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