new module: samtools/getrg (#2123)

* new module: samtools/getrg

* add output file to stub

* add missing config

* Intentionally break prettier linting

* [automated] Fix linting with Prettier

Co-authored-by: Phil Ewels <phil@seqera.io>
Co-authored-by: nf-core-bot <core@nf-co.re>

modules/samtools/getrg/main.nf

@@ -0,0 +1,47 @@
+process SAMTOOLS_GETRG {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+
+    input:
+    tuple val(meta), path(input)
+
+    output:
+    tuple val(meta), file("readgroups.txt"),    emit: readgroup
+    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}"
+    """
+    samtools \\
+        view \\
+        -H \\
+        $args \\
+        $input \\
+    | grep '^@RG' > readgroups.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+
+    echo -e "@RG\\tID:${prefix}\\tSM:${prefix}\\tPL:ILLUMINA" > readgroups.txt
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+}

modules/samtools/getrg/meta.yml

@@ -0,0 +1,43 @@
+name: samtools_getrg
+description: filter/convert SAM/BAM/CRAM file
+keywords:
+  - view
+  - bam
+  - sam
+  - cram
+  - readgroup
+tools:
+  - samtools:
+      description: |
+        SAMtools is a set of utilities for interacting with and post-processing
+        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+        These files are generated as output by short read aligners like BWA.
+      homepage: http://www.htslib.org/
+      documentation: hhttp://www.htslib.org/doc/samtools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - input:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - readgroup:
+      type: stdout
+      description: File containing readgroup string(s)
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@matthdsm"

tests/config/pytest_modules.yml

@@ -2115,6 +2115,10 @@ samtools/flagstat:
   - modules/samtools/flagstat/**
   - tests/modules/samtools/flagstat/**
 
+samtools/getrg:
+  - modules/samtools/getrg/**
+  - tests/modules/samtools/getrg/**
+
 samtools/idxstats:
   - modules/samtools/idxstats/**
   - tests/modules/samtools/idxstats/**

tests/modules/samtools/getrg/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_GETRG } from '../../../../modules/samtools/getrg/main.nf'
+
+workflow test_samtools_getrg {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    SAMTOOLS_GETRG ( input )
+}

tests/modules/samtools/getrg/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}

tests/modules/samtools/getrg/test.yml

@@ -0,0 +1,8 @@
+- name: samtools getrg test_samtools_getrg
+  command: nextflow run ./tests/modules/samtools/getrg -entry test_samtools_getrg -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/getrg/nextflow.config
+  tags:
+    - samtools/getrg
+    - samtools
+  files:
+    - path: output/samtools/readgroups.txt
+      md5sum: 7b1d2d10a82a0c4fa6b22673559e41f6