Merge pull request #749 from maxplanck-ie/dev_ksikora2

Fixes RNA-seq workflows wo sampleSheet
maxplanck-ie · Feb 5, 2021 · 0120aca · 0120aca
2 parents 060bcd4 + 9d9c087
commit 0120aca
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Showing 7 changed files with 30 additions and 14 deletions.
diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh
@@ -181,6 +181,8 @@ WC=`ChIP-seq -d allelic_BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv -
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 331 ]; 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 ] || [ $WC -ne 882 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 892 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
@@ -211,6 +213,8 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 659 ]; then exit 1 ; fi
 WC=`mRNA-seq --mode alignment,alignment-free -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 867 ]; then exit 1 ; fi
 #allelic
+WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1360 ]; then exit 1 ; fi
 WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1370 ]; then exit 1 ; fi
 WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
@@ -219,6 +223,8 @@ WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1370 ]; then exit 1 ; fi
 
 # noncoding-RNA-seq
+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 ] || [ $WC -ne 717 ]; then exit 1 ; fi
 WC=`noncoding-RNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 733 ]; then exit 1 ; fi
 WC=`noncoding-RNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: snakepipes
-  version: 2.4.2
+  version: 2.4.3
 
 source:
   path: ../

diff --git a/docs/content/News.rst b/docs/content/News.rst
@@ -1,6 +1,15 @@
 snakePipes News
 ===============
 
+snakePipes 2.4.3
+----------------
+
+* Fixed noncoding-RNA-seq workflow without sample sheet.
+* Updated links to prebuilt indices on zenodo.
+* Fixed read length estimation for rMats.
+* Cutadapt is set as default read trimming program for both noncoding-RNA-seq and mRNA-seq workflows.
+
+
 snakePipes 2.4.2
 ----------------
 

diff --git a/docs/content/setting_up.rst b/docs/content/setting_up.rst
@@ -34,7 +34,7 @@ The easiest way to install snakePipes is via our conda channel. The following co
 
 .. code:: bash
 
-    conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes==2.4.2
+    conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes==2.4.3
 
 This way, the software used within snakePipes do not conflict with the software pre-installed on your terminal or in your python environment.
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -34,7 +34,7 @@ Quick start
 
 .. code:: bash
 
-    conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes==2.4.2
+    conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes==2.4.3
 
 * You can update snakePipes to the latest version available on conda with:
 

diff --git a/snakePipes/__init__.py b/snakePipes/__init__.py
@@ -1 +1 @@
-__version__ = '2.4.2'
+__version__ = '2.4.3'
diff --git a/snakePipes/shared/rules/tecounts.snakefile b/snakePipes/shared/rules/tecounts.snakefile
@@ -183,16 +183,17 @@ def get_outdir(folder_name,sampleSheet):
     sample_name = os.path.splitext(os.path.basename(str(sampleSheet)))[0]
     return("{}_{}".format(folder_name, sample_name))
 
-rule split_sampleSheet:
-    input:
-        sampleSheet = sampleSheet
-    output:
-        splitSheets = os.path.join("splitSampleSheets",os.path.splitext(os.path.basename(str(sampleSheet)))[0]+".{compGroup}.tsv")
-    params:
-        splitSheetPfx = os.path.join("splitSampleSheets",os.path.splitext(os.path.basename(str(sampleSheet)))[0])
-    run:
-        if isMultipleComparison:
-            cf.splitSampleSheet(input.sampleSheet,params.splitSheetPfx)
+if sampleSheet:
+    rule split_sampleSheet:
+        input:
+            sampleSheet = sampleSheet
+        output:
+            splitSheets = os.path.join("splitSampleSheets",os.path.splitext(os.path.basename(str(sampleSheet)))[0]+".{compGroup}.tsv")
+        params:
+            splitSheetPfx = os.path.join("splitSampleSheets",os.path.splitext(os.path.basename(str(sampleSheet)))[0])
+        run:
+            if isMultipleComparison:
+                cf.splitSampleSheet(input.sampleSheet,params.splitSheetPfx)
 
 
 # TODO: topN, FDR