Skip to content

Commit

Permalink
Fix889 (#904)
Browse files Browse the repository at this point in the history 
* added cluster resources to sambamba flagstat to prevent swapping
* fixes #889 

* fixes #890

* ci tests

---------

Co-authored-by: katarzyna.otylia.sikora@gmail.com <sikora@minimus.ie-freiburg.mpg.de>
Co-authored-by: katarzyna.otylia.sikora@gmail.com <sikora@maximus.ie-freiburg.mpg.de>
  • Loading branch information
@katsikora
3 people committed Jun 7, 2023
1 parent 7d34a84 commit 6e6cf19
Show file tree
Hide file tree
Showing 4 changed files with 43 additions and 38 deletions.
68 changes: 34 additions & 34 deletions .ci_stuff/test_dag.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -129,32 +129,32 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 181 ]; then exit 1 ; fi

# DNA mapping
WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp " | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 763 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 769 ]; then exit 1 ; fi
WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 819 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 825 ]; then exit 1 ; fi
WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs --bcExtract | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 787 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 793 ]; then exit 1 ; fi
WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --UMIDedup --properPairs --bcExtract | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 837 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 843 ]; then exit 1 ; fi
WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --UMIDedup --properPairs | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 869 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 875 ]; then exit 1 ; fi
WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --mapq 20 --UMIDedup --properPairs | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 869 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 875 ]; then exit 1 ; fi
WC=`DNA-mapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 687 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 693 ]; then exit 1 ; fi
WC=`DNA-mapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 743 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 749 ]; then exit 1 ; fi
WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --aligner bwa | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 757 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 763 ]; then exit 1 ; fi
WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --aligner bwa-mem2 | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 757 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 763 ]; then exit 1 ; fi
#allelic
WC=`DNA-mapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1335 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1341 ]; then exit 1 ; fi
WC=`DNA-mapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1318 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1324 ]; then exit 1 ; fi
WC=`DNA-mapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1335 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1341 ]; then exit 1 ; fi

# ChIP-seq
WC=`ChIP-seq -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 "Conda environment" | sed '/^\s*$/d' | wc -l`
Expand All @@ -170,55 +170,55 @@ WC=`ChIP-seq -d outdir --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeO
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 717 ]; then exit 1 ; fi
# spikein
WC=`ChIP-seq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 635 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 637 ]; then exit 1 ; fi
# fromBAM and spikein
WC=`ChIP-seq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 793 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 795 ]; then exit 1 ; fi
WC=`ChIP-seq -d outdir --useSpikeInForNorm --getSizeFactorsFrom TSS --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 593 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 595 ]; then exit 1 ; fi
WC=`ChIP-seq -d outdir --useSpikeInForNorm --getSizeFactorsFrom input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 581 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 583 ]; then exit 1 ; fi
# allelic
WC=`ChIP-seq -d allelic_BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 333 ]; 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 917 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 923 ]; then exit 1 ; fi
WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 927 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 933 ]; then exit 1 ; fi
WC=`mRNA-seq -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 943 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 949 ]; then exit 1 ; fi
WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 637 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 643 ]; then exit 1 ; fi
WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 983 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 989 ]; then exit 1 ; fi
WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1044 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1050 ]; then exit 1 ; fi
WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 951 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 957 ]; then exit 1 ; fi
WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --UMIDedup --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1001 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1007 ]; then exit 1 ; fi
WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 842 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 848 ]; then exit 1 ; fi
WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 561 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 567 ]; then exit 1 ; fi
WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 898 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 904 ]; then exit 1 ; fi
WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 959 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 965 ]; then exit 1 ; fi
WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --fastqc .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1010 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1016 ]; then exit 1 ; fi
WC=`mRNA-seq -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 657 ]; then exit 1 ; fi
#multiple comparison groups
WC=`mRNA-seq --mode alignment,alignment-free -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 907 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 913 ]; then exit 1 ; fi
# three prime sequencing
WC=`mRNA-seq -i PE_input -o output --mode three-prime-seq --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 656 ]; then exit 1 ; fi
WC=`mRNA-seq -i PE_input -o output --mode three-prime-seq,deepTools_qc --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1237 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1243 ]; then exit 1 ; fi
#allelic
WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1395 ]; then exit 1 ; fi
Expand Down Expand Up @@ -251,9 +251,9 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 793 ]; then exit 1 ; fi
#WC=`scRNAseq -i PE_input -o output --mode Gruen --snakemakeOptions " --dryrun --conda-prefix /tmp" --skipRaceID --splitLib .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
#if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1015 ]; then exit 1 ; fi
WC=`scRNAseq -i PE_input -o output --mode STARsolo --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1003 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1009 ]; then exit 1 ; fi
WC=`scRNAseq -i PE_input -o output --mode STARsolo --skipVelocyto --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 895 ]; then exit 1 ; fi
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 901 ]; then exit 1 ; fi
WC=`scRNAseq -i PE_input -o output --mode Alevin --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 450 ]; then exit 1 ; fi
WC=`scRNAseq -i PE_input -o output --mode Alevin --skipVelocyto --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
Expand Down
6 changes: 4 additions & 2 deletions snakePipes/shared/rules/sambamba.snakefile
View file
Original file line number Diff line number Diff line change
Expand Up @@ -31,8 +31,9 @@ rule sambamba_flagstat_sorted:
"Sambamba/{sample}.sorted.markdup.txt"
log: "Sambamba/logs/{sample}.flagstat_sorted.log"
conda: CONDA_SAMBAMBA_ENV
threads: lambda wildcards: 10 if 10<max_thread else max_thread
shell: """
sambamba flagstat -p {input} > {output} 2> {log}
sambamba flagstat -p {input} -t {threads} > {output} 2> {log}
"""

rule sambamba_flagstat:
Expand All @@ -42,8 +43,9 @@ rule sambamba_flagstat:
"Sambamba/{sample}.markdup.txt"
log: "Sambamba/logs/{sample}.flagstat.log"
conda: CONDA_SAMBAMBA_ENV
threads: lambda wildcards: 10 if 10<max_thread else max_thread
shell: """
sambamba flagstat -p {input} > {output} 2> {log}
sambamba flagstat -p {input} -t {threads} > {output} 2> {log}
"""

## index the duplicate marked folder
Expand Down
3 changes: 1 addition & 2 deletions snakePipes/workflows/ChIP-seq/internals.snakefile
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,6 @@ import sys
import pandas as pd
import warnings


### Functions ##################################################################

def get_control(sample):
Expand Down Expand Up @@ -217,7 +216,7 @@ def check_if_spikein_genome(genome_index,spikeinExt):
for line in ifile:
resl.append(re.search(spikeinExt, line))
if any(resl):
print("\n Spikein genome detected - at least one spikeIn chromosome found with extention " + spikeinExt + " .\n\n")
warnings.warn("\n Spikein genome detected - at least one spikeIn chromosome found with extention " + spikeinExt + " .\n\n")
return True
else:
return False
Expand Down
4 changes: 4 additions & 0 deletions snakePipes/workflows/DNA-mapping/cluster.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,3 +16,7 @@ CollectInsertSizeMetrics:
memory: 1G
filter_reads:
memory: 3G
sambamba_flagstat:
memory: 3G
sambamba_flagstat_sorted:
memory: 3G

0 comments on commit 6e6cf19

Please sign in to comment.