From 73a6b3d61df16739eb064507d246c9fa92fefb54 Mon Sep 17 00:00:00 2001 From: Jonathan Gesell <jonathan.gesell@utsouthwestern.edu> Date: Mon, 10 Feb 2020 16:49:56 -0600 Subject: [PATCH] Corrected typo in .gitlab-ci.yml --- .gitlab-ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index a5b5994..a4c2f3e 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -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 -- GitLab