fixes

snakePipes/shared/rules/DESeq2.singleComp.snakefile

@@ -7,7 +7,7 @@ def get_outdir(folder_name,sampleSheet):
 ## DESeq2 (on featureCounts)
 rule DESeq2:
     input:
-        counts_table = lambda wildcards : "featureCounts/counts_allelic.tsv" if 'allelic-mapping' in mode or "allelic-counting" in mode else "featureCounts/counts.tsv",
+        counts_table = lambda wildcards : "featureCounts/counts_allelic.tsv" if 'allelic' in mode else "featureCounts/counts.tsv",
         sampleSheet = sampleSheet,
         symbol_file = "Annotation/genes.filtered.symbol" #get_symbol_file
     output:
@@ -20,7 +20,7 @@ rule DESeq2:
         outdir = get_outdir("DESeq2",sampleSheet),
         fdr = fdr,
         importfunc = os.path.join(maindir, "shared", "rscripts", "DE_functions.R"),
-        allele_info = lambda wildcards : 'TRUE' if 'allelic-mapping' in mode or "allelic-counting" in mode else 'FALSE',
+        allele_info = lambda wildcards : 'TRUE' if 'allelic' in mode else 'FALSE',
         tx2gene_file = 'NA',
         rmdTemplate = os.path.join(maindir, "shared", "rscripts", "DESeq2Report.Rmd"),
         formula = config["formula"],

snakePipes/workflows/mRNAseq/Snakefile

@@ -119,7 +119,7 @@ else:
     include: os.path.join(maindir, "shared", "rules", "LinkBam.snakefile")
 
 
-if "allelic-mapping" in mode or "allelic-counting" in mode or "allelic-whatshap" in mode:
+if "allelic" in mode:
     ## featureCounts_allelic
     include: os.path.join(maindir, "shared", "rules", "featureCounts_allelic.snakefile")
 else:
@@ -254,7 +254,7 @@ def make_nmasked_genome():
         return([])
 
 def run_allelesp_mapping():
-    if "allelic-mapping" in mode or "allelic-counting" in mode or "allelic-whatshap" in mode:
+    if "allelic" in mode:
         allele_suffix = ['allele_flagged', 'genome1', 'genome2', 'unassigned']
         file_list = [
         expand("allelic_bams/{sample}.{suffix}.sorted.bam", sample = samples,