From 5ee467531d9fd6d98b3e9f367d9e7a95c0a6500a Mon Sep 17 00:00:00 2001 From: Steffen Heyne Date: Tue, 25 Jul 2017 08:44:45 +0200 Subject: [PATCH] fix: omit deeptools_qc also for scRNA-seq in case of single samples --- workflows/scRNAseq/Snakefile | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/workflows/scRNAseq/Snakefile b/workflows/scRNAseq/Snakefile index 5f1836102..6e947e608 100755 --- a/workflows/scRNAseq/Snakefile +++ b/workflows/scRNAseq/Snakefile @@ -46,7 +46,19 @@ def run_Trimming(trim): def run_bamCoverage(): return( expand("bamCoverage/{sample}.coverage.bw", sample = samples) ) - +def run_deeptools_qc(): + file_list = [ + expand("bamCoverage/{sample}.RPKM.bw", sample = samples), + expand("bamCoverage/{sample}.coverage.bw", sample = samples), + "deepTools_qc/plotEnrichment/plotEnrichment.png", + "deepTools_qc/plotEnrichment/plotEnrichment.tsv"] + if len(samples)>1: + file_list.append( ["deepTools_qc/multiBigwigSummary/coverage.bed.npz", + "deepTools_qc/plotCorrelation/correlation.pearson.bed_coverage.heatmap.png", + "deepTools_qc/plotCorrelation/correlation.spearman.bed_coverage.heatmap.png", + "deepTools_qc/plotPCA/PCA.bed_coverage.png"] ) + return(file_list) + ### execute before workflow starts ############################################# ################################################################################ onstart: @@ -93,15 +105,7 @@ rule all: expand("Counts/{sample}.featureCounts_summary.txt",sample = samples), "Results/all_samples.gencode_genomic.coutt_merged.csv", "QC_report/QC_report.all_samples.libstats_reads.tsv", - expand("bamCoverage/{sample}.RPKM.bw", sample = samples), - expand("bamCoverage/{sample}.coverage.bw", sample = samples), - "deepTools_qc/plotEnrichment/plotEnrichment.png", - "deepTools_qc/plotEnrichment/plotEnrichment.tsv", - "deepTools_qc/multiBigwigSummary/coverage.bed.npz", - "deepTools_qc/plotCorrelation/correlation.pearson.bed_coverage.heatmap.png", - "deepTools_qc/plotCorrelation/correlation.spearman.bed_coverage.heatmap.png", - "deepTools_qc/plotPCA/PCA.bed_coverage.png", - + run_deeptools_qc(), rule annot: input: "Annotation/genes.filtered.bed",