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Fixed bug in pipeline.nf: parameter gtf_path is now working
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renewiegandt committed Dec 21, 2018
1 parent d70610e commit 13bccda
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions pipeline.nf
Original file line number Diff line number Diff line change
@@ -9,7 +9,7 @@
params.tfbs_path=""
params.create_known_tfbs_path = "./"
params.help = 0
params.get_path=""
params.gtf_path=""
params.out = "./out/"

//peak_calling
@@ -583,15 +583,15 @@ process create_GTF {
file ('*.gtf') into gtf

when:
gtf_path == ""
params.gtf_path == ""

script:
"""
python ${path_bin}/RegGTFExtractor.py ${params.organism} --tissue ${params.tissues} --wd ${path_bin}
"""
}

if (gtf_path == "") {
if (params.gtf_path == "") {
gtf_for_uropa = gtf
} else {
gtf_for_uropa = Channel.fromPath(params.gtf_path)

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