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Commit 91a9ea5f authored by Jonathan Gesell's avatar Jonathan Gesell
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RE-specified the output directory.

parent 30349d74
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2 merge requests!37v0.0.1,!17Resolve "process_dedup"
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......@@ -58,8 +58,8 @@ alignReads:
dedupReads:
stage: unit
script:
- singularity exec 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5JA_1M.pe.sorted.bam O=./test_data/bam/small/Q-Y5JA_1M.pe.deduped.bam M=Q-Y5JA_1M.pe.deduped.Metrics.txt REMOVE_DUPLICATES=true
- singularity exec 'docker://bicf/picard2.21.7:2.0.0' 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 exec 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5JA_1M.pe.sorted.bam O=Q-Y5JA_1M.pe.deduped.bam M=Q-Y5JA_1M.pe.deduped.Metrics.txt REMOVE_DUPLICATES=true
- singularity exec 'docker://bicf/picard2.21.7:2.0.0' 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
- pytest -m dedupData
integration_se:
......
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