Skip to content
Snippets Groups Projects
Commit 06790eb4 authored by Jonathan Gesell's avatar Jonathan Gesell
Browse files

Update .gitlab-ci.yml, removed variable IDs.

parent a28ab789
Branches
Tags
2 merge requests!37v0.0.1,!17Resolve "process_dedup"
Pipeline #5846 failed with stages
in 30 minutes and 39 seconds
......@@ -58,7 +58,8 @@ alignReads:
dedupReads:
stage: unit
script:
- singularity run 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=${sortedBam} O=${repRID}.deduped.bam M=${repRID}.deduped.Metrics.txt REMOVE_DUPLICATES=true
- singularity run 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=Q-Y5JA.sorted.bam O=Q-Y5JA.deduped.bam M=Q-Y5JA.deduped.Metrics.txt REMOVE_DUPLICATES=true
- singularity run 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=16-1ZX4.sorted.bam O=16-1ZX4.deduped.bam M=16-1ZX4.deduped.Metrics.txt REMOVE_DUPLICATES=true
- pytest -m dedupData
integration_se:
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment