diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index d6f9e172e1f622d8b7a1ebb564002b10daaae4b5..5152934a70a1e45f3d56915d4de805222334d14d 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -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: