remove unused param

TheJacksonLaboratory · Jul 18, 2024 · 891c52f · 891c52f
1 parent a3f717f
commit 891c52f
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Showing 8 changed files with 9 additions and 13 deletions.
diff --git a/bin/help/somatic_wes.nf b/bin/help/somatic_wes.nf
@@ -38,8 +38,6 @@ Parameter | Default | Description
 --bait_picard | '/projects/omics_share/human/GRCh38/supporting_files/capture_kit_files/agilent/v7/S31285117_MergedProbes_no_gene_names.picard.interval_list' | A GATK interval file covering WES target intervals. Used in calculating coverage metrics. This file can be the same as the interval file,  NOTE: This file MUST reflect the capture array used to generate your data.
 
 --mismatch_penalty | -B 8 | The BWA penalty for a mismatch.
---call_val | 50 | The minimum phred-scaled confidence threshold at which variants should be called.
---ploidy_val | '-ploidy 2' | Sample ploidy
 
 --gnomad_ref | '/projects/compsci/omics_share/human/GRCh38/genome/annotation/snps_indels/af-only-gnomad.hg38.vcf.gz' | GnomAD germline reference from GATK resource pack. 
 --pon_ref | '/projects/compsci/omics_share/human/GRCh38/genome/annotation/snps_indels/1000g_pon.hg38.vcf.gz' | 1000 genome germline panel of normals from GATK resource pack.

diff --git a/bin/help/somatic_wes_pta.nf b/bin/help/somatic_wes_pta.nf
@@ -40,8 +40,6 @@ Parameter | Default | Description
 --bait_picard | '/projects/omics_share/human/GRCh38/supporting_files/capture_kit_files/agilent/v7/S31285117_MergedProbes_no_gene_names.picard.interval_list' | A GATK interval file covering WES target intervals. Used in calculating coverage metrics. This file can be the same as the interval file,  NOTE: This file MUST reflect the capture array used to generate your data.
 
 --mismatch_penalty | -B 8 | The BWA penalty for a mismatch.
---call_val | 50 | The minimum phred-scaled confidence threshold at which variants should be called.
---ploidy_val | '-ploidy 2' | Sample ploidy
 
 --gnomad_ref | '/projects/compsci/omics_share/human/GRCh38/genome/annotation/snps_indels/af-only-gnomad.hg38.vcf.gz' | GnomAD germline reference from GATK resource pack. 
 --pon_ref | '/projects/compsci/omics_share/human/GRCh38/genome/annotation/snps_indels/1000g_pon.hg38.vcf.gz' | 1000 genome germline panel of normals from GATK resource pack.

diff --git a/bin/log/somatic_wes.nf b/bin/log/somatic_wes.nf
@@ -50,7 +50,6 @@ ______________________________________________________
 --bait_picard                   ${params.bait_picard}
 --snpEff_config                 ${params.snpEff_config}
 --mismatch_penalty              ${params.mismatch_penalty}
---call_val                      ${params.call_val}
 --gen_ver                       ${params.gen_ver}
 --gold_std_indels               ${params.gold_std_indels}
 --phase1_1000G                  ${params.phase1_1000G}

diff --git a/bin/log/somatic_wes_pta.nf b/bin/log/somatic_wes_pta.nf
@@ -47,7 +47,6 @@ ______________________________________________________
 --bait_picard                   ${params.bait_picard}
 --snpEff_config                 ${params.snpEff_config}
 --mismatch_penalty              ${params.mismatch_penalty}
---call_val                      ${params.call_val}
 --gen_ver                       ${params.gen_ver}
 --gold_std_indels               ${params.gold_std_indels}
 --phase1_1000G                  ${params.phase1_1000G}

diff --git a/config/somatic_wes.config b/config/somatic_wes.config
@@ -50,9 +50,8 @@ params {
   target_picard = params.reference_cache+'/human/GRCh38/supporting_files/capture_kit_files/agilent/v7/S31285117_MergedProbes_no_gene_names.picard.interval_list'
   bait_picard = params.reference_cache+'/human/GRCh38/supporting_files/capture_kit_files/agilent/v7/S31285117_MergedProbes_no_gene_names.picard.interval_list'
 
-  // Variant calling parameters
+  // BWA Param
   mismatch_penalty = "-B 8"
-  call_val = "50.0"
 
   gnomad_ref=params.reference_cache+'/human/GRCh38/genome/annotation/snps_indels/af-only-gnomad.hg38.vcf.gz'
   pon_ref=params.reference_cache+'/human/GRCh38/genome/annotation/snps_indels/1000g_pon.hg38.vcf.gz'

diff --git a/config/somatic_wes_pta.config b/config/somatic_wes_pta.config
@@ -52,7 +52,6 @@ params {
 
   // Variant calling parameters
   mismatch_penalty = "-B 8"
-  call_val = "50.0"
 
   gnomad_ref=params.reference_cache+'/human/GRCh38/genome/annotation/snps_indels/af-only-gnomad.hg38.vcf.gz'
   pon_ref=params.reference_cache+'/human/GRCh38/genome/annotation/snps_indels/1000g_pon.hg38.vcf.gz'

diff --git a/config/wes.config b/config/wes.config
@@ -41,8 +41,9 @@ params {
   target_picard = params.reference_cache+'/mouse/GRCm38/supporting_files/capture_kit_files/agilent/v2/S32371113_mouse_exon_V2.bare.picard.primary_assembly.interval_list'
   bait_picard = params.reference_cache+'/mouse/GRCm38/supporting_files/capture_kit_files/agilent/v2/S32371113_mouse_exon_V2.bare.picard.primary_assembly.interval_list'
 
-  // Variant calling parameters
+  // BWA parameter
   mismatch_penalty = "-B 8"
+  // Variant calling parameters
   call_val = "50.0"
   ploidy_val = "-ploidy 2"
 
@@ -75,8 +76,9 @@ if (params.gen_org=='human'){
   params.target_picard = params.reference_cache+'/human/GRCh38/supporting_files/capture_kit_files/agilent/v7/S31285117_MergedProbes_no_gene_names.picard.interval_list'
   params.bait_picard = params.reference_cache+'/human/GRCh38/supporting_files/capture_kit_files/agilent/v7/S31285117_MergedProbes_no_gene_names.picard.interval_list'
 
-  // Variant calling parameters
+  // BWA parameter
   params.mismatch_penalty = "-B 8"
+  // Variant calling parameters
   params.call_val = "50.0"
   params.ploidy_val = "-ploidy 2"
 

diff --git a/config/wgs.config b/config/wgs.config
@@ -49,8 +49,9 @@ params {
   dbSNP_index = params.reference_cache+'/mouse/GRCm38/genome/annotation/snps_indels/GCA_000001635.6_current_ids.vcf.gz.tbi'
   snpEff_config = params.reference_cache+'/mouse/GRCm38/genome/indices/snpEff_5_1/snpEff.config'
 
-  // Variant calling parameters
+  // BWA parameter
   mismatch_penalty = "-B 8"
+  // Variant calling parameters
   ploidy_val = "-ploidy 2"
   call_val = "50.0"
 
@@ -67,8 +68,9 @@ if (params.gen_org=='human'){
   params.chrom_contigs = params.reference_cache+'/human/GRCh38/genome/sequence/gatk/Homo_sapiens_assembly38.primaryChr.contig_list'
   params.primary_chrom_bed = params.reference_cache+'/human/GRCh38/genome/annotation/intervals/Homo_sapiens_assembly38.primary_chrom.bed'
 
-  // Variant calling parameters
+  // BWA parameter
   params.mismatch_penalty = "-B 8"
+  // Variant calling parameters
   params.ploidy_val = "-ploidy 2"
   params.call_val = "50.0"