diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index dfce12b1569ef68362dd7630eefeb5e550a614ed..923f14517ea2ab48ab88e8db8861b152b6686fd5 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -37,7 +37,7 @@ parseMetadata: - stranded=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded) - spike=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike) - species=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species) - - echo -e "\${endsMeta},\${endsManual},\${stranded},\${spike},\${species},\${exp},\${study},\${repRID}" > design.csv + - echo -e "${endsMeta},${endsManual},${stranded},${spike},${species},${exp},${study},${repRID}" > design.csv - pytest -m parseMetadata inferMetadata: