diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index a5b59948d9f0b74838f13abf72b75309bedfb7c0..a4c2f3e5dbc9dc475d9f332c2e82f6b27571a7a3 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -64,8 +64,8 @@ alignData: dedupData: stage: unit script: - - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5JA_1M.se.sorted.bam O=Q-Y5JA_1M.se.deduped.bam M=Q-Y5JA_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true - - singularity run 'docker://bicf/gudmaprbkdedup.2.0.0' samtools sort -@ `nproc` -O BAM -o ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5JA_1M.se.deduped.bam + - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5JA_1M.se.sorted.bam O=./test_data/bam/small/Q-Y5JA_1M.se.deduped.bam M=Q-Y5JA_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true + - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools sort -@ `nproc` -O BAM -o ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5JA_1M.se.deduped.bam - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools index -@ `nproc` -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bai - pytest -m dedupData