HiCExplorer3.5 (#670)

* updated hicexplorer to 3.5 * fixed dag lines * more fix for the number of lines in the dag Co-authored-by: Leily Rabbani <rabbani@maximus.ie-freiburg.mpg.de> Co-authored-by: Leily Rabbani <rabbani@pc390.ie-freiburg.mpg.de>
maxplanck-ie · Aug 7, 2020 · 0706188 · 0706188
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commit 0706188
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diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh
@@ -198,15 +198,15 @@ 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 479 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 487 ]; then exit 1 ; fi
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 447 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 455 ]; then exit 1 ; fi
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 503 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 511 ]; then exit 1 ; fi
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --enzyme DpnII .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 447 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 455 ]; then exit 1 ; fi
 WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --noTAD .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 397 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 405 ]; 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`

diff --git a/snakePipes/shared/rules/envs/hic.yaml b/snakePipes/shared/rules/envs/hic.yaml
@@ -3,6 +3,6 @@ channels:
  - conda-forge
  - bioconda
 dependencies:
- - hicexplorer = 3.4.3
+ - hicexplorer = 3.5
  - bwa = 0.7.17
  - samtools = 1.10
diff --git a/snakePipes/shared/rules/hicexplorer.snakefile b/snakePipes/shared/rules/hicexplorer.snakefile
@@ -68,7 +68,8 @@ else:
     rule build_matrix:
         input:
             R1 = "BWA/{sample}"+reads[0]+".bam",
-            R2 = "BWA/{sample}"+reads[1]+".bam"
+            R2 = "BWA/{sample}"+reads[1]+".bam",
+            bed = enzyme + ".bed"
         output:
             matrix = "HiC_matrices/{sample}_"+matrixFile_suffix+matrix_format,
             qc = "HiC_matrices/QCplots/{sample}_QC/QC.log"
@@ -89,6 +90,7 @@ else:
         shell:
             "hicBuildMatrix -s {input.R1} {input.R2} "
             "-bs {params.bin_size} "
+            "-rs {input.bed} "
             "--restrictionSequence {params.res_seq} "
             "--danglingSequence {params.dang_seq} "
             "--minDistance {params.min_dist} "