From ba9dda86935a569fbca74bdf359285ab292038c9 Mon Sep 17 00:00:00 2001
From: WardDeb <ward@deboutte.be>
Date: Thu, 1 Jun 2023 13:42:39 +0200
Subject: [PATCH] ci update

---
 .ci_stuff/test_dag.sh | 156 +++++++++++++++++++++---------------------
 1 file changed, 78 insertions(+), 78 deletions(-)

diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh
index de1d122d7..d918f0883 100755
--- a/.ci_stuff/test_dag.sh
+++ b/.ci_stuff/test_dag.sh
@@ -117,133 +117,133 @@ snakePipes config
 
 # createIndices
 WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --genome ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtf ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz blah | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 184 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 142 ]; then exit 1 ; fi
 WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --genome ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtf ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz --rmskURL http://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/rmsk.txt.gz blah | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 192 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 148 ]; then exit 1 ; fi
 WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --genome ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtf ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz --rmskURL http://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/rmsk.txt.gz blah | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 192 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 148 ]; then exit 1 ; fi
 # spikein
 WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --genomeURL ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtfURL ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz --spikeinGenomeURL ftp://ftp.ensembl.org/pub/release-79/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.dna_sm.toplevel.fa.gz --spikeinGtfURL  ftp://ftp.ensembl.org/pub/release-96/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.22.96.gtf.gz --rmskURL http://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/rmsk.txt.gz blah | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 239 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 181 ]; then exit 1 ; fi
 
 
 # DNA mapping
 WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp " | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 985 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 763 ]; then exit 1 ; fi
 WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1053 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 819 ]; then exit 1 ; fi
 WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs --bcExtract | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1009 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 787 ]; then exit 1 ; fi
 WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --UMIDedup --properPairs --bcExtract | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1077 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 837 ]; then exit 1 ; fi
 WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --UMIDedup --properPairs | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1121 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 869 ]; then exit 1 ; fi
 WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --mapq 20 --UMIDedup --properPairs | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1121 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 869 ]; then exit 1 ; fi
 WC=`DNA-mapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 885 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 687 ]; then exit 1 ; fi
 WC=`DNA-mapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 953 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 743 ]; then exit 1 ; fi
 WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --aligner bwa | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 973 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 757 ]; then exit 1 ; fi
 WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --aligner bwa-mem2 | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 973 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 757 ]; then exit 1 ; fi
 #allelic
 WC=`DNA-mapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1707 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1335 ]; then exit 1 ; fi
 WC=`DNA-mapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1686 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1318 ]; then exit 1 ; fi
 WC=`DNA-mapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1707 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1335 ]; then exit 1 ; fi
 
 # ChIP-seq
 WC=`ChIP-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 516 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 403 ]; then exit 1 ; fi
 WC=`ChIP-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 522 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 403 ]; then exit 1 ; fi
 WC=`ChIP-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --singleEnd .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 514 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 401 ]; then exit 1 ; fi
 WC=`ChIP-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --bigWigType log2ratio .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 470 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 365 ]; then exit 1 ; fi
 # fromBAM
 WC=`ChIP-seq -d outdir --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 914 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 717 ]; then exit 1 ; fi
 # spikein
 WC=`ChIP-seq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp"  .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 798 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 635 ]; then exit 1 ; fi
 # fromBAM and spikein
 WC=`ChIP-seq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1004 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 793 ]; then exit 1 ; fi
 WC=`ChIP-seq -d outdir --useSpikeInForNorm --getSizeFactorsFrom TSS --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 762 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 593 ]; then exit 1 ; fi
 WC=`ChIP-seq -d outdir --useSpikeInForNorm --getSizeFactorsFrom input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 746 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 581 ]; then exit 1 ; fi
 # allelic
 WC=`ChIP-seq -d allelic_BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp"  .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 421 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 333 ]; then exit 1 ; fi
 
 # mRNA-seq
 WC=`mRNA-seq -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1175 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 917 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1187 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 927 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1207 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 943 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 835 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 637 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1255 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 983 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1327 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1044 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1211 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 951 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --UMIDedup --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1273 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1001 ]; then exit 1 ; fi
 WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1076 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 842 ]; then exit 1 ; fi
 WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 735 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 561 ]; then exit 1 ; fi
 WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1144 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 898 ]; then exit 1 ; fi
 WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1216 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 959 ]; then exit 1 ; fi
 WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --fastqc .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1280 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1010 ]; then exit 1 ; fi
 WC=`mRNA-seq -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 833 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 657 ]; then exit 1 ; fi
 #multiple comparison groups
 WC=`mRNA-seq --mode alignment,alignment-free -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1172 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 907 ]; then exit 1 ; fi
 # three prime sequencing
 WC=`mRNA-seq -i PE_input -o output --mode three-prime-seq --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 866 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 656 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --mode three-prime-seq,deepTools_qc --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1585 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1237 ]; then exit 1 ; fi
 #allelic
 WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1771 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1395 ]; then exit 1 ; fi
 WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i allelic_BAM_input/filtered_bam --fromBAM --bamExt '.filtered.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1408 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1118 ]; then exit 1 ; fi
 WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1783 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1405 ]; then exit 1 ; fi
 WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1762 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1388 ]; then exit 1 ; fi
 WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1783 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1405 ]; then exit 1 ; fi
 WC=`mRNA-seq -m allelic-mapping,deepTools_qc,alignment-free -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2328 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1841 ]; then exit 1 ; fi
 
 WC=`noncoding-RNA-seq -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 968 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 755 ]; then exit 1 ; fi
 WC=`noncoding-RNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 988 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 771 ]; then exit 1 ; fi
 WC=`noncoding-RNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 877 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 686 ]; then exit 1 ; fi
 WC=`noncoding-RNA-seq -i BAM_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 714 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 569 ]; then exit 1 ; fi
 #multiple comparison groups
 WC=`noncoding-RNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1016 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 793 ]; then exit 1 ; fi
 
 # scRNA-seq
 #WC=`scRNAseq -i PE_input -o output --mode Gruen --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
@@ -251,58 +251,58 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1016 ]; then exit 1 ; fi
 #WC=`scRNAseq -i PE_input -o output --mode Gruen --snakemakeOptions " --dryrun --conda-prefix /tmp" --skipRaceID --splitLib .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
 #if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1015 ]; then exit 1 ; fi
 WC=`scRNAseq -i PE_input -o output --mode STARsolo --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1271 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1003 ]; then exit 1 ; fi
 WC=`scRNAseq -i PE_input -o output --mode STARsolo --skipVelocyto --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1137 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 895 ]; then exit 1 ; fi
 WC=`scRNAseq -i PE_input -o output --mode Alevin --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 583 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 450 ]; then exit 1 ; fi
 WC=`scRNAseq -i PE_input -o output --mode Alevin --skipVelocyto --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 511 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 392 ]; then exit 1 ; fi
 
 # WGBS
 WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1034 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 789 ]; then exit 1 ; fi
 WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --aligner bwameth2 --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1034 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 789 ]; then exit 1 ; fi
 WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1045 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 798 ]; then exit 1 ; fi
 WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 759 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 590 ]; then exit 1 ; fi
 WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --fastqc --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 759 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 590 ]; then exit 1 ; fi
 WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --skipBamQC --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 400 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 310 ]; then exit 1 ; fi
 
 # ATAC-seq
 WC=`ATAC-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 527 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 408 ]; then exit 1 ; fi
 WC=`ATAC-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 615 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 474 ]; then exit 1 ; fi
 WC=`ATAC-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller HMMRATAC .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 600 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 466 ]; then exit 1 ; fi
 WC=`ATAC-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --maxFragmentSize 120 --qval 0.1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 527 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 408 ]; then exit 1 ; fi
 WC=`ATAC-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 869 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 678 ]; then exit 1 ; fi
 
 # HiC
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --correctionMethod ICE .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 697 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 533 ]; then exit 1 ; fi
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 653 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 501 ]; then exit 1 ; fi
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 721 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 557 ]; then exit 1 ; fi
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --enzyme DpnII .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 653 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 501 ]; then exit 1 ; fi
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --noTAD .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 591 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 451 ]; then exit 1 ; fi
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --aligner bwa-mem2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 653 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 501 ]; then exit 1 ; fi
 
 # preprocessing
 WC=`preprocessing -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp"  --fastqc --optDedupDist 2500 | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 558 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 424 ]; then exit 1 ; fi
 WC=`preprocessing -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp"  --DAG --fastqc --optDedupDist 2500 | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 558 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 424 ]; then exit 1 ; fi
 
 rm -rf SE_input PE_input BAM_input output allelic_input allelic_BAM_input /tmp/genes.gtf /tmp/genome.fa /tmp/genome.fa.fai /tmp/rmsk.txt /tmp/genes.bed /tmp/spikein_genes.gtf