From 8951821ff5076ad5d9b073d4850c5e186636bc06 Mon Sep 17 00:00:00 2001 From: "katarzyna.otylia.sikora@gmail.com" Date: Tue, 14 Jan 2025 10:51:51 +0100 Subject: [PATCH] allelic-counting --- .ci_stuff/test_dag.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh index bfd63921a..ab214dd89 100755 --- a/.ci_stuff/test_dag.sh +++ b/.ci_stuff/test_dag.sh @@ -338,7 +338,7 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2408 ]; then exit 1 ; fi WC=`mRNAseq -m allelic-mapping,deepTools_qc,alignment-free -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 3105 ]; then exit 1 ; fi WC=`mRNAseq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` -if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 638 ]; then exit 1 ; fi +if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 637 ]; then exit 1 ; fi WC=`mRNAseq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 637 ]; then exit 1 ; fi #allelic+multicomp