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Clean up module file

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This commit is contained in:
Gregor Sturm 2020-07-14 11:49:08 +02:00
parent a5306b33da
commit 167067a92e
2 changed files with 3 additions and 17 deletions
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2
software/fastqc/environment.yml
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@ -6,4 +6,4 @@ channels:
- bioconda - bioconda
- defaults - defaults
dependencies: dependencies:
- fastqc=0.11.8 - fastqc=0.11.9

18
software/fastqc/main.nf
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@ -1,37 +1,23 @@
nextflow.preview.dsl = 2 nextflow.preview.dsl = 2
process FASTQC { process FASTQC {
// tag "FastQC - $sample_id"
input: input:
tuple val(name), path(reads) tuple val(name), path(reads)
val (outputdir)
// fastqc_args are best passed into the workflow in the following manner:
// --fastqc_args="--nogroup -a custom_adapter_file.txt"
val (fastqc_args) val (fastqc_args)
val (verbose) val (outputdir)
output: output:
tuple val(name), path ("*fastqc*"), emit: all tuple val(name), path ("*fastqc*"), emit: all
path "*.zip", emit: report // e.g. for MultiQC later path "*.zip", emit: report // e.g. for MultiQC later
// container 'quay.io/biocontainers/fastqc:0.11.8--2' container 'quay.io/biocontainers/fastqc:0.11.8--2'
publishDir "$outputdir", publishDir "$outputdir",
mode: "copy", overwrite: true mode: "copy", overwrite: true
script: script:
if (verbose){
println ("[MODULE] FASTQC ARGS: " + fastqc_args)
}
""" """
module load fastqc
fastqc $fastqc_args -q -t 2 $reads fastqc $fastqc_args -q -t 2 $reads
fastqc --version &> fastqc.version.txt fastqc --version &> fastqc.version.txt
""" """
} }