Commit a1c370ff authored by Brandi Cantarel's avatar Brandi Cantarel

update skip dea

parent bb6e7948
Pipeline #3575 canceled with stage
...@@ -158,9 +158,9 @@ workflow_parameters: ...@@ -158,9 +158,9 @@ workflow_parameters:
- id: genome - id: genome
type: select type: select
choices: choices:
- [ '/project/shared/bicf_workflow_ref/GRCh38', 'Human GRCh38'] - [ '/project/shared/bicf_workflow_ref/human/GRCh38', 'Human GRCh38']
- [ '/project/shared/bicf_workflow_ref/GRCh37', 'Human GRCh37'] - [ '/project/shared/bicf_workflow_ref/human/GRCh37', 'Human GRCh37']
- [ '/project/shared/bicf_workflow_ref/GRCm38', 'Mouse GRCm38'] - [ '/project/shared/bicf_workflow_ref/mouse/GRCm38', 'Mouse GRCm38']
required: true required: true
description: | description: |
Reference genome for alignment Reference genome for alignment
......
...@@ -6,7 +6,7 @@ params.output= "$baseDir/output" ...@@ -6,7 +6,7 @@ params.output= "$baseDir/output"
params.fastqs="$params.input/*.fastq.gz" params.fastqs="$params.input/*.fastq.gz"
params.design="$params.input/design.txt" params.design="$params.input/design.txt"
params.genome="/project/shared/bicf_workflow_ref/GRCh38/" params.genome="/project/shared/bicf_workflow_ref/human/GRCh38/"
params.markdups="picard" params.markdups="picard"
params.stranded="0" params.stranded="0"
params.pairs="pe" params.pairs="pe"
...@@ -20,7 +20,8 @@ fastqs=file(params.fastqs) ...@@ -20,7 +20,8 @@ fastqs=file(params.fastqs)
design_file = file(params.design) design_file = file(params.design)
gtf_file = file("$params.genome/gencode.gtf") gtf_file = file("$params.genome/gencode.gtf")
genenames = file("$params.genome/genenames.txt") genenames = file("$params.genome/genenames.txt")
geneset = file("$params.genome/gsea_gmt/$params.geneset")
geneset = file("$params.genome/../gsea_gmt/$params.geneset")
dbsnp="$params.genome/dbSnp.vcf.gz" dbsnp="$params.genome/dbSnp.vcf.gz"
indel="$params.genome/GoldIndels.vcf.gz" indel="$params.genome/GoldIndels.vcf.gz"
knownindel=file(indel) knownindel=file(indel)
......
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