diff --git a/workflow/scripts/createTestData.sh b/workflow/scripts/createTestData.sh index 2b76481c0dd539518596a7cba916cc76cd257cc4..47c73d46fba5510f64fe5f9bb5c540eb4ad618cc 100644 --- a/workflow/scripts/createTestData.sh +++ b/workflow/scripts/createTestData.sh @@ -63,6 +63,7 @@ cp Q-Y5F6_1M.pe.alignSummary.txt ./NEW_test_data/meta/Q-Y5F6_1M.pe.alignSummary. singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./NEW_test_data/bam/small/Q-Y5F6_1M.se.sorted.bam O=Q-Y5F6_1M.se.deduped.bam M=Q-Y5F6_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.se.sorted.deduped.bam Q-Y5F6_1M.se.deduped.bam singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools index -@ 20 -b Q-Y5F6_1M.se.sorted.deduped.bam Q-Y5F6_1M.se.sorted.deduped.bam.bai +cp Q-Y5F6_1M.se.deduped.bam ./NEW_test_data/bam/small/Q-Y5F6_1M.se.deduped.bam cp Q-Y5F6_1M.se.sorted.deduped.bam ./NEW_test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam cp Q-Y5F6_1M.se.sorted.deduped.bam.bai ./NEW_test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam.bai cp Q-Y5F6_1M.se.deduped.Metrics.txt /NEW_test_data/meta/Q-Y5F6_1M.se.deduped.Metrics.txt