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The MetaPhlAn3 module computes the input type from the file extension without the possibility to configure an override. Since AdapterRemoval2 creates files without `.fastq` extensions, MetaPhlAn3 input was determined to be SAM.
31 lines
900 B
Text
31 lines
900 B
Text
process ENSURE_FASTQ_EXTENSION {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "conda-forge::bash=5.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
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'biocontainers/biocontainers:v1.2.0_cv2' }"
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path('*.fastq.gz'), emit: reads
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script:
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if (meta.single_end) {
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fastq = "${reads.baseName}.fastq.gz"
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"""
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ln -s '${reads}' '${fastq}'
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"""
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} else {
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first = "${reads[0].baseName}.fastq.gz"
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second = "${reads[1].baseName}.fastq.gz"
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"""
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ln -s '${reads[0]}' '${first}'
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ln -s '${reads[1]}' '${second}'
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"""
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}
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}
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