diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 4d7f37b00efa2a89272e1eb69d5fea366c2aac3d..d1a71e5685aaff3d0545975b8c7e72e2200db9a9 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -21,13 +21,13 @@ getData: - singularity run 'docker://bicf/gudmaprbkfilexfer:1.1' sh ./workflow/scripts/bdbagFetch.sh Replicate_16-1ZX4 16-1ZX4 trimData_se: - tage: unit + stage: unit script: - if [ `nproc` -gt 8 ]; then ncore=8; else ncore=`nproc`; fi - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --basename 16-1ZX4 -j ${ncore} ./test_data/fastq/16-1ZX4.R1.fastq.gz trimData_pe: - tage: unit + stage: unit script: - if [ `nproc` -gt 8 ]; then ncore=8; else ncore=`nproc`; fi - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --paired --basename Q-Y5JA -j ${ncore} ./test_data/fastq/Q-Y5JA.R1.fastq.gz ./test_data/fastq/Q-Y5JA.R2.fastq.gz \ No newline at end of file