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 + """ + } + } -- GitLab