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Commit 73a6b3d6 authored by Jonathan Gesell's avatar Jonathan Gesell
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Corrected typo in .gitlab-ci.yml

parent 819e87c2
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2 merge requests!37v0.0.1,!19Resolve "process_makeBigWig"
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......@@ -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
......
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