Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.4.0/modules/fastqc/main.nf @ 101:ce6d9548fe89
"planemo upload"
| author | kkonganti |
|---|---|
| date | Thu, 04 Aug 2022 10:45:55 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@101 | 1 process FASTQC { |
| kkonganti@101 | 2 tag "$meta.id" |
| kkonganti@101 | 3 label 'process_low' |
| kkonganti@101 | 4 |
| kkonganti@101 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}fastqc${params.fs}0.11.9" : null) |
| kkonganti@101 | 6 conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) |
| kkonganti@101 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@101 | 8 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : |
| kkonganti@101 | 9 'quay.io/biocontainers/fastqc:0.11.9--0' }" |
| kkonganti@101 | 10 |
| kkonganti@101 | 11 input: |
| kkonganti@101 | 12 tuple val(meta), path(reads) |
| kkonganti@101 | 13 |
| kkonganti@101 | 14 output: |
| kkonganti@101 | 15 tuple val(meta), path("*.html"), emit: html |
| kkonganti@101 | 16 tuple val(meta), path("*.zip") , emit: zip |
| kkonganti@101 | 17 path "versions.yml" , emit: versions |
| kkonganti@101 | 18 |
| kkonganti@101 | 19 when: |
| kkonganti@101 | 20 task.ext.when == null || task.ext.when |
| kkonganti@101 | 21 |
| kkonganti@101 | 22 script: |
| kkonganti@101 | 23 def args = task.ext.args ?: '' |
| kkonganti@101 | 24 // Add soft-links to original FastQs for consistent naming in pipeline |
| kkonganti@101 | 25 def prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@101 | 26 if (meta.single_end) { |
| kkonganti@101 | 27 """ |
| kkonganti@101 | 28 [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz |
| kkonganti@101 | 29 fastqc $args --threads $task.cpus ${prefix}.fastq.gz |
| kkonganti@101 | 30 |
| kkonganti@101 | 31 cat <<-END_VERSIONS > versions.yml |
| kkonganti@101 | 32 "${task.process}": |
| kkonganti@101 | 33 fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) |
| kkonganti@101 | 34 END_VERSIONS |
| kkonganti@101 | 35 """ |
| kkonganti@101 | 36 } else { |
| kkonganti@101 | 37 """ |
| kkonganti@101 | 38 [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz |
| kkonganti@101 | 39 [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz |
| kkonganti@101 | 40 fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz |
| kkonganti@101 | 41 |
| kkonganti@101 | 42 cat <<-END_VERSIONS > versions.yml |
| kkonganti@101 | 43 "${task.process}": |
| kkonganti@101 | 44 fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) |
| kkonganti@101 | 45 END_VERSIONS |
| kkonganti@101 | 46 """ |
| kkonganti@101 | 47 } |
| kkonganti@101 | 48 } |