added reference genome index on germline indel calling (which is requ…

…ired when only indel calling has been activated & remove -C from BWA mem call (on DNAseq data) which causes issues on Illumina identifier

CHANGELOG.md

@@ -16,6 +16,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Prioritization of neoantigens is now done separately for each variant type (speeds up the process)
 - NMD information (e.g., escape rule,...) is now also calculated for all variants
 
+## [0.2.6] - 2024-06-20
+
+### Fix 
+
+- Added routines to catch errors when rnaseq data is not provided but exitron/alternative splicing calling is activated
+- Added reference genome index as input to germline indel calling (necessary when only indel calling is activated)
+- removed -C from BWA mem call (on DNAseq data) to avoid error on Illumina identifiers
+
 ## [0.2.5] - 2024-06-19
 
 ### Fix 

workflow/rules/align.smk

@@ -231,10 +231,9 @@ if config['data']['dnaseq_filetype'] in ['.fq','.fastq']:
     threads: config['threads']
     shell:
       """
-        bwa mem -t{threads} -C resources/refs/bwa/genome {input.reads} \
-        | samtools addreplacerg -r ID:{wildcards.group} -r SM:{wildcards.sample} \
-        -r LB:{wildcards.sample} -r PL:ILLUMINA -r PU:{wildcards.group} - - \
-        | samtools sort -@ 6 -n -m1g - -o {output} > {log} 2>&1
+        bwa mem -t{threads} resources/refs/bwa/genome \
+            -R '@RG\\tID:{wildcards.group}\\tSM:{wildcards.sample}\\tLB:{wildcards.sample}\\tPL:ILLUMINA' \
+            {input.reads} | samtools sort -@ 6 -n -m1g - -o {output} > {log} 2>&1
       """
 
   rule dnaseq_postproc:

workflow/rules/common.smk

@@ -124,7 +124,6 @@ def all_identical(l):
 
 # load up the config
 config['data'] = data_structure(config['data'])
-print(config)
 
 ########### PREPROCESSING ##########
 def get_raw_reads(wildcards):