From d9cb16e47041166d89c6afd898142e47e710f5a9 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 11 Aug 2023 11:28:23 +0200
Subject: [PATCH 1/4] wgsmetrics

---
 .github/workflows/test.yml                    |  2 +
 modules/nf-core/sentieon/wgsmetrics/main.nf   | 81 +++++++++++++++++++
 modules/nf-core/sentieon/wgsmetrics/meta.yml  | 73 +++++++++++++++++
 tests/config/pytest_modules.yml               |  4 +
 .../nf-core/sentieon/wgsmetrics/main.nf       | 24 ++++++
 .../sentieon/wgsmetrics/nextflow.config       | 10 +++
 .../nf-core/sentieon/wgsmetrics/test.yml      |  8 ++
 7 files changed, 202 insertions(+)
 create mode 100644 modules/nf-core/sentieon/wgsmetrics/main.nf
 create mode 100644 modules/nf-core/sentieon/wgsmetrics/meta.yml
 create mode 100644 tests/modules/nf-core/sentieon/wgsmetrics/main.nf
 create mode 100644 tests/modules/nf-core/sentieon/wgsmetrics/nextflow.config
 create mode 100644 tests/modules/nf-core/sentieon/wgsmetrics/test.yml

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index ae42931b6fa..aa9c56b60df 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -228,6 +228,8 @@ jobs:
             tags: sentieon/readwriter
           - profile: "conda"
             tags: sentieon/varcal
+          - profile: "conda"
+            tags: sentieon/wgmetrics
           - profile: "conda"
             tags: spaceranger/count
           - profile: "conda"
diff --git a/modules/nf-core/sentieon/wgsmetrics/main.nf b/modules/nf-core/sentieon/wgsmetrics/main.nf
new file mode 100644
index 00000000000..b325e38fd42
--- /dev/null
+++ b/modules/nf-core/sentieon/wgsmetrics/main.nf
@@ -0,0 +1,81 @@
+process SENTIEON_WGSMETRICS {
+    tag "$meta.id"
+    label 'process_medium'
+    label 'sentieon'
+
+    secret 'SENTIEON_LICENSE_BASE64'
+
+    container 'nf-core/sentieon:202112.06'
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta3), path(intervals_list)
+
+
+    output:
+    tuple val(meta), path('*.txt'), emit: wgs_metrics
+    path  "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args     = task.ext.args ?: ''
+    def input    = bam.sort().collect{"-i $it"}.join(' ')
+    def prefix   = task.ext.prefix ?: "${meta.id}"
+    def interval = intervals_list ? "--interval ${intervals_list}" : ""
+    def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
+    def sentieon_auth_data_base64 = task.ext.sentieon_auth_data_base64 ?: ''
+    """
+    if [ "\${#SENTIEON_LICENSE_BASE64}" -lt "1500" ]; then  # If the string SENTIEON_LICENSE_BASE64 is short, then it is an encrypted url.
+        export SENTIEON_LICENSE=\$(echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d)
+    else  # Localhost license file
+        # The license file is stored as a nextflow variable like, for instance, this:
+        # nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
+        export SENTIEON_LICENSE=\$(mktemp)
+        echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d > \$SENTIEON_LICENSE
+    fi
+
+    if  [ ${sentieon_auth_mech_base64} ] && [ ${sentieon_auth_data_base64} ]; then
+        # If sentieon_auth_mech_base64 and sentieon_auth_data_base64 are non-empty strings, then Sentieon is mostly likely being run with some test-license.
+        export SENTIEON_AUTH_MECH=\$(echo -n "${sentieon_auth_mech_base64}" | base64 -d)
+        export SENTIEON_AUTH_DATA=\$(echo -n "${sentieon_auth_data_base64}" | base64 -d)
+        echo "Decoded and exported Sentieon test-license system environment variables"
+    fi
+
+    sentieon \\
+        driver \\
+        -t $task.cpus \\
+        -r $fasta \\
+        $input \\
+        $interval \\
+        $args \\
+        --algo WgsMetricsAlgo ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
+    END_VERSIONS
+    """
+
+    stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/sentieon/wgsmetrics/meta.yml b/modules/nf-core/sentieon/wgsmetrics/meta.yml
new file mode 100644
index 00000000000..85e39faa8d7
--- /dev/null
+++ b/modules/nf-core/sentieon/wgsmetrics/meta.yml
@@ -0,0 +1,73 @@
+name: "sentieon_datametrics"
+description: Collects multiple quality metrics from a bam file
+keywords:
+  - metrics
+  - bam
+  - sentieon
+tools:
+  - sentieon:
+      description: |
+        Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.
+        Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
+      homepage: https://www.sentieon.com/
+      documentation: https://www.sentieon.com/
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. `[ id:'test' ]`
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. `[ id:'test' ]`
+  - meta4:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. `[ id:'test' ]`
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - bai:
+      type: file
+      description: Index of th sorted BAM/CRAM/SAM file
+      pattern: "*.{bai,crai,sai}"
+  - fasta:
+      type: file
+      description: Genome fasta file
+      pattern: "*.{fa,fasta}"
+  - fai:
+      type: file
+      description: Index of the genome fasta file
+      pattern: "*.fai"
+  - interval_list:
+      type: file
+      description: bed or interval_list file containing interval in the reference that will be used in the analysis
+      pattern: "*.{bed,interval_list}"
+
+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"
+  - wgs_metrics:
+      type: file
+      description: File containing the information about mean base quality score for each sequencing cycle
+      pattern: "*.txt"
+
+authors:
+  - "@ramprasadn"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 2f32193488f..8a11a58ea8b 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -3287,6 +3287,10 @@ sentieon/readwriter:
   - modules/nf-core/sentieon/readwriter/**
   - tests/modules/nf-core/sentieon/readwriter/**
 
+sentieon/wgsmetrics:
+  - modules/nf-core/sentieon/wgsmetrics/**
+  - tests/modules/nf-core/sentieon/wgsmetrics/**
+
 sentieon/varcal:
   - modules/nf-core/sentieon/varcal/**
   - tests/modules/nf-core/sentieon/varcal/**
diff --git a/tests/modules/nf-core/sentieon/wgsmetrics/main.nf b/tests/modules/nf-core/sentieon/wgsmetrics/main.nf
new file mode 100644
index 00000000000..b5f3e1a0f54
--- /dev/null
+++ b/tests/modules/nf-core/sentieon/wgsmetrics/main.nf
@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SENTIEON_WGSMETRICS } from '../../../../../modules/nf-core/sentieon/wgsmetrics/main.nf'
+
+workflow test_sentieon_wgsmetrics {
+
+    input = [
+                [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+            ]
+    fasta = [
+        [id:'genome'],
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+    fai = [
+        [id:'genome'],
+        file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    ]
+
+    SENTIEON_WGSMETRICS ( input, fasta, fai, [[:],[]] )
+}
diff --git a/tests/modules/nf-core/sentieon/wgsmetrics/nextflow.config b/tests/modules/nf-core/sentieon/wgsmetrics/nextflow.config
new file mode 100644
index 00000000000..ccf30410f8d
--- /dev/null
+++ b/tests/modules/nf-core/sentieon/wgsmetrics/nextflow.config
@@ -0,0 +1,10 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withLabel: 'sentieon' {
+        ext.sentieon_auth_mech_base64 = secrets.SENTIEON_AUTH_MECH_BASE64
+        ext.sentieon_auth_data_base64 = secrets.SENTIEON_AUTH_DATA_BASE64
+    }
+
+}
diff --git a/tests/modules/nf-core/sentieon/wgsmetrics/test.yml b/tests/modules/nf-core/sentieon/wgsmetrics/test.yml
new file mode 100644
index 00000000000..257bcec1a94
--- /dev/null
+++ b/tests/modules/nf-core/sentieon/wgsmetrics/test.yml
@@ -0,0 +1,8 @@
+- name: "sentieon wgsmetrics"
+  command: nextflow run ./tests/modules/nf-core/sentieon/wgsmetrics -entry test_sentieon_wgsmetrics -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/sentieon/wgsmetrics/nextflow.config
+  tags:
+    - "sentieon"
+    - "sentieon/wgsmetrics"
+  files:
+    - path: "output/sentieon/test.txt"
+    - path: "output/sentieon/versions.yml"

From e03f2e4d94cea632883818cf1949418f4ae191ce Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 11 Aug 2023 11:32:27 +0200
Subject: [PATCH 2/4] fix lint error

---
 modules/nf-core/sentieon/wgsmetrics/meta.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/sentieon/wgsmetrics/meta.yml b/modules/nf-core/sentieon/wgsmetrics/meta.yml
index 85e39faa8d7..09fb9ecaaf6 100644
--- a/modules/nf-core/sentieon/wgsmetrics/meta.yml
+++ b/modules/nf-core/sentieon/wgsmetrics/meta.yml
@@ -1,5 +1,5 @@
-name: "sentieon_datametrics"
-description: Collects multiple quality metrics from a bam file
+name: "sentieon_wgsmetrics"
+description: Collects whole genome quality metrics from a bam file
 keywords:
   - metrics
   - bam

From 2244e3de9ef9186181a892a36bfefcaa0d533dc6 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 11 Aug 2023 12:15:45 +0200
Subject: [PATCH 3/4] typo

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index aa9c56b60df..3b62ffebbe6 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -229,7 +229,7 @@ jobs:
           - profile: "conda"
             tags: sentieon/varcal
           - profile: "conda"
-            tags: sentieon/wgmetrics
+            tags: sentieon/wgsmetrics
           - profile: "conda"
             tags: spaceranger/count
           - profile: "conda"

From 741a6a043d8feb3e6dd64ab4f5083c64f0d87f00 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 15 Aug 2023 11:51:17 +0200
Subject: [PATCH 4/4] Update modules/nf-core/sentieon/wgsmetrics/main.nf

Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com>
---
 modules/nf-core/sentieon/wgsmetrics/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/sentieon/wgsmetrics/main.nf b/modules/nf-core/sentieon/wgsmetrics/main.nf
index b325e38fd42..fd7fdae5f1e 100644
--- a/modules/nf-core/sentieon/wgsmetrics/main.nf
+++ b/modules/nf-core/sentieon/wgsmetrics/main.nf
@@ -11,7 +11,7 @@ process SENTIEON_WGSMETRICS {
     tuple val(meta), path(bam), path(bai)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(fai)
-    tuple val(meta3), path(intervals_list)
+    tuple val(meta4), path(intervals_list)
 
 
     output: