Merge pull request #776 from maxplanck-ie/hic_multiqc

multiqc version has been updated

.ci_stuff/test_dag.sh

@@ -275,15 +275,15 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 686 ]; 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 487 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 495 ]; then exit 1 ; fi
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 455 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 463 ]; then exit 1 ; fi
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 511 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 519 ]; then exit 1 ; fi
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --enzyme DpnII .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 455 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 463 ]; then exit 1 ; fi
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --noTAD .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 405 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 413 ]; 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`

snakePipes/shared/rules/envs/shared.yaml

@@ -11,6 +11,6 @@ dependencies:
  - fastqc = 0.11.9
  - cutadapt = 2.8
  - trim-galore = 0.6.5
- - multiqc = 1.8
+ - multiqc = 1.10.1
  - fastp = 0.20.0
  - umi_tools = 1.0.1

snakePipes/workflows/HiC/Snakefile

@@ -147,7 +147,7 @@ rule all:
         run_build_matrices(),
         expand("HiC_matrices/QCplots/{sample}_QC/QC.log", sample = samples),
         run_dist_vs_count(),
-        #"multiQC/multiqc_report.html"
+        "multiQC/multiqc_report.html"
 
 ### execute after workflow finished ############################################
 ################################################################################