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Commit f3c034a7 authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Add in trimming step into workflow.

parent 5532fa6d
1 merge request!5Resolve "Add mapping and trimming"
...@@ -40,6 +40,8 @@ documentation_files: ...@@ -40,6 +40,8 @@ documentation_files:
# A list of cluster environment modules that this workflow requires to run. # A list of cluster environment modules that this workflow requires to run.
# Specify versioned module names to ensure reproducability. # Specify versioned module names to ensure reproducability.
workflow_modules: workflow_modules:
- 'python/3.6.1-2-anaconda'
- 'trimgalore/0.4.1'
- 'fastqc/0.11.5' - 'fastqc/0.11.5'
- 'deeptools/2.3.5' - 'deeptools/2.3.5'
- 'meme/4.11.1-gcc-openmpi' - 'meme/4.11.1-gcc-openmpi'
...@@ -114,7 +116,7 @@ vizapp_cran_packages: ...@@ -114,7 +116,7 @@ vizapp_cran_packages:
- shiny - shiny
- shinyFiles - shinyFiles
# List of any Bioconductor packages, not provided by the modules, # List of any Bioconductor packages, not provided by the modules,
# that must be made available to the vizapp # that must be made available to the vizapp
vizapp_bioc_packages: vizapp_bioc_packages:
- qusage - qusage
......
...@@ -62,7 +62,7 @@ rawReads = designFilePaths ...@@ -62,7 +62,7 @@ rawReads = designFilePaths
process trimReads { process trimReads {
tag "$sampleId-$replicate" tag "$sampleId-$replicate"
publishDir "$baseDir/output/{task.process}/$sampleId-$replicate$/", mode: 'copy' publishDir "$baseDir/output/{task.process}/$sampleId-$replicate/", mode: 'copy'
input: input:
...@@ -71,10 +71,19 @@ process trimReads { ...@@ -71,10 +71,19 @@ process trimReads {
output: output:
set sampleId, file('*.fq.gz'), biosample, factor, treatment, replicate, controlId into trimmedReads set sampleId, file('*.fq.gz'), biosample, factor, treatment, replicate, controlId into trimmedReads
file '*trimming_report.txt' into trimgalore_results
script: script:
""" if (pairedEnd) {
python $baseDir/scripts/trim_reads.py -f $reads """
""" python $baseDir/scripts/trim_reads.py -f $reads -p
"""
}
else {
"""
python $baseDir/scripts/check_design.py -f $reads
"""
}
} }
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