allelic feature counts

maxplanck-ie · Jan 10, 2025 · f4a881d · f4a881d
1 parent 9b0ba53
commit f4a881d
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Showing 2 changed files with 1 addition and 14 deletions.
diff --git 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
@@ -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: