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Commit e6fda180 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Change seqwho ref location in ci

parent fe1d95b4
2 merge requests!95Update rna-seq.nf,!94Resolve "Move seqwho reference"
Pipeline #10532 failed with stages
in 13 seconds
......@@ -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
......
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