Add trimgalore

software/trimgalore/functions.nf

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+../lib/functions.nf

software/trimgalore/main.nf

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+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process TRIMGALORE {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${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/trim-galore:0.6.5--0"
+    //container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.5--0"
+
+    conda (params.conda ? "bioconda::trim-galore=0.6.5" : null)
+
+    input:
+    tuple val(meta), path(reads)
+    val options
+
+    output:
+    tuple val(meta), path("*.fq.gz"), emit: reads
+    tuple val(meta), path("*.html"), emit: html optional true
+    tuple val(meta), path("*.zip"), emit: zip optional true
+    tuple val(meta), path("*report.txt"), emit: log
+    path "*.version.txt", emit: version
+
+    script:
+    // Calculate number of --cores for TrimGalore based on value of task.cpus
+    // See: https://github.com/FelixKrueger/TrimGalore/blob/master/Changelog.md#version-060-release-on-1-mar-2019
+    // See: https://github.com/nf-core/atacseq/pull/65
+    def cores = 1
+    if (task.cpus) {
+        cores = (task.cpus as int) - 4
+        if (meta.single_end) cores = (task.cpus as int) - 3
+        if (cores < 1) cores = 1
+        if (cores > 4) cores = 4
+    }
+
+    // Clipping presets have to be evaluated in the context of SE/PE
+    def c_r1 = params.clip_r1 > 0 ? "--clip_r1 ${params.clip_r1}" : ''
+    def c_r2 = params.clip_r2 > 0 ? "--clip_r2 ${params.clip_r2}" : ''
+    def tpc_r1 = params.three_prime_clip_r1 > 0 ? "--three_prime_clip_r1 ${params.three_prime_clip_r1}" : ''
+    def tpc_r2 = params.three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${params.three_prime_clip_r2}" : ''
+
+    // Added soft-links to original fastqs for consistent naming in MultiQC
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    if (meta.single_end) {
+        """
+        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
+        trim_galore \\
+            $ioptions.args \\
+            --cores $cores \\
+            --gzip \\
+            $c_r1 \\
+            $tpc_r1 \\
+            ${prefix}.fastq.gz
+        echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//' > ${software}.version.txt
+        """
+    } else {
+        """
+        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
+        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
+        trim_galore \\
+            $ioptions.args \\
+            --cores $cores \\
+            --paired \\
+            --gzip \\
+            $c_r1 \\
+            $c_r2 \\
+            $tpc_r1 \\
+            $tpc_r2 \\
+            ${prefix}_1.fastq.gz \\
+            ${prefix}_2.fastq.gz
+        echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//' > ${software}.version.txt
+        """
+    }
+}