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BICF
Astrocyte
rnaseq
Commits
19ca68db
Commit
19ca68db
authored
Nov 09, 2018
by
Brandi Cantarel
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updating process scripts
parent
e550dccd
Pipeline
#2594
failed with stage
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README.md
README.md
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workflow/main.nf
workflow/main.nf
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workflow/process_scripts
workflow/process_scripts
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README.md
View file @
19ca68db
## RNASeq Analysis Worklow
```
module load nextflow
/0.24.1-SNAPSHOT
module load nextflow
nextflow run workflow/main.nf
```
workflow/main.nf
View file @
19ca68db
...
...
@@ -201,14 +201,15 @@ process statanal {
file "*.txt" into txtfiles
file "*.png" into psfiles
file("bg.rda") into rdafiles
file("geneset.shiny.gmt") into gmtfile
when:
script:
if (params.dea == 'skip')
"""
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
"""
...
...
process_scripts
@
75a4aa68
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636e989b
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75a4aa68
Subproject commit
636e989b65cc76352111cedac9a8762fbe570384
Subproject commit
75a4aa688f82c607794e109e4ee0ec8e12418a2d
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