diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 0fc6736e0de68c5316cdb95abb87e212bc3d4226..b7a8ba1c50f6afbea814e25865d65261ea896263 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -69,7 +69,7 @@ dedupData: - 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 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 Q-Y5JA_1M.se.sorted.deduped.bam.bai - - for i in "chr8","chr4","chrY"}; do + - for i in {"chr8","chr4","chrY"}; do echo "samtools view -b Q-Y5JA_1M.se.sorted.deduped.bam ${i} > Q-Y5JA_1M.se.sorted.deduped.${i}.bam; samtools index -@ `nproc` -b Q-Y5JA_1M.se.sorted.deduped.${i}.bam Q-Y5JA_1M.se.sorted.deduped.${i}.bam.bai;"; done | singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' parallel -j `nproc` -k - pytest -m dedupData