From f3c034a75d73878e33a75765f4b887f02ea823af Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 3 Oct 2017 14:33:53 -0500
Subject: [PATCH] Add in trimming step into workflow.
---
astrocyte_pkg.yml | 4 +++-
workflow/main.nf | 17 +++++++++++++----
2 files changed, 16 insertions(+), 5 deletions(-)
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index b812c4a..c7ff94f 100644
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -40,6 +40,8 @@ documentation_files:
# A list of cluster environment modules that this workflow requires to run.
# Specify versioned module names to ensure reproducability.
workflow_modules:
+ - 'python/3.6.1-2-anaconda'
+ - 'trimgalore/0.4.1'
- 'fastqc/0.11.5'
- 'deeptools/2.3.5'
- 'meme/4.11.1-gcc-openmpi'
@@ -114,7 +116,7 @@ vizapp_cran_packages:
- shiny
- 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
vizapp_bioc_packages:
- qusage
diff --git a/workflow/main.nf b/workflow/main.nf
index 7648445..6ee87c6 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -62,7 +62,7 @@ rawReads = designFilePaths
process trimReads {
tag "$sampleId-$replicate"
- publishDir "$baseDir/output/{task.process}/$sampleId-$replicate$/", mode: 'copy'
+ publishDir "$baseDir/output/{task.process}/$sampleId-$replicate/", mode: 'copy'
input:
@@ -71,10 +71,19 @@ process trimReads {
output:
set sampleId, file('*.fq.gz'), biosample, factor, treatment, replicate, controlId into trimmedReads
+ file '*trimming_report.txt' into trimgalore_results
script:
- """
- python $baseDir/scripts/trim_reads.py -f $reads
- """
+ if (pairedEnd) {
+ """
+ python $baseDir/scripts/trim_reads.py -f $reads -p
+ """
+ }
+ else {
+ """
+ python $baseDir/scripts/check_design.py -f $reads
+ """
+ }
+
}
--
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