--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/modules/cat/fastq/main.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,89 @@
+process CAT_FASTQ {
+    tag "$meta.id"
+    label 'process_micro'
+
+    conda (params.enable_conda ? "conda-forge::sed=4.7 conda-forge::gzip" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
+        'biocontainers/biocontainers:v1.2.0_cv1' }"
+
+    input:
+        tuple val(meta), path(reads, stageAs: "input*/*")
+
+    output:
+        tuple val(meta), path("*.merged.fastq.gz"), emit: catted_reads
+        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}"
+        def readList = reads.collect{ it.toString() }
+        def is_in_gz = readList[0].endsWith('.gz')
+        def gz_or_ungz = (is_in_gz ? '' : ' | gzip')
+        def pigz_or_ungz = (is_in_gz ? '' : " | pigz -p ${task.cpus}")
+        if (meta.single_end) {
+            if (readList.size > 1) {
+                """
+                zcmd="gzip"
+                zver=""
+
+                if type pigz > /dev/null 2>&1; then
+                    cat ${readList.join(' ')} ${pigz_or_ungz} > ${prefix}.merged.fastq.gz
+                    zcmd="pigz"
+                    zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
+                else
+                    cat ${readList.join(' ')} ${gz_or_ungz} > ${prefix}.merged.fastq.gz
+                    zcmd="gzip"
+
+                    if [ "${workflow.containerEngine}" != "null" ]; then
+                        zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
+                    else
+                        zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
+                    fi
+                fi
+
+                cat <<-END_VERSIONS > versions.yml
+                "${task.process}":
+                    cat: \$( echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//' )
+                    \$zcmd: \$zver
+                END_VERSIONS
+                """
+            }
+        } else {
+            if (readList.size > 2) {
+                def read1 = []
+                def read2 = []
+                readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
+                """
+                zcmd="gzip"
+                zver=""
+
+                if type pigz > /dev/null 2>&1; then
+                    cat ${read1.join(' ')} ${pigz_or_ungz} > ${prefix}_1.merged.fastq.gz
+                    cat ${read2.join(' ')} ${pigz_or_ungz} > ${prefix}_2.merged.fastq.gz
+                    zcmd="pigz"
+                    zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
+                else
+                    cat ${read1.join(' ')} ${gz_or_ungz} > ${prefix}_1.merged.fastq.gz
+                    cat ${read2.join(' ')} ${gz_or_ungz} > ${prefix}_2.merged.fastq.gz
+                    zcmd="gzip"
+
+                    if [ "${workflow.containerEngine}" != "null" ]; then
+                        zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
+                    else
+                        zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
+                    fi
+                fi
+
+                cat <<-END_VERSIONS > versions.yml
+                "${task.process}":
+                    cat: \$( echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//' )
+                    \$zcmd: \$zver
+                END_VERSIONS
+                """
+            }
+        }
+}
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