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Commit f2dd8009 authored by Jonathan Gesell's avatar Jonathan Gesell
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Corrected input and output BAM file paths.

parent 06790eb4
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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 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
- 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.sorted.bam O=./test_data/bam/small/Q-Y5JA.deduped.bam M=Q-Y5JA.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/16-1ZX4.sorted.bam O=./test_data/bam/small/16-1ZX4.deduped.bam M=16-1ZX4.deduped.Metrics.txt REMOVE_DUPLICATES=true
- pytest -m dedupData
integration_se:
......
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