ci tests for allelic multicom

maxplanck-ie · Apr 11, 2024 · 770ae19 · 770ae19
1 parent 833e1e1
commit 770ae19
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Showing 4 changed files with 10 additions and 5 deletions.
diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh
@@ -340,8 +340,13 @@ WC=`mRNA-seq -m allelic-mapping,deepTools_qc,alignment-free -i PE_input -o outpu
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 3294 ]; then exit 1 ; fi
 WC=`mRNA-seq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp"  .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "conda installation\|Conda environment" | sed '/^\s*$/d' | wc -l`
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 659 ]; then exit 1 ; fi
-
-
+#allelic+multicomp
+WC=`mRNA-seq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp"  .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "conda installation\|Conda environment" | sed '/^\s*$/d' | wc -l`
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 659 ]; then exit 1 ; fi
+WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i allelic_BAM_input/filtered_bam --fromBAM --bamExt '.filtered.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "conda installation\|Conda environment" | sed '/^\s*$/d' | wc -l`
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1408 ]; then exit 1 ; fi
+WC=`mRNA-seq -m allelic-mapping,deepTools_qc,alignment-free -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "conda installation\|Conda environment" | sed '/^\s*$/d' | wc -l`
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 3294 ]; 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 installation\|Conda environment" | sed '/^\s*$/d' | wc -l`
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1370 ]; then exit 1 ; fi

diff --git a/snakePipes/shared/rscripts/DESeq2.R b/snakePipes/shared/rscripts/DESeq2.R
@@ -34,7 +34,7 @@ importfunc <- snakemake@params[["importfunc"]]
 allelic_info <- as.logical(snakemake@params[["allele_info"]])
 tx2gene_file <- snakemake@params[["tx2gene_file"]]
 rmdTemplate <- snakemake@params[["rmdTemplate"]]
-formulaInput <- snakemake@params[["formula"]]
+formulaInput <- as.character(snakemake@params[["formula"]])
 wdir <- snakemake@params[["outdir"]]
 
 setwd(wdir)

diff --git a/snakePipes/workflows/mRNA-seq/defaults.yaml b/snakePipes/workflows/mRNA-seq/defaults.yaml
@@ -64,7 +64,7 @@ clusterPAS:
 ## further options
 mode: alignment,deepTools_qc
 sampleSheet:
-formula:
+formula: ""
 rMats: False
 bwBinSize: 25
 fastqc: False

diff --git a/snakePipes/workflows/mRNA-seq/mRNA-seq b/snakePipes/workflows/mRNA-seq/mRNA-seq
@@ -27,7 +27,7 @@ def parse_args(defaults={"verbose": False, "configFile": None,
                          "alignerOptions": None,
                          "featureCountsOptions": "-C -Q 10 --primary",
                          "filterGTF": None, "sampleSheet": None,
-                         "formula": None,
+                         "formula": "",
                          "reads": ["_R1", "_R2"], "ext": ".fastq.gz",
                          "bwBinSize": 25, "dnaContam": False, "plotFormat": "png",
                          "fromBAM": False, "bamExt": ".bam", "pairedEnd": True,