--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/modules/samtools/fastq/main.nf	Mon Mar 31 14:50:40 2025 -0400
@@ -0,0 +1,53 @@
+process SAMTOOLS_FASTQ {
+    tag "$meta.id"
+    label 'process_micro'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}samtools${params.fs}1.13" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::bzip2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' :
+        'quay.io/biocontainers/samtools:1.18--h50ea8bc_1' }"
+
+    input:
+        tuple val(meta), path(input)
+        val(interleave)
+
+    output:
+        tuple val(meta), path("*_{1,2}.fastq.gz")      , optional:true, emit: fastq
+        tuple val(meta), path("*_{1,2}.fastq.gz")      , optional:true, emit: mapped_refs
+        tuple val(meta), path("*_interleaved.fastq")   , optional:true, emit: interleaved
+        tuple val(meta), path("*_singleton.fastq.gz")  , optional:true, emit: singleton
+        tuple val(meta), path("*_other.fastq.gz")      , optional:true, emit: other
+        path  "versions.yml"                           , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args = task.ext.args ?: ''
+        def prefix = task.ext.prefix ?: "${meta.id}"
+        def output = ( interleave && ! meta.single_end ) ? "> ${prefix}_interleaved.fastq" :
+            meta.single_end ? "-1 ${prefix}_1.fastq.gz -s ${prefix}_singleton.fastq.gz" :
+            "-1 ${prefix}_1.fastq.gz -2 ${prefix}_2.fastq.gz -s ${prefix}_singleton.fastq.gz"
+        """
+        samtools \\
+            fastq \\
+            $args \\
+            --threads ${task.cpus-1} \\
+            -0 ${prefix}_other.fastq.gz \\
+            $input \\
+            $output
+
+        samtools \\
+            view \\
+            $args2 \\
+            --threads ${task.cpus-1} \\
+            $input \\
+            | grep -v '*' | cut -f3 | sort -u > mapped_refs.txt
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        END_VERSIONS
+        """
+}
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