removing nfragments.post_mapq_widow_filter

Author: kopardev

workflow/rules/qc.smk

@@ -52,7 +52,6 @@ rule get_nfragments_json:
         fastuniqlanestxt=rules.get_fastq_nreads.output.o3, # fastuniq lanes.txt
         postsecondarysupplementaryfilterbamflagstat=rules.star.output.postsecondarysupplementaryfilterbamflagstat,
         postinsertionfilterbamflagstat=rules.star.output.postinsertionfilterbamflagstat,
-        postmapqwidowfilterbamflagstat=rules.star.output.bamflagstat,
         pluspostmapqwidowfilterbamflagstat=rules.star.output.plusbamflagstat,
         minuspostmapqwidowfilterbamflagstat=rules.star.output.minusbamflagstat,
         plustoSNPcallingbamflagstat=rules.create_toSNPcalling_BAM.output.plustoSNPcallingbamflagstat,
@@ -78,7 +77,6 @@ python {params.pyscript} {params.sample} {output.json} \
     {input.fastuniqlanestxt} \
     {input.postsecondarysupplementaryfilterbamflagstat} \
     {input.postinsertionfilterbamflagstat} \
-    {input.postmapqwidowfilterbamflagstat} \
     {input.pluspostmapqwidowfilterbamflagstat} \
     {input.minuspostmapqwidowfilterbamflagstat} \
     {input.plustoSNPcallingbamflagstat} \

workflow/scripts/get_per_sample_nfragments.py

@@ -44,16 +44,15 @@ def get_nmutations_from_vcf(filename):
 fastuniqlanestxt=sys.argv[5] # fastuniq lanes.txt
 postsecondarysupplementaryfilterbamflagstat=sys.argv[6]
 postinsertionfilterbamflagstat=sys.argv[7]
-postmapqwidowfilterbamflagstat=sys.argv[8]
-pluspostmapqwidowfilterbamflagstat=sys.argv[9]
-minuspostmapqwidowfilterbamflagstat=sys.argv[10]
-plustoSNPcallingbamflagstat=sys.argv[11]
-minustoSNPcallingbamflagstat=sys.argv[12]
-mutatedbamflagstat=sys.argv[13]
-unmutatedbamflagstat=sys.argv[14]
-vcf=sys.argv[15]
-plusvcf=sys.argv[16]
-minusvcf=sys.argv[17]
+pluspostmapqwidowfilterbamflagstat=sys.argv[8]
+minuspostmapqwidowfilterbamflagstat=sys.argv[9]
+plustoSNPcallingbamflagstat=sys.argv[10]
+minustoSNPcallingbamflagstat=sys.argv[11]
+mutatedbamflagstat=sys.argv[12]
+unmutatedbamflagstat=sys.argv[13]
+vcf=sys.argv[14]
+plusvcf=sys.argv[15]
+minusvcf=sys.argv[16]
 
 data=dict()
 data['samplename']=samplename
@@ -63,7 +62,6 @@ def get_nmutations_from_vcf(filename):
 data['nfragments']['fastuniq'] = get_nreads_from_labels(fastuniqlanestxt,samplename)
 data['nfragments']['post_secondary_supplementary_filter'] = get_nfragments_from_flagstat(postsecondarysupplementaryfilterbamflagstat)
 data['nfragments']['post_insertion_filter'] = get_nfragments_from_flagstat(postinsertionfilterbamflagstat)
-data['nfragments']['post_mapq_widow_filter'] = get_nfragments_from_flagstat(postmapqwidowfilterbamflagstat)
 data['nfragments']['post_mapq_widow_filter_plus_strand'] = get_nfragments_from_flagstat(pluspostmapqwidowfilterbamflagstat)
 data['nfragments']['post_mapq_widow_filter_minus_strand'] = get_nfragments_from_flagstat(minuspostmapqwidowfilterbamflagstat)
 data['nfragments']['to_SNP_calling_plus_strand'] = get_nfragments_from_flagstat(plustoSNPcallingbamflagstat)