Adding a few more commonly used modules

modules/cat_fastq/main.nf

@@ -0,0 +1,36 @@
+process CAT_FASTQ {
+    tag "$meta.sample_id"
+    label 'process_single'
+
+    conda 'conda-forge::sed=4.7'
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"
+
+    input:
+    tuple val(meta), path(reads, stageAs: 'input*/*')
+
+    output:
+    tuple val(meta), path('*.merged.fastq.gz'), emit: reads
+    path 'versions.yml'                       , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = meta.sample_id
+    def readList = reads instanceof List ? reads.collect { r -> r.toString() } : [reads.toString()]
+
+    def read1 = []
+    def read2 = []
+    readList.eachWithIndex { v, ix -> (ix & 1 ? read2 : read1) << v }
+    """
+    zcat ${read1.join(' ')} > ${prefix}_1.merged.fastq.gz
+    zcat ${read2.join(' ')} > ${prefix}_2.merged.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/fastp/main.nf

@@ -15,7 +15,6 @@ process FASTP {
     path('versions.yml'), emit: versions
 
     script:
-    r1 = file(reads[0])
 
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: r1.getBaseName()
@@ -25,6 +24,8 @@ process FASTP {
     json = prefix + '.fastp.json'
     html = prefix + '.fastp.html'
 
+    r1 = reads[0]
+
     if (meta.single_end) {
         r1_trim = r1.getBaseName() + suffix
         """
@@ -40,7 +41,7 @@ process FASTP {
         END_VERSIONS
         """
     } else {
-        r2 = file(reads[1])
+        r2 = reads[1]
         r1_trim = r1.getBaseName() + suffix
         r2_trim = r2.getBaseName() + suffix
         """

modules/gunzip/main.nf

@@ -0,0 +1,35 @@
+process GUNZIP {
+    tag "${meta.target}|${zipped}"
+
+    label 'medium_serial'
+
+    publishDir "${params.outdir}/${meta.target}/${meta.tool}", mode: 'copy'
+
+    conda 'sed=4.7'
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"
+
+    input:
+    tuple val(meta), path(zipped)
+
+    output:
+    tuple val(meta), path(unzipped), emit: gunzip
+    path("versions.yml"), emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: zipped.getBaseName()
+
+    unzipped = prefix
+
+    """
+    gunzip $args -c $zipped > $unzipped
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
+    END_VERSIONS
+
+    """
+}