From 1ff8affb320baae2dd058cb359140e8b998b9c4c Mon Sep 17 00:00:00 2001 From: "katarzyna.otylia.sikora@gmail.com" Date: Fri, 20 Dec 2024 11:24:28 +0100 Subject: [PATCH] test dag --- .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 56302c942..f4458bb12 100755 --- a/.ci_stuff/test_dag.sh +++ b/.ci_stuff/test_dag.sh @@ -384,7 +384,7 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1370 ]; then exit 1 ; fi WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --aligner bwameth2 --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1370 ]; then exit 1 ; fi WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` -if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1353 ]; then exit 1 ; fi +if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1380 ]; then exit 1 ; fi WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 974 ]; then exit 1 ; fi WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --fastqc --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l `