Add samtools

software/samtools/flagstat/functions.nf

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+../../lib/functions.nf

software/samtools/flagstat/main.nf

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+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process SAMTOOLS_FLAGSTAT {
+    tag "$meta.id"
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+    //container " https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+
+    conda (params.conda ? "bioconda::samtools=1.10" : null)
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    val options
+
+    output:
+    tuple val(meta), path("*.flagstat"), emit: flagstat
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    samtools flagstat $bam > ${bam}.flagstat
+    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    """
+}

software/samtools/idxstats/functions.nf

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+../../lib/functions.nf

software/samtools/idxstats/main.nf

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+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process SAMTOOLS_IDXSTATS {
+    tag "$meta.id"
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+    //container " https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+
+    conda (params.conda ? "bioconda::samtools=1.10" : null)
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    val options
+
+    output:
+    tuple val(meta), path("*.idxstats"), emit: idxstats
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    samtools idxstats $bam > ${bam}.idxstats
+    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    """
+}

software/samtools/index/functions.nf

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+../../lib/functions.nf

software/samtools/index/main.nf

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+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process SAMTOOLS_INDEX {
+    tag "$meta.id"
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+    //container " https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+
+    conda (params.conda ? "bioconda::samtools=1.10" : null)
+
+    input:
+    tuple val(meta), path(bam)
+    val options
+
+    output:
+    tuple val(meta), path("*.bai"), emit: bai
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    samtools index $bam
+    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    """
+}

software/samtools/sort/functions.nf

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+../../lib/functions.nf

software/samtools/sort/main.nf

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+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process SAMTOOLS_SORT {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+    //container " https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+
+    conda (params.conda ? "bioconda::samtools=1.10" : null)
+
+    input:
+    tuple val(meta), path(bam)
+    val options
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    """
+    samtools sort $ioptions.args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam
+    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    """
+}

software/samtools/stats/functions.nf

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+../../lib/functions.nf

software/samtools/stats/main.nf

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+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process SAMTOOLS_STATS {
+    tag "$meta.id"
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+    //container " https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+
+    conda (params.conda ? "bioconda::samtools=1.10" : null)
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    val options
+
+    output:
+    tuple val(meta), path("*.stats"), emit: stats
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    samtools stats $bam > ${bam}.stats
+    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    """
+}