate-r-base.sh"
-        . "/usr/local/etc/conda/activate.d/augustus.sh"
-        . "/usr/local/etc/conda/activate.d/openjdk_activate.sh"
+        set +u  # Otherwise, errors out because of various unbound variables
+        . "/usr/local/env-activate.sh"
+        set -u
     fi
 
     # If the augustus config directory is not writable, then copy to writeable area

From f02cd618b89e57f7d7a92bcdd8c654c85897c14c Mon Sep 17 00:00:00 2001
From: "Jill V. Hagey, PhD" <jvhagey@gmail.com>
Date: Tue, 3 May 2022 10:09:19 -0400
Subject: [PATCH 10/19] Update meta.yml

---
 modules/busco/meta.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/busco/meta.yml b/modules/busco/meta.yml
index 1301e091837..007d5e7cbc5 100644
--- a/modules/busco/meta.yml
+++ b/modules/busco/meta.yml
@@ -54,3 +54,4 @@ authors:
   - "@charles-plessy"
   - "@mahesh-panchal"
   - "@muffato"
+  - "@jvhagey"

From 8df20218bf2f348a4f30b7a9b2f72bdb8e9e23a5 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Wed, 4 May 2022 09:22:43 +0000
Subject: [PATCH 11/19] Add more tests and capture summaries

Co-authored-by: Jill V. Hagey, PhD <jvhagey@gmail.com>
---
 modules/busco/main.nf               |  11 +-
 tests/modules/busco/main.nf         | 304 +++++++++++++++++++++++++++-
 tests/modules/busco/nextflow.config |  24 ++-
 tests/modules/busco/test.yml        |  60 +++++-
 4 files changed, 392 insertions(+), 7 deletions(-)

diff --git a/modules/busco/main.nf b/modules/busco/main.nf
index c011b05ba0e..59ac20f8595 100644
--- a/modules/busco/main.nf
+++ b/modules/busco/main.nf
@@ -14,8 +14,11 @@ process BUSCO {
     path config_file                                      // Optional:    busco configuration file
 
     output:
-    tuple val(meta), path("*-busco"), emit: busco_dir
-    path "versions.yml"             , emit: versions
+    tuple val(meta), path("*-busco.batch_summary.txt"), emit: batch_summary
+    tuple val(meta), path("short_summary.*.txt")      , emit: short_summaries_txt
+    tuple val(meta), path("short_summary.*.json")     , emit: short_summaries_json
+    tuple val(meta), path("*-busco")                  , emit: busco_dir
+    path "versions.yml"                               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -68,6 +71,10 @@ process BUSCO {
     # clean up
     rm -rf "\$INPUT_SEQS"
 
+    # Move files to avoid staging/publishing issues
+    mv ${prefix}-busco/batch_summary.txt ${prefix}-busco.batch_summary.txt
+    mv ${prefix}-busco/*/short_summary.*.{json,txt} .
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         busco: \$( busco --version 2>&1 | sed 's/^BUSCO //' )
diff --git a/tests/modules/busco/main.nf b/tests/modules/busco/main.nf
index bdd5f40d450..a678d371163 100644
--- a/tests/modules/busco/main.nf
+++ b/tests/modules/busco/main.nf
@@ -5,7 +5,70 @@ nextflow.enable.dsl = 2
 include { BUSCO } from '../../../modules/busco/main.nf'
 
 // This tests genome decompression, empty input channels and data download
-workflow test_busco {
+workflow test_busco_genome_single_fasta {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+    ]
+
+    BUSCO (
+        input,
+        ['bacteria_odb10', 'bacteroidetes_odb10'],
+        [], // Download busco lineage
+        [], // No config
+    )
+
+    /* Output tree:
+    /tmp/tmpimsfk4sj/busco/
+    ├── test-bacteria_odb10-busco -> /tmp/tmp1sz7013h/b7/fdeaab567e1c5bccc475a4c19b8582/test-bacteria_odb10-busco/
+    │   ├── batch_summary.txt
+    │   ├── genome.fna/
+    │   │   ├── logs/
+    │   │   │   ├── hmmsearch_err.log
+    │   │   │   ├── hmmsearch_out.log
+    │   │   │   ├── prodigal_err.log
+    │   │   │   └── prodigal_out.log
+    │   │   ├── prodigal_output/
+    │   │   │   └── predicted_genes/
+    │   │   ├── run_bacteria_odb10/
+    │   │   │   ├── busco_sequences/
+    │   │   │   ├── full_table.tsv
+    │   │   │   ├── hmmer_output/
+    │   │   │   ├── missing_busco_list.tsv
+    │   │   │   ├── short_summary.json
+    │   │   │   └── short_summary.txt
+    │   │   ├── short_summary.specific.bacteria_odb10.genome.fna.json
+    │   │   └── short_summary.specific.bacteria_odb10.genome.fna.txt
+    │   └── logs/
+    │       └── busco.log
+    ├── test-bacteroidetes_odb10-busco -> /tmp/tmp1sz7013h/75/0da56f59ee44bd2b85e0172906de49/test-bacteroidetes_odb10-busco/
+    │   ├── batch_summary.txt
+    │   ├── genome.fna/
+    │   │   ├── logs/
+    │   │   │   ├── hmmsearch_err.log
+    │   │   │   ├── hmmsearch_out.log
+    │   │   │   ├── prodigal_err.log
+    │   │   │   └── prodigal_out.log
+    │   │   ├── prodigal_output/
+    │   │   │   └── predicted_genes/
+    │   │   ├── run_bacteroidetes_odb10/
+    │   │   │   ├── busco_sequences/
+    │   │   │   ├── full_table.tsv
+    │   │   │   ├── hmmer_output/
+    │   │   │   ├── missing_busco_list.tsv
+    │   │   │   ├── short_summary.json
+    │   │   │   └── short_summary.txt
+    │   │   ├── short_summary.specific.bacteroidetes_odb10.genome.fna.json
+    │   │   └── short_summary.specific.bacteroidetes_odb10.genome.fna.txt
+    │   └── logs/
+    │       └── busco.log
+    └── versions.yml -> /tmp/tmp1sz7013h/b7/fdeaab567e1c5bccc475a4c19b8582/versions.yml
+    */
+
+}
+
+workflow test_busco_genome_multi_fasta {
 
     input = [
         [ id:'test', single_end:false ], // meta map
@@ -22,4 +85,243 @@ workflow test_busco {
         [], // No config
     )
 
+    /* Output tree:
+    /tmp/tmpt22rjxzq/busco/
+    ├── test-bacteria_odb10-busco -> /tmp/tmpfxt64xr_/36/425acbe5e9b27ba0bac8861f735494/test-bacteria_odb10-busco/
+    │   ├── batch_summary.txt
+    │   ├── genome.fasta/
+    │   │   ├── logs/
+    │   │   │   ├── hmmsearch_err.log
+    │   │   │   ├── hmmsearch_out.log
+    │   │   │   ├── prodigal_err.log
+    │   │   │   └── prodigal_out.log
+    │   │   ├── prodigal_output/
+    │   │   │   └── predicted_genes/
+    │   │   ├── run_bacteria_odb10/
+    │   │   │   ├── busco_sequences/
+    │   │   │   ├── full_table.tsv
+    │   │   │   ├── hmmer_output/
+    │   │   │   ├── missing_busco_list.tsv
+    │   │   │   ├── short_summary.json
+    │   │   │   └── short_summary.txt
+    │   │   ├── short_summary.specific.bacteria_odb10.genome.fasta.json
+    │   │   └── short_summary.specific.bacteria_odb10.genome.fasta.txt
+    │   ├── genome.fna/
+    │   │   ├── logs/
+    │   │   │   ├── hmmsearch_err.log
+    │   │   │   ├── hmmsearch_out.log
+    │   │   │   ├── prodigal_err.log
+    │   │   │   └── prodigal_out.log
+    │   │   ├── prodigal_output/
+    │   │   │   └── predicted_genes/
+    │   │   ├── run_bacteria_odb10/
+    │   │   │   ├── busco_sequences/
+    │   │   │   ├── full_table.tsv
+    │   │   │   ├── hmmer_output/
+    │   │   │   ├── missing_busco_list.tsv
+    │   │   │   ├── short_summary.json
+    │   │   │   └── short_summary.txt
+    │   │   ├── short_summary.specific.bacteria_odb10.genome.fna.json
+    │   │   └── short_summary.specific.bacteria_odb10.genome.fna.txt
+    │   └── logs/
+    │       └── busco.log
+    └── versions.yml -> /tmp/tmpfxt64xr_/36/425acbe5e9b27ba0bac8861f735494/versions.yml
+    */
+
+}
+
+workflow test_busco_eukaryote_metaeuk {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file( params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    BUSCO (
+        input,
+        'eukaryota_odb10',
+        [], // Download busco lineage
+        [], // No config
+    )
+
+    /* Output tree:
+    /tmp/tmp22sf7kg9/busco/
+    ├── test-eukaryota_odb10-busco -> /tmp/tmpmic8qsk6/d5/d8cb6681c0fcaa6da34b57ec174d59/test-eukaryota_odb10-busco/
+    │   ├── batch_summary.txt
+    │   ├── genome.fasta/
+    │   │   ├── logs/
+    │   │   │   ├── hmmsearch_err.log
+    │   │   │   ├── hmmsearch_out.log
+    │   │   │   ├── metaeuk_err.log
+    │   │   │   └── metaeuk_out.log
+    │   │   ├── run_eukaryota_odb10/
+    │   │   │   ├── busco_sequences/
+    │   │   │   ├── full_table.tsv
+    │   │   │   ├── hmmer_output/
+    │   │   │   ├── metaeuk_output/
+    │   │   │   ├── missing_busco_list.tsv
+    │   │   │   ├── short_summary.json
+    │   │   │   └── short_summary.txt
+    │   │   ├── short_summary.specific.eukaryota_odb10.genome.fasta.json
+    │   │   └── short_summary.specific.eukaryota_odb10.genome.fasta.txt
+    │   └── logs/
+    │       └── busco.log
+    └── versions.yml -> /tmp/tmpmic8qsk6/d5/d8cb6681c0fcaa6da34b57ec174d59/versions.yml
+    */
+
+}
+
+workflow test_busco_eukaryote_augustus {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file( params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    BUSCO (
+        input,
+        'eukaryota_odb10',
+        [], // Download busco lineage
+        [], // No config
+    )
+
+    /* Output tree:
+    /tmp/tmpo77wyvb9/busco/
+    ├── test-eukaryota_odb10-busco -> /tmp/tmpshljnwcg/25/9891a19cbabda15a5c10fb5e34987f/test-eukaryota_odb10-busco/
+    │   ├── batch_summary.txt
+    │   ├── genome.fasta/
+    │   │   ├── blast_db/
+    │   │   │   ├── genome.fasta.ndb
+    │   │   │   ├── genome.fasta.nhr
+    │   │   │   ├── genome.fasta.nin
+    │   │   │   ├── genome.fasta.not
+    │   │   │   ├── genome.fasta.nsq
+    │   │   │   ├── genome.fasta.ntf
+    │   │   │   └── genome.fasta.nto
+    │   │   ├── logs/
+    │   │   │   ├── makeblastdb_err.log
+    │   │   │   ├── makeblastdb_out.log
+    │   │   │   ├── tblastn_err.log
+    │   │   │   └── tblastn_out.log
+    │   │   └── run_eukaryota_odb10/
+    │   │       ├── augustus_output/
+    │   │       ├── blast_output/
+    │   │       ├── busco_sequences/
+    │   │       └── hmmer_output/
+    │   └── logs/
+    │       └── busco.log
+    └── versions.yml -> /tmp/tmpshljnwcg/25/9891a19cbabda15a5c10fb5e34987f/versions.yml
+    */
+
+}
+
+workflow test_busco_protein {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file( params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true)
+    ]
+
+    BUSCO (
+        input,
+        'bacteria_odb10',
+        [], // Download busco lineage
+        [], // No config
+    )
+
+    /* Output tree:
+    /tmp/tmplju98s42/busco/
+    ├── test-bacteria_odb10-busco -> /tmp/tmp0oru9_61/9c/e992f5eee84806770002e4510f51cb/test-bacteria_odb10-busco/
+    │   ├── batch_summary.txt
+    │   ├── logs/
+    │   │   └── busco.log
+    │   └── proteome.fasta/
+    │       ├── logs/
+    │       │   ├── hmmsearch_err.log
+    │       │   └── hmmsearch_out.log
+    │       ├── run_bacteria_odb10/
+    │       │   ├── busco_sequences/
+    │       │   ├── full_table.tsv
+    │       │   ├── hmmer_output/
+    │       │   ├── missing_busco_list.tsv
+    │       │   ├── short_summary.json
+    │       │   └── short_summary.txt
+    │       ├── short_summary.specific.bacteria_odb10.proteome.fasta.json
+    │       └── short_summary.specific.bacteria_odb10.proteome.fasta.txt
+    └── versions.yml -> /tmp/tmp0oru9_61/9c/e992f5eee84806770002e4510f51cb/versions.yml
+    */
+}
+workflow test_busco_transcriptome {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file( params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
+    ]
+
+    BUSCO (
+        input,
+        'bacteria_odb10',
+        [], // Download busco lineage
+        [], // No config
+    )
+
+    /* Output tree:
+    /tmp/tmp5twpr8o9/busco/
+    ├── test-bacteria_odb10-busco -> /tmp/tmp_qyjiads/0d/886515d0f06686b2227517398ef8ce/test-bacteria_odb10-busco/
+    │   ├── batch_summary.txt
+    │   ├── logs/
+    │   │   └── busco.log
+    │   └── test1.contigs.fa/
+    │       ├── blast_db/
+    │       │   ├── test1.contigs.fa.ndb
+    │       │   ├── test1.contigs.fa.nhr
+    │       │   ├── test1.contigs.fa.nin
+    │       │   ├── test1.contigs.fa.not
+    │       │   ├── test1.contigs.fa.nsq
+    │       │   ├── test1.contigs.fa.ntf
+    │       │   └── test1.contigs.fa.nto
+    │       ├── logs/
+    │       │   ├── hmmsearch_err.log
+    │       │   ├── hmmsearch_out.log
+    │       │   ├── makeblastdb_err.log
+    │       │   ├── makeblastdb_out.log
+    │       │   ├── tblastn_err.log
+    │       │   └── tblastn_out.log
+    │       ├── run_bacteria_odb10/
+    │       │   ├── blast_output/
+    │       │   ├── busco_sequences/
+    │       │   ├── full_table.tsv
+    │       │   ├── hmmer_output/
+    │       │   ├── missing_busco_list.tsv
+    │       │   ├── short_summary.json
+    │       │   ├── short_summary.txt
+    │       │   └── single_copy_proteins.faa
+    │       ├── short_summary.specific.bacteria_odb10.test1.contigs.fa.json
+    │       ├── short_summary.specific.bacteria_odb10.test1.contigs.fa.txt
+    │       └── translated_proteins/
+    │           ├── 1024388at2.faa
+    │           ├── 1054741at2.faa
+    │           ├── 1093223at2.faa
+    │           ├── 1151822at2.faa
+    │           ├── 143460at2.faa
+    │           ├── 1491686at2.faa
+    │           ├── 1504821at2.faa
+    │           ├── 1574817at2.faa
+    │           ├── 1592033at2.faa
+    │           ├── 1623045at2.faa
+    │           ├── 1661836at2.faa
+    │           ├── 1674344at2.faa
+    │           ├── 1698718at2.faa
+    │           ├── 1990650at2.faa
+    │           ├── 223233at2.faa
+    │           ├── 402899at2.faa
+    │           ├── 505485at2.faa
+    │           ├── 665824at2.faa
+    │           ├── 776861at2.faa
+    │           ├── 874197at2.faa
+    │           ├── 932854at2.faa
+    │           └── 95696at2.faa
+    └── versions.yml -> /tmp/tmp_qyjiads/0d/886515d0f06686b2227517398ef8ce/versions.yml
+    */
+
 }
diff --git a/tests/modules/busco/nextflow.config b/tests/modules/busco/nextflow.config
index feea8d40035..9e8f718f676 100644
--- a/tests/modules/busco/nextflow.config
+++ b/tests/modules/busco/nextflow.config
@@ -1,6 +1,28 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    ext.args = '--mode genome'
 
+    withName: 'test_busco_genome_single_fasta:BUSCO' {
+        ext.args = '--mode genome'
+    }
+
+    withName: 'test_busco_genome_multi_fasta:BUSCO' {
+        ext.args = '--mode genome'
+    }
+
+    withName: 'test_busco_eukaryote_metaeuk:BUSCO' {
+        ext.args = '--mode genome'
+    }
+
+    withName: 'test_busco_eukaryote_augustus:BUSCO' {
+        ext.args = '--mode genome --augustus'
+    }
+
+    withName: 'test_busco_protein:BUSCO' {
+        ext.args = '--mode proteins'
+    }
+
+    withName: 'test_busco_transcriptome:BUSCO'{
+        ext.args = '--mode transcriptome'
+    }
 }
diff --git a/tests/modules/busco/test.yml b/tests/modules/busco/test.yml
index 3e7c1bf647d..2125c3a4340 100644
--- a/tests/modules/busco/test.yml
+++ b/tests/modules/busco/test.yml
@@ -1,7 +1,61 @@
-- name: busco test_busco
-  command: nextflow run tests/modules/busco -entry test_busco -c tests/config/nextflow.config
+- name: busco test_busco_genome_single_fasta
+  command: nextflow run tests/modules/busco -entry test_busco_genome_single_fasta -c tests/config/nextflow.config
   tags:
     - busco
+    - bacteria
+    - genome
   files:
     - path: output/busco/versions.yml
-      md5sum: 921e2abe85bf73e63a8b494453dc83cf
+      md5sum: 8aa830f71587d859df35c6cfab59f35d
+
+- name: busco test_busco_genome_multi_fasta
+  command: nextflow run tests/modules/busco -entry test_busco_genome_multi_fasta -c tests/config/nextflow.config
+  tags:
+    - busco
+    - bacteria
+    - genome
+  files:
+    - path: output/busco/versions.yml
+      md5sum: 9a959eb0a1f765777dff1ea2f5c139c0
+
+- name: busco test_busco_eukaryote_metaeuk
+  command: nextflow run tests/modules/busco -entry test_busco_eukaryote_metaeuk -c tests/config/nextflow.config
+  tags:
+    - busco
+    - eukaryote
+    - genome
+    - metaeuk
+  files:
+    - path: output/busco/versions.yml
+      md5sum: 34a808c257e6db1b0456f3b4372bc477
+
+- name: busco test_busco_eukaryote_augustus
+  command: nextflow run tests/modules/busco -entry test_busco_eukaryote_augustus -c tests/config/nextflow.config
+  tags:
+    - busco
+    - eukaryote
+    - genome
+    - augustus
+  files:
+    - path: output/busco/versions.yml
+      md5sum: 2caac915461410b16a1524ac064cd0df
+
+- name: busco test_busco_protein
+  command: nextflow run tests/modules/busco -entry test_busco_protein -c tests/config/nextflow.config
+  tags:
+    - busco
+    - bacteria
+    - proteins
+  files:
+    - path: output/busco/versions.yml
+      md5sum: d7392261a57960a7e6aea609dce824f5
+
+- name: busco test_busco_transcriptome
+  command: nextflow run tests/modules/busco -entry test_busco_transcriptome -c tests/config/nextflow.config
+  tags:
+    - busco
+    - bacteria
+    - transcriptome
+  files:
+    - path: output/busco/versions.yml
+      md5sum: 30eacbc7df70f6b1e72e0a7b6d02a7e1

From 73a8df9522e31eaa34f9f611d8a5a42d6a8c53fe Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Wed, 4 May 2022 11:52:42 +0000
Subject: [PATCH 12/19] Fix no genes found test and update test.yml

---
 modules/busco/main.nf        |   6 +-
 tests/modules/busco/main.nf  | 166 +++++++++++++++++------------------
 tests/modules/busco/test.yml | 126 +++++++++++++++++++++++---
 3 files changed, 198 insertions(+), 100 deletions(-)

diff --git a/modules/busco/main.nf b/modules/busco/main.nf
index 59ac20f8595..f6bd63e205d 100644
--- a/modules/busco/main.nf
+++ b/modules/busco/main.nf
@@ -15,8 +15,8 @@ process BUSCO {
 
     output:
     tuple val(meta), path("*-busco.batch_summary.txt"), emit: batch_summary
-    tuple val(meta), path("short_summary.*.txt")      , emit: short_summaries_txt
-    tuple val(meta), path("short_summary.*.json")     , emit: short_summaries_json
+    tuple val(meta), path("short_summary.*.txt")      , emit: short_summaries_txt, optional: true
+    tuple val(meta), path("short_summary.*.json")     , emit: short_summaries_json, optional: true
     tuple val(meta), path("*-busco")                  , emit: busco_dir
     path "versions.yml"                               , emit: versions
 
@@ -73,7 +73,7 @@ process BUSCO {
 
     # Move files to avoid staging/publishing issues
     mv ${prefix}-busco/batch_summary.txt ${prefix}-busco.batch_summary.txt
-    mv ${prefix}-busco/*/short_summary.*.{json,txt} .
+    mv ${prefix}-busco/*/short_summary.*.{json,txt} . || echo "Short summaries were not available: No genes were found."
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/tests/modules/busco/main.nf b/tests/modules/busco/main.nf
index a678d371163..f0201d21a75 100644
--- a/tests/modules/busco/main.nf
+++ b/tests/modules/busco/main.nf
@@ -20,9 +20,12 @@ workflow test_busco_genome_single_fasta {
     )
 
     /* Output tree:
-    /tmp/tmpimsfk4sj/busco/
-    ├── test-bacteria_odb10-busco -> /tmp/tmp1sz7013h/b7/fdeaab567e1c5bccc475a4c19b8582/test-bacteria_odb10-busco/
-    │   ├── batch_summary.txt
+    /tmp/tmpisa3ktco/busco/
+    ├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmpm91x0mn2/8a/ff5c15baba0942cca15a8d53e98009/short_summary.specific.bacteria_odb10.genome.fna.json
+    ├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmpm91x0mn2/8a/ff5c15baba0942cca15a8d53e98009/short_summary.specific.bacteria_odb10.genome.fna.txt
+    ├── short_summary.specific.bacteroidetes_odb10.genome.fna.json -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/short_summary.specific.bacteroidetes_odb10.genome.fna.json
+    ├── short_summary.specific.bacteroidetes_odb10.genome.fna.txt -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
+    ├── test-bacteria_odb10-busco -> /tmp/tmpm91x0mn2/8a/ff5c15baba0942cca15a8d53e98009/test-bacteria_odb10-busco/
     │   ├── genome.fna/
     │   │   ├── logs/
     │   │   │   ├── hmmsearch_err.log
@@ -31,19 +34,17 @@ workflow test_busco_genome_single_fasta {
     │   │   │   └── prodigal_out.log
     │   │   ├── prodigal_output/
     │   │   │   └── predicted_genes/
-    │   │   ├── run_bacteria_odb10/
-    │   │   │   ├── busco_sequences/
-    │   │   │   ├── full_table.tsv
-    │   │   │   ├── hmmer_output/
-    │   │   │   ├── missing_busco_list.tsv
-    │   │   │   ├── short_summary.json
-    │   │   │   └── short_summary.txt
-    │   │   ├── short_summary.specific.bacteria_odb10.genome.fna.json
-    │   │   └── short_summary.specific.bacteria_odb10.genome.fna.txt
+    │   │   └── run_bacteria_odb10/
+    │   │       ├── busco_sequences/
+    │   │       ├── full_table.tsv
+    │   │       ├── hmmer_output/
+    │   │       ├── missing_busco_list.tsv
+    │   │       ├── short_summary.json
+    │   │       └── short_summary.txt
     │   └── logs/
     │       └── busco.log
-    ├── test-bacteroidetes_odb10-busco -> /tmp/tmp1sz7013h/75/0da56f59ee44bd2b85e0172906de49/test-bacteroidetes_odb10-busco/
-    │   ├── batch_summary.txt
+    ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpm91x0mn2/8a/ff5c15baba0942cca15a8d53e98009/test-bacteria_odb10-busco.batch_summary.txt
+    ├── test-bacteroidetes_odb10-busco -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/test-bacteroidetes_odb10-busco/
     │   ├── genome.fna/
     │   │   ├── logs/
     │   │   │   ├── hmmsearch_err.log
@@ -52,18 +53,17 @@ workflow test_busco_genome_single_fasta {
     │   │   │   └── prodigal_out.log
     │   │   ├── prodigal_output/
     │   │   │   └── predicted_genes/
-    │   │   ├── run_bacteroidetes_odb10/
-    │   │   │   ├── busco_sequences/
-    │   │   │   ├── full_table.tsv
-    │   │   │   ├── hmmer_output/
-    │   │   │   ├── missing_busco_list.tsv
-    │   │   │   ├── short_summary.json
-    │   │   │   └── short_summary.txt
-    │   │   ├── short_summary.specific.bacteroidetes_odb10.genome.fna.json
-    │   │   └── short_summary.specific.bacteroidetes_odb10.genome.fna.txt
+    │   │   └── run_bacteroidetes_odb10/
+    │   │       ├── busco_sequences/
+    │   │       ├── full_table.tsv
+    │   │       ├── hmmer_output/
+    │   │       ├── missing_busco_list.tsv
+    │   │       ├── short_summary.json
+    │   │       └── short_summary.txt
     │   └── logs/
     │       └── busco.log
-    └── versions.yml -> /tmp/tmp1sz7013h/b7/fdeaab567e1c5bccc475a4c19b8582/versions.yml
+    ├── test-bacteroidetes_odb10-busco.batch_summary.txt -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/test-bacteroidetes_odb10-busco.batch_summary.txt
+    └── versions.yml -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/versions.yml
     */
 
 }
@@ -86,9 +86,12 @@ workflow test_busco_genome_multi_fasta {
     )
 
     /* Output tree:
-    /tmp/tmpt22rjxzq/busco/
-    ├── test-bacteria_odb10-busco -> /tmp/tmpfxt64xr_/36/425acbe5e9b27ba0bac8861f735494/test-bacteria_odb10-busco/
-    │   ├── batch_summary.txt
+    /tmp/tmpk19byek7/busco/
+    ├── short_summary.specific.bacteria_odb10.genome.fasta.json -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fasta.json
+    ├── short_summary.specific.bacteria_odb10.genome.fasta.txt -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fasta.txt
+    ├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fna.json
+    ├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fna.txt
+    ├── test-bacteria_odb10-busco -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/test-bacteria_odb10-busco/
     │   ├── genome.fasta/
     │   │   ├── logs/
     │   │   │   ├── hmmsearch_err.log
@@ -97,15 +100,13 @@ workflow test_busco_genome_multi_fasta {
     │   │   │   └── prodigal_out.log
     │   │   ├── prodigal_output/
     │   │   │   └── predicted_genes/
-    │   │   ├── run_bacteria_odb10/
-    │   │   │   ├── busco_sequences/
-    │   │   │   ├── full_table.tsv
-    │   │   │   ├── hmmer_output/
-    │   │   │   ├── missing_busco_list.tsv
-    │   │   │   ├── short_summary.json
-    │   │   │   └── short_summary.txt
-    │   │   ├── short_summary.specific.bacteria_odb10.genome.fasta.json
-    │   │   └── short_summary.specific.bacteria_odb10.genome.fasta.txt
+    │   │   └── run_bacteria_odb10/
+    │   │       ├── busco_sequences/
+    │   │       ├── full_table.tsv
+    │   │       ├── hmmer_output/
+    │   │       ├── missing_busco_list.tsv
+    │   │       ├── short_summary.json
+    │   │       └── short_summary.txt
     │   ├── genome.fna/
     │   │   ├── logs/
     │   │   │   ├── hmmsearch_err.log
@@ -114,18 +115,17 @@ workflow test_busco_genome_multi_fasta {
     │   │   │   └── prodigal_out.log
     │   │   ├── prodigal_output/
     │   │   │   └── predicted_genes/
-    │   │   ├── run_bacteria_odb10/
-    │   │   │   ├── busco_sequences/
-    │   │   │   ├── full_table.tsv
-    │   │   │   ├── hmmer_output/
-    │   │   │   ├── missing_busco_list.tsv
-    │   │   │   ├── short_summary.json
-    │   │   │   └── short_summary.txt
-    │   │   ├── short_summary.specific.bacteria_odb10.genome.fna.json
-    │   │   └── short_summary.specific.bacteria_odb10.genome.fna.txt
+    │   │   └── run_bacteria_odb10/
+    │   │       ├── busco_sequences/
+    │   │       ├── full_table.tsv
+    │   │       ├── hmmer_output/
+    │   │       ├── missing_busco_list.tsv
+    │   │       ├── short_summary.json
+    │   │       └── short_summary.txt
     │   └── logs/
     │       └── busco.log
-    └── versions.yml -> /tmp/tmpfxt64xr_/36/425acbe5e9b27ba0bac8861f735494/versions.yml
+    ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/test-bacteria_odb10-busco.batch_summary.txt
+    └── versions.yml -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/versions.yml
     */
 
 }
@@ -145,28 +145,28 @@ workflow test_busco_eukaryote_metaeuk {
     )
 
     /* Output tree:
-    /tmp/tmp22sf7kg9/busco/
-    ├── test-eukaryota_odb10-busco -> /tmp/tmpmic8qsk6/d5/d8cb6681c0fcaa6da34b57ec174d59/test-eukaryota_odb10-busco/
-    │   ├── batch_summary.txt
+    /tmp/tmpeq4dsir5/busco/
+    ├── short_summary.specific.eukaryota_odb10.genome.fasta.json -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/short_summary.specific.eukaryota_odb10.genome.fasta.json
+    ├── short_summary.specific.eukaryota_odb10.genome.fasta.txt -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/short_summary.specific.eukaryota_odb10.genome.fasta.txt
+    ├── test-eukaryota_odb10-busco -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/test-eukaryota_odb10-busco/
     │   ├── genome.fasta/
     │   │   ├── logs/
     │   │   │   ├── hmmsearch_err.log
     │   │   │   ├── hmmsearch_out.log
     │   │   │   ├── metaeuk_err.log
     │   │   │   └── metaeuk_out.log
-    │   │   ├── run_eukaryota_odb10/
-    │   │   │   ├── busco_sequences/
-    │   │   │   ├── full_table.tsv
-    │   │   │   ├── hmmer_output/
-    │   │   │   ├── metaeuk_output/
-    │   │   │   ├── missing_busco_list.tsv
-    │   │   │   ├── short_summary.json
-    │   │   │   └── short_summary.txt
-    │   │   ├── short_summary.specific.eukaryota_odb10.genome.fasta.json
-    │   │   └── short_summary.specific.eukaryota_odb10.genome.fasta.txt
+    │   │   └── run_eukaryota_odb10/
+    │   │       ├── busco_sequences/
+    │   │       ├── full_table.tsv
+    │   │       ├── hmmer_output/
+    │   │       ├── metaeuk_output/
+    │   │       ├── missing_busco_list.tsv
+    │   │       ├── short_summary.json
+    │   │       └── short_summary.txt
     │   └── logs/
     │       └── busco.log
-    └── versions.yml -> /tmp/tmpmic8qsk6/d5/d8cb6681c0fcaa6da34b57ec174d59/versions.yml
+    ├── test-eukaryota_odb10-busco.batch_summary.txt -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/test-eukaryota_odb10-busco.batch_summary.txt
+    └── versions.yml -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/versions.yml
     */
 
 }
@@ -186,9 +186,8 @@ workflow test_busco_eukaryote_augustus {
     )
 
     /* Output tree:
-    /tmp/tmpo77wyvb9/busco/
-    ├── test-eukaryota_odb10-busco -> /tmp/tmpshljnwcg/25/9891a19cbabda15a5c10fb5e34987f/test-eukaryota_odb10-busco/
-    │   ├── batch_summary.txt
+    /tmp/tmp2xqaygjj/busco/
+    ├── test-eukaryota_odb10-busco -> /tmp/tmpjqs61x9o/3f/67cc14e873c0ceb45e2a27594d624c/test-eukaryota_odb10-busco/
     │   ├── genome.fasta/
     │   │   ├── blast_db/
     │   │   │   ├── genome.fasta.ndb
@@ -210,7 +209,8 @@ workflow test_busco_eukaryote_augustus {
     │   │       └── hmmer_output/
     │   └── logs/
     │       └── busco.log
-    └── versions.yml -> /tmp/tmpshljnwcg/25/9891a19cbabda15a5c10fb5e34987f/versions.yml
+    ├── test-eukaryota_odb10-busco.batch_summary.txt -> /tmp/tmpjqs61x9o/3f/67cc14e873c0ceb45e2a27594d624c/test-eukaryota_odb10-busco.batch_summary.txt
+    └── versions.yml -> /tmp/tmpjqs61x9o/3f/67cc14e873c0ceb45e2a27594d624c/versions.yml
     */
 
 }
@@ -230,25 +230,25 @@ workflow test_busco_protein {
     )
 
     /* Output tree:
-    /tmp/tmplju98s42/busco/
-    ├── test-bacteria_odb10-busco -> /tmp/tmp0oru9_61/9c/e992f5eee84806770002e4510f51cb/test-bacteria_odb10-busco/
-    │   ├── batch_summary.txt
+    /tmp/tmpzwd5dn56/busco/
+    ├── short_summary.specific.bacteria_odb10.proteome.fasta.json -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/short_summary.specific.bacteria_odb10.proteome.fasta.json
+    ├── short_summary.specific.bacteria_odb10.proteome.fasta.txt -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/short_summary.specific.bacteria_odb10.proteome.fasta.txt
+    ├── test-bacteria_odb10-busco -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/test-bacteria_odb10-busco/
     │   ├── logs/
     │   │   └── busco.log
     │   └── proteome.fasta/
     │       ├── logs/
     │       │   ├── hmmsearch_err.log
     │       │   └── hmmsearch_out.log
-    │       ├── run_bacteria_odb10/
-    │       │   ├── busco_sequences/
-    │       │   ├── full_table.tsv
-    │       │   ├── hmmer_output/
-    │       │   ├── missing_busco_list.tsv
-    │       │   ├── short_summary.json
-    │       │   └── short_summary.txt
-    │       ├── short_summary.specific.bacteria_odb10.proteome.fasta.json
-    │       └── short_summary.specific.bacteria_odb10.proteome.fasta.txt
-    └── versions.yml -> /tmp/tmp0oru9_61/9c/e992f5eee84806770002e4510f51cb/versions.yml
+    │       └── run_bacteria_odb10/
+    │           ├── busco_sequences/
+    │           ├── full_table.tsv
+    │           ├── hmmer_output/
+    │           ├── missing_busco_list.tsv
+    │           ├── short_summary.json
+    │           └── short_summary.txt
+    ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/test-bacteria_odb10-busco.batch_summary.txt
+    └── versions.yml -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/versions.yml
     */
 }
 workflow test_busco_transcriptome {
@@ -266,9 +266,10 @@ workflow test_busco_transcriptome {
     )
 
     /* Output tree:
-    /tmp/tmp5twpr8o9/busco/
-    ├── test-bacteria_odb10-busco -> /tmp/tmp_qyjiads/0d/886515d0f06686b2227517398ef8ce/test-bacteria_odb10-busco/
-    │   ├── batch_summary.txt
+    /tmp/tmpitjyvo9g/busco/
+    ├── short_summary.specific.bacteria_odb10.test1.contigs.fa.json -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/short_summary.specific.bacteria_odb10.test1.contigs.fa.json
+    ├── short_summary.specific.bacteria_odb10.test1.contigs.fa.txt -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/short_summary.specific.bacteria_odb10.test1.contigs.fa.txt
+    ├── test-bacteria_odb10-busco -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/test-bacteria_odb10-busco/
     │   ├── logs/
     │   │   └── busco.log
     │   └── test1.contigs.fa/
@@ -296,8 +297,6 @@ workflow test_busco_transcriptome {
     │       │   ├── short_summary.json
     │       │   ├── short_summary.txt
     │       │   └── single_copy_proteins.faa
-    │       ├── short_summary.specific.bacteria_odb10.test1.contigs.fa.json
-    │       ├── short_summary.specific.bacteria_odb10.test1.contigs.fa.txt
     │       └── translated_proteins/
     │           ├── 1024388at2.faa
     │           ├── 1054741at2.faa
@@ -321,7 +320,8 @@ workflow test_busco_transcriptome {
     │           ├── 874197at2.faa
     │           ├── 932854at2.faa
     │           └── 95696at2.faa
-    └── versions.yml -> /tmp/tmp_qyjiads/0d/886515d0f06686b2227517398ef8ce/versions.yml
+    ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/test-bacteria_odb10-busco.batch_summary.txt
+    └── versions.yml -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/versions.yml
     */
 
 }
diff --git a/tests/modules/busco/test.yml b/tests/modules/busco/test.yml
index 2125c3a4340..b838d9b7ffc 100644
--- a/tests/modules/busco/test.yml
+++ b/tests/modules/busco/test.yml
@@ -2,9 +2,39 @@
   command: nextflow run tests/modules/busco -entry test_busco_genome_single_fasta -c tests/config/nextflow.config
   tags:
     - busco
-    - bacteria
-    - genome
   files:
+    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
+      contains:
+        - 'one_line_summary'
+        - 'input_file'
+        - 'mode'
+        - 'dataset'
+    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.txt
+      contains:
+        - 'BUSCO version'
+        - 'The lineage dataset is'
+        - 'BUSCO was run in mode'
+        - 'Complete BUSCOs'
+        - 'Missing BUSCOs'
+        - 'Dependencies and versions'
+    - path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.json
+      contains:
+        - 'one_line_summary'
+        - 'input_file'
+        - 'mode'
+        - 'dataset'
+    - path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
+      contains:
+        - 'BUSCO version'
+        - 'The lineage dataset is'
+        - 'BUSCO was run in mode'
+        - 'Complete BUSCOs'
+        - 'Missing BUSCOs'
+        - 'Dependencies and versions'
+    - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
+      md5sum: e50690742e9ae6abdd2bf99334ff9e12
+    - path: output/busco/test-bacteroidetes_odb10-busco.batch_summary.txt
+      md5sum: 4c1b2c4317c88398eddc30877ed740d9
     - path: output/busco/versions.yml
       md5sum: 8aa830f71587d859df35c6cfab59f35d
 
@@ -12,9 +42,37 @@
   command: nextflow run tests/modules/busco -entry test_busco_genome_multi_fasta -c tests/config/nextflow.config
   tags:
     - busco
-    - bacteria
-    - genome
   files:
+    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.json
+      contains:
+        - 'one_line_summary'
+        - 'input_file'
+        - 'mode'
+        - 'dataset'
+    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.txt
+      contains:
+        - 'BUSCO version'
+        - 'The lineage dataset is'
+        - 'BUSCO was run in mode'
+        - 'Complete BUSCOs'
+        - 'Missing BUSCOs'
+        - 'Dependencies and versions'
+    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
+      contains:
+        - 'one_line_summary'
+        - 'input_file'
+        - 'mode'
+        - 'dataset'
+    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.txt
+      contains:
+        - 'BUSCO version'
+        - 'The lineage dataset is'
+        - 'BUSCO was run in mode'
+        - 'Complete BUSCOs'
+        - 'Missing BUSCOs'
+        - 'Dependencies and versions'
+    - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
+      md5sum: 5360dfe83bec1f5741ee115e53e6b517
     - path: output/busco/versions.yml
       md5sum: 9a959eb0a1f765777dff1ea2f5c139c0
 
@@ -22,10 +80,23 @@
   command: nextflow run tests/modules/busco -entry test_busco_eukaryote_metaeuk -c tests/config/nextflow.config
   tags:
     - busco
-    - eukaryote
-    - genome
-    - metaeuk
   files:
+    - path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.json
+      contains:
+        - 'one_line_summary'
+        - 'input_file'
+        - 'mode'
+        - 'dataset'
+    - path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.txt
+      contains:
+        - 'BUSCO version'
+        - 'The lineage dataset is'
+        - 'BUSCO was run in mode'
+        - 'Complete BUSCOs'
+        - 'Missing BUSCOs'
+        - 'Dependencies and versions'
+    - path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
+      md5sum: a70806f99ba5706d7353d3353b3f1d2b
     - path: output/busco/versions.yml
       md5sum: 34a808c257e6db1b0456f3b4372bc477
 
@@ -33,10 +104,9 @@
   command: nextflow run tests/modules/busco -entry test_busco_eukaryote_augustus -c tests/config/nextflow.config
   tags:
     - busco
-    - eukaryote
-    - genome
-    - augustus
   files:
+    - path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
+      md5sum: 660393dd43cd6a093b952d4b8ad41e40
     - path: output/busco/versions.yml
       md5sum: 2caac915461410b16a1524ac064cd0df
 
@@ -44,9 +114,23 @@
   command: nextflow run tests/modules/busco -entry test_busco_protein -c tests/config/nextflow.config
   tags:
     - busco
-    - bacteria
-    - proteins
   files:
+    - path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.json
+      contains:
+        - 'one_line_summary'
+        - 'input_file'
+        - 'mode'
+        - 'dataset'
+    - path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.txt
+      contains:
+        - 'BUSCO version'
+        - 'The lineage dataset is'
+        - 'BUSCO was run in mode'
+        - 'Complete BUSCOs'
+        - 'Missing BUSCOs'
+        - 'Dependencies and versions'
+    - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
+      md5sum: fd3b4e30ce74d1fcb95d6286d6e2049f
     - path: output/busco/versions.yml
       md5sum: d7392261a57960a7e6aea609dce824f5
 
@@ -54,8 +138,22 @@
   command: nextflow run tests/modules/busco -entry test_busco_transcriptome -c tests/config/nextflow.config
   tags:
     - busco
-    - bacteria
-    - transcriptome
   files:
+    - path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.json
+      contains:
+        - 'one_line_summary'
+        - 'input_file'
+        - 'mode'
+        - 'dataset'
+    - path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.txt
+      contains:
+        - 'BUSCO version'
+        - 'The lineage dataset is'
+        - 'BUSCO was run in mode'
+        - 'Complete BUSCOs'
+        - 'Missing BUSCOs'
+        - 'Dependencies and versions'
+    - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
+      md5sum: 9a176cafe66ac0adca89dc34ad2be13f
     - path: output/busco/versions.yml
       md5sum: 30eacbc7df70f6b1e72e0a7b6d02a7e1

From f65abe1e9a4e9d9932772a4d2355666b9cac9e61 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Wed, 4 May 2022 11:54:51 +0000
Subject: [PATCH 13/19] Prettier

---
 tests/modules/busco/test.yml | 140 +++++++++++++++++------------------
 1 file changed, 70 insertions(+), 70 deletions(-)

diff --git a/tests/modules/busco/test.yml b/tests/modules/busco/test.yml
index b838d9b7ffc..43b810ba192 100644
--- a/tests/modules/busco/test.yml
+++ b/tests/modules/busco/test.yml
@@ -5,32 +5,32 @@
   files:
     - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
       contains:
-        - 'one_line_summary'
-        - 'input_file'
-        - 'mode'
-        - 'dataset'
+        - "one_line_summary"
+        - "input_file"
+        - "mode"
+        - "dataset"
     - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.txt
       contains:
-        - 'BUSCO version'
-        - 'The lineage dataset is'
-        - 'BUSCO was run in mode'
-        - 'Complete BUSCOs'
-        - 'Missing BUSCOs'
-        - 'Dependencies and versions'
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
     - path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.json
       contains:
-        - 'one_line_summary'
-        - 'input_file'
-        - 'mode'
-        - 'dataset'
+        - "one_line_summary"
+        - "input_file"
+        - "mode"
+        - "dataset"
     - path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
       contains:
-        - 'BUSCO version'
-        - 'The lineage dataset is'
-        - 'BUSCO was run in mode'
-        - 'Complete BUSCOs'
-        - 'Missing BUSCOs'
-        - 'Dependencies and versions'
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
     - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
       md5sum: e50690742e9ae6abdd2bf99334ff9e12
     - path: output/busco/test-bacteroidetes_odb10-busco.batch_summary.txt
@@ -45,32 +45,32 @@
   files:
     - path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.json
       contains:
-        - 'one_line_summary'
-        - 'input_file'
-        - 'mode'
-        - 'dataset'
+        - "one_line_summary"
+        - "input_file"
+        - "mode"
+        - "dataset"
     - path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.txt
       contains:
-        - 'BUSCO version'
-        - 'The lineage dataset is'
-        - 'BUSCO was run in mode'
-        - 'Complete BUSCOs'
-        - 'Missing BUSCOs'
-        - 'Dependencies and versions'
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
     - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
       contains:
-        - 'one_line_summary'
-        - 'input_file'
-        - 'mode'
-        - 'dataset'
+        - "one_line_summary"
+        - "input_file"
+        - "mode"
+        - "dataset"
     - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.txt
       contains:
-        - 'BUSCO version'
-        - 'The lineage dataset is'
-        - 'BUSCO was run in mode'
-        - 'Complete BUSCOs'
-        - 'Missing BUSCOs'
-        - 'Dependencies and versions'
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
     - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
       md5sum: 5360dfe83bec1f5741ee115e53e6b517
     - path: output/busco/versions.yml
@@ -83,18 +83,18 @@
   files:
     - path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.json
       contains:
-        - 'one_line_summary'
-        - 'input_file'
-        - 'mode'
-        - 'dataset'
+        - "one_line_summary"
+        - "input_file"
+        - "mode"
+        - "dataset"
     - path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.txt
       contains:
-        - 'BUSCO version'
-        - 'The lineage dataset is'
-        - 'BUSCO was run in mode'
-        - 'Complete BUSCOs'
-        - 'Missing BUSCOs'
-        - 'Dependencies and versions'
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
     - path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
       md5sum: a70806f99ba5706d7353d3353b3f1d2b
     - path: output/busco/versions.yml
@@ -117,18 +117,18 @@
   files:
     - path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.json
       contains:
-        - 'one_line_summary'
-        - 'input_file'
-        - 'mode'
-        - 'dataset'
+        - "one_line_summary"
+        - "input_file"
+        - "mode"
+        - "dataset"
     - path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.txt
       contains:
-        - 'BUSCO version'
-        - 'The lineage dataset is'
-        - 'BUSCO was run in mode'
-        - 'Complete BUSCOs'
-        - 'Missing BUSCOs'
-        - 'Dependencies and versions'
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
     - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
       md5sum: fd3b4e30ce74d1fcb95d6286d6e2049f
     - path: output/busco/versions.yml
@@ -141,18 +141,18 @@
   files:
     - path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.json
       contains:
-        - 'one_line_summary'
-        - 'input_file'
-        - 'mode'
-        - 'dataset'
+        - "one_line_summary"
+        - "input_file"
+        - "mode"
+        - "dataset"
     - path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.txt
       contains:
-        - 'BUSCO version'
-        - 'The lineage dataset is'
-        - 'BUSCO was run in mode'
-        - 'Complete BUSCOs'
-        - 'Missing BUSCOs'
-        - 'Dependencies and versions'
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
     - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
       md5sum: 9a176cafe66ac0adca89dc34ad2be13f
     - path: output/busco/versions.yml

From 865ad3447a2b74167a25f36e0471f7dbe42fce97 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Thu, 5 May 2022 08:23:54 +0000
Subject: [PATCH 14/19] Update meta.yml output files

---
 modules/busco/meta.yml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/modules/busco/meta.yml b/modules/busco/meta.yml
index 007d5e7cbc5..19c2c991b9f 100644
--- a/modules/busco/meta.yml
+++ b/modules/busco/meta.yml
@@ -40,6 +40,18 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
+  - batch_summary:
+      type: file
+      description: Summary of all sequence files analyzed
+      pattern: "*-busco.batch_summary.txt"
+  - short_summaries_txt:
+      type: file
+      description: Short Busco summary in plain text format
+      pattern: "short_summary.*.txt"
+  - short_summaries_json:
+      type: file
+      description: Short Busco summary in JSON format
+      pattern: "short_summary.*.json"
   - busco_dir:
       type: directory
       description: BUSCO lineage specific output

From 2542ae1823d57777434a63849e217eabf97b3a8e Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Thu, 5 May 2022 16:33:32 +0200
Subject: [PATCH 15/19] Update modules/busco/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
---
 modules/busco/main.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/busco/main.nf b/modules/busco/main.nf
index f6bd63e205d..15e7ce5c25c 100644
--- a/modules/busco/main.nf
+++ b/modules/busco/main.nf
@@ -8,10 +8,10 @@ process BUSCO {
         'quay.io/biocontainers/busco:5.3.2--pyhdfd78af_0' }"
 
     input:
-    tuple val(meta), path(fasta, stageAs: 'tmp_input/*')  // Required:    meta map, and fasta sequence files
-    each lineage                                          // Required:    lineage to check against
-    path busco_lineages_path                              // Recommended: path to busco lineages - downloads if not set
-    path config_file                                      // Optional:    busco configuration file
+    tuple val(meta), path('tmp_input/*')  // Required:    meta map, and fasta sequence files
+    each lineage                          // Required:    lineage to check against
+    path busco_lineages_path              // Recommended: path to busco lineages - downloads if not set
+    path config_file                      // Optional:    busco configuration file
 
     output:
     tuple val(meta), path("*-busco.batch_summary.txt"), emit: batch_summary

From 1289626cc99eecb3436bd067cd90a85028957d5f Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Thu, 5 May 2022 16:09:45 +0100
Subject: [PATCH 16/19] Update modules/busco/main.nf

---
 modules/busco/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/busco/main.nf b/modules/busco/main.nf
index 15e7ce5c25c..8c1b1dad518 100644
--- a/modules/busco/main.nf
+++ b/modules/busco/main.nf
@@ -8,7 +8,7 @@ process BUSCO {
         'quay.io/biocontainers/busco:5.3.2--pyhdfd78af_0' }"
 
     input:
-    tuple val(meta), path('tmp_input/*')  // Required:    meta map, and fasta sequence files
+    tuple val(meta), path('tmp_input/*')
     each lineage                          // Required:    lineage to check against
     path busco_lineages_path              // Recommended: path to busco lineages - downloads if not set
     path config_file                      // Optional:    busco configuration file

From 35c5828f43b50bc029b20b133d3878b3bc16ca9d Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Fri, 6 May 2022 11:48:21 +0000
Subject: [PATCH 17/19] Add --auto-lineage option and remove single_end

Co-authored-by: Jill V. Hagey, PhD <jvhagey@gmail.com>
---
 modules/busco/main.nf        |  5 +--
 tests/modules/busco/main.nf  | 67 ++++++++++++++++++++++++++----------
 tests/modules/busco/test.yml | 30 ++++++++++++++++
 3 files changed, 82 insertions(+), 20 deletions(-)

diff --git a/modules/busco/main.nf b/modules/busco/main.nf
index 8c1b1dad518..f0713862439 100644
--- a/modules/busco/main.nf
+++ b/modules/busco/main.nf
@@ -9,7 +9,7 @@ process BUSCO {
 
     input:
     tuple val(meta), path('tmp_input/*')
-    each lineage                          // Required:    lineage to check against
+    each lineage                          // Required:    lineage to check against, "auto" enables --auto-lineage instead
     path busco_lineages_path              // Recommended: path to busco lineages - downloads if not set
     path config_file                      // Optional:    busco configuration file
 
@@ -27,6 +27,7 @@ process BUSCO {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}-${lineage}"
     def busco_config = config_file ? "--config $config_file" : ''
+    def busco_lineage = lineage.equals('auto') ? '--auto-lineage' : "--lineage_dataset ${lineage}"
     def busco_lineage_dir = busco_lineages_path ? "--offline --download_path ${busco_lineages_path}" : ''
     """
     # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
@@ -63,7 +64,7 @@ process BUSCO {
         --cpu $task.cpus \\
         --in "\$INPUT_SEQS" \\
         --out ${prefix}-busco \\
-        --lineage_dataset $lineage \\
+        $busco_lineage \\
         $busco_lineage_dir \\
         $busco_config \\
         $args
diff --git a/tests/modules/busco/main.nf b/tests/modules/busco/main.nf
index f0201d21a75..e290b9651a9 100644
--- a/tests/modules/busco/main.nf
+++ b/tests/modules/busco/main.nf
@@ -4,28 +4,59 @@ nextflow.enable.dsl = 2
 
 include { BUSCO } from '../../../modules/busco/main.nf'
 
-// This tests genome decompression, empty input channels and data download
 workflow test_busco_genome_single_fasta {
 
     input = [
-        [ id:'test', single_end:false ], // meta map
+        [ id:'test' ], // meta map
         file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
     ]
 
     BUSCO (
         input,
-        ['bacteria_odb10', 'bacteroidetes_odb10'],
+        ['auto','bacteria_odb10', 'bacteroidetes_odb10'],  // Launch with auto to use --auto-lineage, and specified lineages
         [], // Download busco lineage
         [], // No config
     )
 
     /* Output tree:
-    /tmp/tmpisa3ktco/busco/
-    ├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmpm91x0mn2/8a/ff5c15baba0942cca15a8d53e98009/short_summary.specific.bacteria_odb10.genome.fna.json
-    ├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmpm91x0mn2/8a/ff5c15baba0942cca15a8d53e98009/short_summary.specific.bacteria_odb10.genome.fna.txt
-    ├── short_summary.specific.bacteroidetes_odb10.genome.fna.json -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/short_summary.specific.bacteroidetes_odb10.genome.fna.json
-    ├── short_summary.specific.bacteroidetes_odb10.genome.fna.txt -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
-    ├── test-bacteria_odb10-busco -> /tmp/tmpm91x0mn2/8a/ff5c15baba0942cca15a8d53e98009/test-bacteria_odb10-busco/
+    /tmp/tmp846crjv2/busco/
+    ├── short_summary.generic.bacteria_odb10.genome.fna.json -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.json
+    ├── short_summary.generic.bacteria_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.txt
+    ├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/short_summary.specific.bacteria_odb10.genome.fna.json
+    ├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/short_summary.specific.bacteria_odb10.genome.fna.txt
+    ├── short_summary.specific.bacteroidales_odb10.genome.fna.json -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.specific.bacteroidales_odb10.genome.fna.json
+    ├── short_summary.specific.bacteroidales_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.specific.bacteroidales_odb10.genome.fna.txt
+    ├── short_summary.specific.bacteroidetes_odb10.genome.fna.json -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/short_summary.specific.bacteroidetes_odb10.genome.fna.json
+    ├── short_summary.specific.bacteroidetes_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
+    ├── test-auto-busco -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco/
+    │   ├── genome.fna/
+    │   │   ├── auto_lineage/
+    │   │   │   ├── run_archaea_odb10/
+    │   │   │   ├── run_bacteria_odb10/
+    │   │   │   └── run_eukaryota_odb10/
+    │   │   ├── logs/
+    │   │   │   ├── hmmsearch_err.log
+    │   │   │   ├── hmmsearch_out.log
+    │   │   │   ├── metaeuk_err.log
+    │   │   │   ├── metaeuk_out.log
+    │   │   │   ├── prodigal_err.log
+    │   │   │   ├── prodigal_out.log
+    │   │   │   ├── sepp_err.log
+    │   │   │   └── sepp_out.log
+    │   │   ├── prodigal_output/
+    │   │   │   └── predicted_genes/
+    │   │   ├── run_bacteria_odb10 -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco/genome.fna/auto_lineage/run_bacteria_odb10/  [recursive, not followed]
+    │   │   └── run_bacteroidales_odb10/
+    │   │       ├── busco_sequences/
+    │   │       ├── full_table.tsv
+    │   │       ├── hmmer_output/
+    │   │       ├── missing_busco_list.tsv
+    │   │       ├── short_summary.json
+    │   │       └── short_summary.txt
+    │   └── logs/
+    │       └── busco.log
+    ├── test-auto-busco.batch_summary.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco.batch_summary.txt
+    ├── test-bacteria_odb10-busco -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/test-bacteria_odb10-busco/
     │   ├── genome.fna/
     │   │   ├── logs/
     │   │   │   ├── hmmsearch_err.log
@@ -43,8 +74,8 @@ workflow test_busco_genome_single_fasta {
     │   │       └── short_summary.txt
     │   └── logs/
     │       └── busco.log
-    ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpm91x0mn2/8a/ff5c15baba0942cca15a8d53e98009/test-bacteria_odb10-busco.batch_summary.txt
-    ├── test-bacteroidetes_odb10-busco -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/test-bacteroidetes_odb10-busco/
+    ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/test-bacteria_odb10-busco.batch_summary.txt
+    ├── test-bacteroidetes_odb10-busco -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/test-bacteroidetes_odb10-busco/
     │   ├── genome.fna/
     │   │   ├── logs/
     │   │   │   ├── hmmsearch_err.log
@@ -62,8 +93,8 @@ workflow test_busco_genome_single_fasta {
     │   │       └── short_summary.txt
     │   └── logs/
     │       └── busco.log
-    ├── test-bacteroidetes_odb10-busco.batch_summary.txt -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/test-bacteroidetes_odb10-busco.batch_summary.txt
-    └── versions.yml -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/versions.yml
+    ├── test-bacteroidetes_odb10-busco.batch_summary.txt -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/test-bacteroidetes_odb10-busco.batch_summary.txt
+    └── versions.yml -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/versions.yml
     */
 
 }
@@ -71,7 +102,7 @@ workflow test_busco_genome_single_fasta {
 workflow test_busco_genome_multi_fasta {
 
     input = [
-        [ id:'test', single_end:false ], // meta map
+        [ id:'test' ], // meta map
         [
             file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true),
             file( params.test_data['candidatus_portiera_aleyrodidarum']['genome']['genome_fasta'], checkIfExists: true)
@@ -133,7 +164,7 @@ workflow test_busco_genome_multi_fasta {
 workflow test_busco_eukaryote_metaeuk {
 
     input = [
-        [ id:'test', single_end:false ], // meta map
+        [ id:'test' ], // meta map
         file( params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     ]
 
@@ -174,7 +205,7 @@ workflow test_busco_eukaryote_metaeuk {
 workflow test_busco_eukaryote_augustus {
 
     input = [
-        [ id:'test', single_end:false ], // meta map
+        [ id:'test' ], // meta map
         file( params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     ]
 
@@ -218,7 +249,7 @@ workflow test_busco_eukaryote_augustus {
 workflow test_busco_protein {
 
     input = [
-        [ id:'test', single_end:false ], // meta map
+        [ id:'test' ], // meta map
         file( params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true)
     ]
 
@@ -254,7 +285,7 @@ workflow test_busco_protein {
 workflow test_busco_transcriptome {
 
     input = [
-        [ id:'test', single_end:false ], // meta map
+        [ id:'test' ], // meta map
         file( params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
     ]
 
diff --git a/tests/modules/busco/test.yml b/tests/modules/busco/test.yml
index 43b810ba192..2a801e64f3e 100644
--- a/tests/modules/busco/test.yml
+++ b/tests/modules/busco/test.yml
@@ -3,6 +3,20 @@
   tags:
     - busco
   files:
+    - path: output/busco/short_summary.generic.bacteria_odb10.genome.fna.json
+      contains:
+        - "one_line_summary"
+        - "input_file"
+        - "mode"
+        - "dataset"
+    - path: output/busco/short_summary.generic.bacteria_odb10.genome.fna.txt
+      contains:
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
     - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
       contains:
         - "one_line_summary"
@@ -17,6 +31,20 @@
         - "Complete BUSCOs"
         - "Missing BUSCOs"
         - "Dependencies and versions"
+    - path: output/busco/short_summary.specific.bacteroidales_odb10.genome.fna.json
+      contains:
+        - "one_line_summary"
+        - "input_file"
+        - "mode"
+        - "dataset"
+    - path: output/busco/short_summary.specific.bacteroidales_odb10.genome.fna.txt
+      contains:
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
     - path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.json
       contains:
         - "one_line_summary"
@@ -31,6 +59,8 @@
         - "Complete BUSCOs"
         - "Missing BUSCOs"
         - "Dependencies and versions"
+    - path: output/busco/test-auto-busco.batch_summary.txt
+      md5sum: 32f7765c310f33555c31c7a3e64c990e
     - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
       md5sum: e50690742e9ae6abdd2bf99334ff9e12
     - path: output/busco/test-bacteroidetes_odb10-busco.batch_summary.txt

From 9fa6b6c1fc930830c1d819a9273b4ec12ffacb0a Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Fri, 6 May 2022 11:56:19 +0000
Subject: [PATCH 18/19] Update meta.yml

---
 modules/busco/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/busco/meta.yml b/modules/busco/meta.yml
index 19c2c991b9f..ef8c5245c7f 100644
--- a/modules/busco/meta.yml
+++ b/modules/busco/meta.yml
@@ -26,7 +26,7 @@ input:
       pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}"
   - lineage:
       type: value
-      description: The BUSCO lineage to use.
+      description: The BUSCO lineage to use, or "auto" to automatically select lineage
   - busco_lineages_path:
       type: directory
       description: Path to local BUSCO lineages directory.

From 7a85760d080d74ea8b883f9255a6d3861fd7d44b Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Fri, 6 May 2022 13:33:27 +0000
Subject: [PATCH 19/19] remove 'auto' test

---
 tests/modules/busco/main.nf  | 48 +++++++++++++++++++++++++++++++++++-
 tests/modules/busco/test.yml | 30 ----------------------
 2 files changed, 47 insertions(+), 31 deletions(-)

diff --git a/tests/modules/busco/main.nf b/tests/modules/busco/main.nf
index e290b9651a9..598e148add2 100644
--- a/tests/modules/busco/main.nf
+++ b/tests/modules/busco/main.nf
@@ -13,12 +13,58 @@ workflow test_busco_genome_single_fasta {
 
     BUSCO (
         input,
-        ['auto','bacteria_odb10', 'bacteroidetes_odb10'],  // Launch with auto to use --auto-lineage, and specified lineages
+        ['bacteria_odb10', 'bacteroidetes_odb10'],  // Launch with 'auto' to use --auto-lineage, and specified lineages // 'auto' removed from test due to memory issues
         [], // Download busco lineage
         [], // No config
     )
 
     /* Output tree:
+    /tmp/tmpyz_hi62i/busco/
+    ├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmpza_0dth3/33/7d8c9b2c8931d9ad6a67aa843895e7/short_summary.specific.bacteria_odb10.genome.fna.json
+    ├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmpza_0dth3/33/7d8c9b2c8931d9ad6a67aa843895e7/short_summary.specific.bacteria_odb10.genome.fna.txt
+    ├── short_summary.specific.bacteroidetes_odb10.genome.fna.json -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/short_summary.specific.bacteroidetes_odb10.genome.fna.json
+    ├── short_summary.specific.bacteroidetes_odb10.genome.fna.txt -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
+    ├── test-bacteria_odb10-busco -> /tmp/tmpza_0dth3/33/7d8c9b2c8931d9ad6a67aa843895e7/test-bacteria_odb10-busco/
+    │   ├── genome.fna/
+    │   │   ├── logs/
+    │   │   │   ├── hmmsearch_err.log
+    │   │   │   ├── hmmsearch_out.log
+    │   │   │   ├── prodigal_err.log
+    │   │   │   └── prodigal_out.log
+    │   │   ├── prodigal_output/
+    │   │   │   └── predicted_genes/
+    │   │   └── run_bacteria_odb10/
+    │   │       ├── busco_sequences/
+    │   │       ├── full_table.tsv
+    │   │       ├── hmmer_output/
+    │   │       ├── missing_busco_list.tsv
+    │   │       ├── short_summary.json
+    │   │       └── short_summary.txt
+    │   └── logs/
+    │       └── busco.log
+    ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpza_0dth3/33/7d8c9b2c8931d9ad6a67aa843895e7/test-bacteria_odb10-busco.batch_summary.txt
+    ├── test-bacteroidetes_odb10-busco -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/test-bacteroidetes_odb10-busco/
+    │   ├── genome.fna/
+    │   │   ├── logs/
+    │   │   │   ├── hmmsearch_err.log
+    │   │   │   ├── hmmsearch_out.log
+    │   │   │   ├── prodigal_err.log
+    │   │   │   └── prodigal_out.log
+    │   │   ├── prodigal_output/
+    │   │   │   └── predicted_genes/
+    │   │   └── run_bacteroidetes_odb10/
+    │   │       ├── busco_sequences/
+    │   │       ├── full_table.tsv
+    │   │       ├── hmmer_output/
+    │   │       ├── missing_busco_list.tsv
+    │   │       ├── short_summary.json
+    │   │       └── short_summary.txt
+    │   └── logs/
+    │       └── busco.log
+    ├── test-bacteroidetes_odb10-busco.batch_summary.txt -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/test-bacteroidetes_odb10-busco.batch_summary.txt
+    └── versions.yml -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/versions.yml
+
+    Former Output tree -w 'auto':
     /tmp/tmp846crjv2/busco/
     ├── short_summary.generic.bacteria_odb10.genome.fna.json -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.json
     ├── short_summary.generic.bacteria_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.txt
diff --git a/tests/modules/busco/test.yml b/tests/modules/busco/test.yml
index 2a801e64f3e..43b810ba192 100644
--- a/tests/modules/busco/test.yml
+++ b/tests/modules/busco/test.yml
@@ -3,20 +3,6 @@
   tags:
     - busco
   files:
-    - path: output/busco/short_summary.generic.bacteria_odb10.genome.fna.json
-      contains:
-        - "one_line_summary"
-        - "input_file"
-        - "mode"
-        - "dataset"
-    - path: output/busco/short_summary.generic.bacteria_odb10.genome.fna.txt
-      contains:
-        - "BUSCO version"
-        - "The lineage dataset is"
-        - "BUSCO was run in mode"
-        - "Complete BUSCOs"
-        - "Missing BUSCOs"
-        - "Dependencies and versions"
     - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
       contains:
         - "one_line_summary"
@@ -31,20 +17,6 @@
         - "Complete BUSCOs"
         - "Missing BUSCOs"
         - "Dependencies and versions"
-    - path: output/busco/short_summary.specific.bacteroidales_odb10.genome.fna.json
-      contains:
-        - "one_line_summary"
-        - "input_file"
-        - "mode"
-        - "dataset"
-    - path: output/busco/short_summary.specific.bacteroidales_odb10.genome.fna.txt
-      contains:
-        - "BUSCO version"
-        - "The lineage dataset is"
-        - "BUSCO was run in mode"
-        - "Complete BUSCOs"
-        - "Missing BUSCOs"
-        - "Dependencies and versions"
     - path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.json
       contains:
         - "one_line_summary"
@@ -59,8 +31,6 @@
         - "Complete BUSCOs"
         - "Missing BUSCOs"
         - "Dependencies and versions"
-    - path: output/busco/test-auto-busco.batch_summary.txt
-      md5sum: 32f7765c310f33555c31c7a3e64c990e
     - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
       md5sum: e50690742e9ae6abdd2bf99334ff9e12
     - path: output/busco/test-bacteroidetes_odb10-busco.batch_summary.txt