From f4a881da92069525a53a5034e78420e68d64c75a Mon Sep 17 00:00:00 2001 From: "katarzyna.otylia.sikora@gmail.com" Date: Fri, 10 Jan 2025 10:08:02 +0100 Subject: [PATCH] allelic feature counts --- snakePipes/shared/rules/whatshap.snakefile | 13 ------------- snakePipes/workflows/mRNAseq/Snakefile | 2 +- 2 files changed, 1 insertion(+), 14 deletions(-) diff --git a/snakePipes/shared/rules/whatshap.snakefile b/snakePipes/shared/rules/whatshap.snakefile index 0c69e2aa4..f47683f37 100644 --- a/snakePipes/shared/rules/whatshap.snakefile +++ b/snakePipes/shared/rules/whatshap.snakefile @@ -30,19 +30,6 @@ rule whatshap_split: whatshap split --output-h1 {output.h1bam} --output-h2 {output.h2bam} --output-untagged {output.unbam} {input.hbam} {input.hlist} """ -#wildcard_constraints: -# suffix = ['allele_flagged', 'genome1', 'genome2', 'unassigned'] - - -#def collect_split_bams(wildcards): -# checkpoint_output_a = checkpoints.whatshap_haplotag.get(**wildcards).output["hbam"] -# checkpoint_output_b = checkpoints.whatshap_split.get(**wildcards).output -# checkpoint_output = checkpoint_output_a + checkpoint_output_b -# return expand("allelic_bams/{{sample}}.{suffix}.sorted.bam", -# suffix = glob_wildcards("allelic_bams/{sample}.{suffix}.sorted.bam").suffix) - -#_ , suffix = glob_wildcards("allelic_bams/{sample}.{suffix}.sorted.bam") - rule BAMindex_allelic: input: diff --git a/snakePipes/workflows/mRNAseq/Snakefile b/snakePipes/workflows/mRNAseq/Snakefile index 227d3c99e..54f3ee09e 100755 --- a/snakePipes/workflows/mRNAseq/Snakefile +++ b/snakePipes/workflows/mRNAseq/Snakefile @@ -118,7 +118,7 @@ else: include: os.path.join(maindir, "shared", "rules", "LinkBam.snakefile") -if "allelic-mapping" in mode or "allelic-counting" in mode: +if "allelic-mapping" in mode or "allelic-counting" in mode or "allelic-whatshap" in mode: ## featureCounts_allelic include: os.path.join(maindir, "shared", "rules", "featureCounts_allelic.snakefile") else: