diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh
index 78f7db4b1..7e5dcf8ae 100755
--- a/.ci_stuff/test_dag.sh
+++ b/.ci_stuff/test_dag.sh
@@ -166,206 +166,206 @@ snakePipes config --tempDir /tmp
 
 # 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 -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 229 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 213 ]; then exit 1 ; fi
 WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --genome ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtf ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz --rmskURL http://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/rmsk.txt.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 237 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 221 ]; then exit 1 ; fi
 WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --genome ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtf ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz --rmskURL http://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/rmsk.txt.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 237 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 221 ]; then exit 1 ; fi
 # spikein
 WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --genomeURL ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtfURL ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz --spikeinGenomeURL ftp://ftp.ensembl.org/pub/release-79/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.dna_sm.toplevel.fa.gz --spikeinGtfURL  ftp://ftp.ensembl.org/pub/release-96/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.22.96.gtf.gz --rmskURL http://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/rmsk.txt.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 284 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 268 ]; then exit 1 ; fi
 
 
 # DNA mapping
 WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp " | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1420 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1332 ]; then exit 1 ; fi
 WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1521 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1424 ]; then exit 1 ; fi
 WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs --bcExtract | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1456 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1350 ]; then exit 1 ; fi
 WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --UMIDedup --properPairs --bcExtract | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1557 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1433 ]; then exit 1 ; fi
 WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --UMIDedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1622 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1507 ]; then exit 1 ; fi
 WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --mapq 20 --UMIDedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1622 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1507 ]; then exit 1 ; fi
 WC=`DNAmapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1272 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1184 ]; then exit 1 ; fi
 WC=`DNAmapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1373 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1276 ]; then exit 1 ; fi
 WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --aligner bwa | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1402 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1314 ]; then exit 1 ; fi
 WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --aligner bwa-mem2 | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1402 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1314 ]; then exit 1 ; fi
 #allelic
 WC=`DNAmapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2466 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2273 ]; then exit 1 ; fi
 WC=`DNAmapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2445 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2254 ]; then exit 1 ; fi
 WC=`DNAmapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2466 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2273 ]; then exit 1 ; fi
 
 # ChIPseq
 WC=`ChIPseq -d BAM_input --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 407 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 377 ]; then exit 1 ; fi
 WC=`ChIPseq -d BAM_input --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 399 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 365 ]; then exit 1 ; fi
 WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 630 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 580 ]; then exit 1 ; fi
 WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_broad_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 840 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 778 ]; then exit 1 ; fi
 WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 609 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 556 ]; then exit 1 ; fi
 WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --singleEnd .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 628 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 578 ]; then exit 1 ; fi
 WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --bigWigType log2ratio .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 562 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 518 ]; then exit 1 ; fi
 WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 927 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 853 ]; then exit 1 ; fi
 WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR --useSpikeInForNorm .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1371 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1256 ]; then exit 1 ; fi
 #noInput
 WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 403 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 374 ]; then exit 1 ; fi
 WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 349 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 320 ]; then exit 1 ; fi
 WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 637 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 590 ]; then exit 1 ; fi
 WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR --useSpikeInForNorm .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 864 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 796 ]; then exit 1 ; fi
 # fromBAM
 WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1187 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1104 ]; then exit 1 ; fi
 # fromBam and noInput
 WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 801 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 748 ]; then exit 1 ; fi
 # spikein
 WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp"  .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1142 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1045 ]; then exit 1 ; fi
 # spikein and noInput
 WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp"  .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 698 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 642 ]; then exit 1 ; fi
 # fromBAM and spikein
 WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1447 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1341 ]; then exit 1 ; fi
 WC=`ChIPseq -d outdir --useSpikeInForNorm --getSizeFactorsFrom TSS --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1178 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1098 ]; then exit 1 ; fi
 WC=`ChIPseq -d outdir --useSpikeInForNorm --getSizeFactorsFrom input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1149 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1070 ]; then exit 1 ; fi
 # allelic
 WC=`ChIPseq -d allelic_BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp"  .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_short_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 423 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 391 ]; then exit 1 ; fi
 #multiComp
 WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 842 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 772 ]; then exit 1 ; fi
 WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 861 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 784 ]; then exit 1 ; fi
 WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_broad_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1052 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 970 ]; then exit 1 ; fi
 #multiComp and fromBam
 WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1399 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1296 ]; then exit 1 ; fi
 WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1418 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1308 ]; then exit 1 ; fi
 #multiComp and spikein
 WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp"  .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1335 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1220 ]; then exit 1 ; fi
 WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1354 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1232 ]; then exit 1 ; fi
 #multiComp and spikein and noInput
 WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp"  .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 853 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 783 ]; then exit 1 ; fi
 WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 839 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 765 ]; then exit 1 ; fi
 #multiComp and spikein and fromBam
 WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1640 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1516 ]; then exit 1 ; fi
 WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1045 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 965 ]; then exit 1 ; fi
 #multiComp and spikein and fromBam and noInput
 WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1059 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 983 ]; then exit 1 ; fi
 WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1045 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 965 ]; then exit 1 ; fi
 #multiComp and noInput and fromBam
 WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1190 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1105 ]; then exit 1 ; fi
 
 
 # mRNAseq
 WC=`mRNAseq -i PE_input -o output --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' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1673 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1563 ]; then exit 1 ; fi
 WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1685 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1574 ]; then exit 1 ; fi
 WC=`mRNAseq -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1705 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1593 ]; then exit 1 ; fi
 WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1201 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1133 ]; then exit 1 ; fi
 WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1786 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1666 ]; then exit 1 ; fi
 WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1876 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1754 ]; then exit 1 ; fi
 WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1721 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1592 ]; then exit 1 ; fi
 WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --UMIDedup --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1813 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1666 ]; then exit 1 ; fi
 WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1526 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1416 ]; then exit 1 ; fi
 WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1053 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 985 ]; then exit 1 ; fi
 WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1627 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1508 ]; then exit 1 ; fi
 WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1717 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1596 ]; then exit 1 ; fi
 WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --fastqc .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1829 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1692 ]; then exit 1 ; fi
 WC=`mRNAseq -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1151 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1067 ]; then exit 1 ; fi
 #multiple comparison groups
 WC=`mRNAseq --mode alignment,alignment-free -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1598 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1503 ]; then exit 1 ; fi
 # three prime sequencing
 WC=`mRNAseq -i PE_input -o output --mode three-prime-seq --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1775 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1692 ]; then exit 1 ; fi
 WC=`mRNAseq -i PE_input -o output --mode three-prime-seq,deepTools_qc --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2259 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2133 ]; then exit 1 ; fi
 #allelic
 WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2527 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2331 ]; then exit 1 ; fi
 WC=`mRNAseq -m allelic-mapping,deepTools_qc -i allelic_BAM_input/filtered_bam --fromBAM --bamExt '.filtered.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1408 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1291 ]; then exit 1 ; fi
 WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2539 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2342 ]; then exit 1 ; fi
 WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2518 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2323 ]; then exit 1 ; fi
 WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2539 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2342 ]; then exit 1 ; fi
 WC=`mRNAseq -m allelic-mapping,deepTools_qc,alignment-free -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 3294 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 3039 ]; then exit 1 ; fi
 WC=`mRNAseq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp"  .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 659 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 638 ]; then exit 1 ; fi
 WC=`mRNAseq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp"  .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 659 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 638 ]; then exit 1 ; fi
 #allelic+multicomp
 WC=`mRNAseq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp"  .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 690 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 668 ]; then exit 1 ; fi
 WC=`mRNAseq -m allelic-mapping,deepTools_qc -i allelic_BAM_input/filtered_bam --fromBAM --bamExt '.filtered.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1439 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1321 ]; then exit 1 ; fi
 WC=`mRNAseq -m allelic-mapping,deepTools_qc,alignment-free -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 3302 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 3048 ]; then exit 1 ; fi
 
 #ncRNAseq
 WC=`ncRNAseq -i PE_input -o output --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' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1370 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1290 ]; then exit 1 ; fi
 WC=`ncRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1390 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1310 ]; then exit 1 ; fi
 WC=`ncRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1231 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1152 ]; then exit 1 ; fi
 WC=`ncRNAseq -i BAM_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 984 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 904 ]; then exit 1 ; fi
 #multiple comparison groups
 WC=`ncRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1418 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1338 ]; then exit 1 ; fi
 
 # scRNAseq
 #WC=`scRNAseq -i PE_input -o output --mode Gruen --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' | wc -l`
@@ -373,74 +373,74 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1418 ]; then exit 1 ; fi
 #WC=`scRNAseq -i PE_input -o output --mode Gruen --snakemakeOptions " --dryrun --conda-prefix /tmp" --skipRaceID --splitLib .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
 #if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1015 ]; then exit 1 ; fi
 WC=`scRNAseq -i PE_input -o output --mode STARsolo --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1790 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1642 ]; then exit 1 ; fi
 WC=`scRNAseq -i PE_input -o output --mode STARsolo --skipVelocyto --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1614 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1485 ]; then exit 1 ; fi
 WC=`scRNAseq -i PE_input -o output --mode Alevin --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 761 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 723 ]; then exit 1 ; fi
 WC=`scRNAseq -i PE_input -o output --mode Alevin --skipVelocyto --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 641 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 613 ]; then exit 1 ; fi
 
 # WGBS
 WC=`WGBS -i PE_input -o output --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' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1430 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1337 ]; then exit 1 ; fi
 WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1475 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1380 ]; then exit 1 ; fi
 WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --aligner bwameth2 --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1475 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1380 ]; then exit 1 ; fi
 WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1486 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1390 ]; then exit 1 ; fi
 WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1062 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 984 ]; then exit 1 ; fi
 WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --fastqc --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1062 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 984 ]; then exit 1 ; fi
 WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --skipBamQC --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 559 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 530 ]; then exit 1 ; fi
 
 # ATACseq
 WC=`ATACseq -d BAM_input --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' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 524 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 478 ]; then exit 1 ; fi
 WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 686 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 626 ]; then exit 1 ; fi
 WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 807 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 736 ]; then exit 1 ; fi
 WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller HMMRATAC .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 789 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 719 ]; then exit 1 ; fi
 WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --maxFragmentSize 120 --qval 0.1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 686 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 626 ]; then exit 1 ; fi
 WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1160 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1076 ]; then exit 1 ; fi
 #multicomp
 WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 841 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 767 ]; then exit 1 ; fi
 WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 980 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 893 ]; then exit 1 ; fi
 WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller HMMRATAC .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 944 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 860 ]; then exit 1 ; fi
 WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --maxFragmentSize 120 --qval 0.1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 841 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 767 ]; then exit 1 ; fi
 WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1315 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1217 ]; 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 -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1012 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 974 ]; then exit 1 ; fi
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 947 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 900 ]; then exit 1 ; fi
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1048 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 992 ]; then exit 1 ; fi
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --enzyme DpnII .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 947 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 900 ]; then exit 1 ; fi
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --noTAD .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 855 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 817 ]; then exit 1 ; fi
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --aligner bwa-mem2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 947 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 900 ]; 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 -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 807 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 779 ]; then exit 1 ; fi
 WC=`preprocessing -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp"  --DAG --fastqc --optDedupDist 2500 | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 807 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 779 ]; 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