Commit d3570757 authored by Brandi Cantarel's avatar Brandi Cantarel
Browse files

update statanal into bash

parent 422f4fa1
Pipeline #2915 passed with stage
in 106 minutes
...@@ -177,13 +177,13 @@ process geneabund { ...@@ -177,13 +177,13 @@ process geneabund {
publishDir "$params.output", mode: 'copy' publishDir "$params.output", mode: 'copy'
input: input:
set pair_id, file(sbam) from deduped1 set pair_id, file(sbam) from deduped1
file gtf_file
output: output:
file("${pair_id}.cts") into counts file("${pair_id}.cts") into counts
file("${pair_id}.cts.summary") into ctsum
file("${pair_id}_stringtie") into strcts file("${pair_id}_stringtie") into strcts
file("${pair_id}.fpkm.txt") into fpkm file("${pair_id}.fpkm.txt") into fpkm
""" """
bash $baseDir/process_scripts/diff_exp/geneabundance.sh -s $params.stranded -g ${gtf_file} -p ${pair_id} -b ${sbam} bash $baseDir/process_scripts/genect_rnaseq/geneabundance.sh -s $params.stranded -g ${gtf_file} -p ${pair_id} -b ${sbam}
""" """
} }
...@@ -192,6 +192,7 @@ process statanal { ...@@ -192,6 +192,7 @@ process statanal {
publishDir "$params.output", mode: 'copy' publishDir "$params.output", mode: 'copy'
input: input:
file count_file from counts.toList() file count_file from counts.toList()
file count_sum from ctsum.toList()
file newdesign name 'design.txt' file newdesign name 'design.txt'
file genenames file genenames
file geneset name 'geneset.gmt' file geneset name 'geneset.gmt'
...@@ -204,24 +205,8 @@ process statanal { ...@@ -204,24 +205,8 @@ process statanal {
file("geneset.shiny.gmt") into gmtfile file("geneset.shiny.gmt") into gmtfile
when: when:
script: script:
if (params.dea == 'skip') """
""" bash $baseDir/process_scripts/genect_rnaseq/statanal.sh
perl $baseDir/scripts/concat_cts.pl -o ./ *.cts
perl $baseDir/scripts/concat_fpkm.pl -o ./ *.fpkm.txt
touch empty.png
touch bg.rda
cp geneset.gmt geneset.shiny.gmt
"""
else
"""
module load R/3.2.1-intel
perl $baseDir/scripts/concat_cts.pl -o ./ *.cts
cp design.txt design.shiny.txt
cp geneset.gmt geneset.shiny.gmt
Rscript $baseDir/scripts/dea.R
Rscript $baseDir/scripts/build_ballgown.R *_stringtie
perl $baseDir/scripts/concat_edgeR.pl *.edgeR.txt
perl $baseDir/scripts/concat_fpkm.pl -o ./ *.fpkm.txt
""" """
} }
process gatkbam { process gatkbam {
......
Subproject commit 7adcb10cc4b0159f22faf630fba29ad31c48bf9d Subproject commit cba11424a989582e446c69894a5b166beb132899
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