--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.2/modules/seqkit/grep/main.nf	Wed Jul 03 15:16:39 2024 -0400
@@ -0,0 +1,89 @@
+process SEQKIT_GREP {
+    tag "$meta.id"
+    label 'process_low'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}seqkit${params.fs}2.2.0" : null)
+    conda (params.enable_conda ? "bioconda::seqkit=2.2.0 conda-forge::sed=4.7 conda-forge::coreutils" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0':
+        'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(reads), path(pattern_file)
+
+    output:
+    tuple val(meta), path("*.gz"), emit: fastx
+    path "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def extension = "fastq"
+    if ("$reads" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/) {
+        extension = "fasta"
+    }
+
+    if (meta.single_end) {
+        """
+        pattern_file_contents=\$(sed '1!d' $pattern_file)
+        if [ "\$pattern_file_contents" != "DuMmY" ]; then
+            additional_args="-f $pattern_file $args"
+        else
+            additional_args="$args"
+        fi
+
+        seqkit \\
+            grep \\
+            -j $task.cpus \\
+            -o ${prefix}.seqkit-grep.${extension}.gz \\
+            \$additional_args \\
+            $reads
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            seqkit: \$( seqkit | sed '3!d; s/Version: //' )
+        END_VERSIONS
+        """
+    } else {
+        """
+        pattern_file_contents=\$(sed '1!d' $pattern_file)
+        if [ "\$pattern_file_contents" != "DuMmY" ]; then
+            additional_args="-f $pattern_file $args"
+        else
+            additional_args="$args"
+        fi
+
+        seqkit \\
+            grep \\
+            -j $task.cpus \\
+            -o ${prefix}.R1.seqkit-grep.${extension}.gz \\
+            \$additional_args \\
+            ${reads[0]}
+        
+        seqkit \\
+            grep \\
+            -j $task.cpus \\
+            -o ${prefix}.R2.seqkit-grep.${extension}.gz \\
+            \$additional_args \\
+            ${reads[1]}
+
+        seqkit \\
+            pair \\
+            -j $task.cpus \\
+            -1 ${prefix}.R1.seqkit-grep.${extension}.gz \\
+            -2 ${prefix}.R2.seqkit-grep.${extension}.gz
+
+        rm ${prefix}.R1.seqkit-grep.${extension}.gz
+        rm ${prefix}.R2.seqkit-grep.${extension}.gz
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            seqkit: \$( seqkit | sed '3!d; s/Version: //' )
+        END_VERSIONS
+        """
+    }
+}