diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 4519e674866692619c2439246a2430c2d305acf5..aa9e446d0369a9ba68e912c89635f360348ee76c 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -255,7 +255,7 @@ seqwho: - seqwhoImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f1) - seqwhoVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f2) - echo ${dir}${seqwhoImg}_${seqwhoVar}.sif - - wget -O SeqWho.ix https://cloud.biohpc.swmed.edu/index.php/s/eeNWqZz8jqN5zWY/download + - wget -O SeqWho.ix https://cloud.biohpc.swmed.edu/index.php/s/sP48taKmymSkJBM/download - mkdir -p SeqWho_call_plots/test_data/fastq/small/ - singularity run ${dir}${seqwhoImg}_${seqwhoVar}.sif seqwho.py -f test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -x SeqWho.ix - pytest -m seqwho