Commit a25480f0 authored by Brandi Cantarel's avatar Brandi Cantarel

add support mouse

parent f1e9fed0
Pipeline #1688 failed with stage
in 247 minutes and 6 seconds
......@@ -64,7 +64,7 @@ else {
spltnames
.splitCsv()
.filter { fileMap.get(it[1]) != null }
.map { it -> tuple(it[0], fileMap.get(it[1]),fileMap.get(it[1])) }
.map { it -> tuple(it[0], fileMap.get(it[1]),'') }
.set { read }
}
if( ! read ) { error "Didn't match any input files with entries in the design file" }
......@@ -232,7 +232,7 @@ process gatkbam {
output:
set file("${pair_id}.final.bam"),file("${pair_id}.final.bai") into gatkbam
when:
params.align == 'hisat'
params.align == 'hisat' && $index_path == '/project/shared/bicf_workflow_ref/GRCh38/'
script:
"""
bash $baseDir/process_scripts/variants/gatkrunner.sh -a gatkbam_rna -b $rbam -r ${index_path}/hisat_index -p $pair_id
......
Subproject commit b6d2f6898ecc1890b4df305e9505bdaa5eace4a6
Subproject commit 012a37c5f66ad4c20312642904416c4c493fa75e
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