Commit 7b474afc authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Add fastqc (needs input file optimization)

parent 6e722372
Pipeline #3462 passed with stages
in 1 minute and 21 seconds
......@@ -81,7 +81,7 @@ process mkfastq {
output:
file("**/outs/fastq_path/**/*") into fastqPaths
file("**/outs/fastq_path/Stats/Stats.json") into qc
file("**/outs/fastq_path/Stats/Stats.json") into bqcPaths
script:
......@@ -94,16 +94,40 @@ process mkfastq {
"""
}
process fastqc {
publishDir "$outDir/${task.process}", mode: 'copy'
input:
file("outs/fastq_path/*/*") from fastqPaths
output:
file("*fastqc.*") into fqcPaths
script:
"""
hostname
ulimit -a
module load fastqc/0.11.5
module load parallel
sh $baseDir/scripts/fastqc.sh
"""
}
process multiqc {
publishDir "$outDir/${task.process}", mode: 'copy'
input:
file qc
file bqcPaths
file fqcPaths
output:
file("*") into qcPaths
file("*") into mqcPaths
script:
......@@ -111,6 +135,6 @@ process multiqc {
hostname
ulimit -a
module load multiqc/1.7
multiqc Stats.json
multiqc .
"""
}
#!/bin/bash
find . -name '*.fastq.gz' | awk '{printf("fastqc \"%s\"\n", $0)}' | parallel -j 25 --verbose
find . -name '*fastqc.*' | xargs -I '{}' mv '{}' ./
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