Merge pull request #38 from CCRGeneticsBranch/develop

Develop
CCRGeneticsBranch · Jan 15, 2025 · eb6fb89 · eb6fb89
2 parents 9d2e302 + e6d20f7
commit eb6fb89
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Showing 4 changed files with 14 additions and 8 deletions.
diff --git a/bin/tsv2html.sh b/bin/tsv2html.sh
@@ -19,6 +19,7 @@ Options:
 
   --Name   To include in Mail
   --Diagnosis To include in the mail body
+  --Pipeline_version To include in mail body
 Examples:
 
   1. $(basename $0) --Name NCI00001 input.csv
@@ -57,6 +58,10 @@ while true; do
       shift
       diagnosis="$1"
       ;;
+    --pipeline)
+      shift
+      pipeline="$1"
+      ;;
     --help)
       usage
       exit 0
@@ -121,7 +126,7 @@ echo "<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www
 <body>
 <p>
 Hello,<br><br>
-     ngs-pipeline version v5.1 finished successfully on biowulf.nih.gov<br><br>
+     ngs-pipeline version $pipeline finished successfully on biowulf.nih.gov<br><br>
      Please check the genotyping result on <b>$diagnosis</b> patient \"$name\"; a cell with <font color=\"red\">red</font> color indicate that corresponding library might not belong to the patient $name.<br><br>
 </p>
 "

diff --git a/config/biowulf_small_test_params.config b/config/biowulf_small_test_params.config
@@ -1,5 +1,5 @@
 params {
-    Pipeline_version = "5.1.1"
+    Pipeline_version = "5.1.2"
     genome_version = "19"
     genome_version_tcellextrect = "hg19"
     genome_version_fusion_annotation = "v37lift37"
@@ -38,8 +38,8 @@ params {
     access_hotspot = "/data/Clinomics/Ref/khanlab/hotspot/hg19_Hotspot.08.08.16_merged.bed"
     hg19_hotspot_pos = "/data/Clinomics/Ref/khanlab/annotation/hg19_hotspot_pos.txt"
     Biowulf_snpEff_config  = "/data/Clinomics/Tools/ngs_pipeline_4.2/Tools_config/Biowulf_snpEff.config"
-    dbNSFP2_4 = "/fdb/dbNSFP2/dbNSFP2.4.txt.gz"
-    dbNSFP2_4_tbi = "/fdb/dbNSFP2/dbNSFP2.4.txt.gz.tbi"
+    dbNSFP2_4 = "/vf/users/khanlab/projects/Nextflow_dev/dev/dbNSFP/dbNSFP2.4.txt.gz"
+	  dbNSFP2_4_tbi = "/vf/users/khanlab/projects/Nextflow_dev/dev/dbNSFP/dbNSFP2.4.txt.gz.tbi"
     strelka_config = "/data/Clinomics/Tools/ngs_pipeline_4.3/Tools_config/Biowulf_Strelka.config.ini"
     recode_vcf = "/data/Clinomics/Ref/khanlab/verifyBamID/Clinical_Research_Exome.recode.vcf"
     cosmic_v67_hg19_vcf = "/data/khanlab/projects/ngs_pipeline_testing/References_4.0/New_GRCh37/cosmic_v67.hg19.vcf"

diff --git a/modules/qc/qc.nf b/modules/qc/qc.nf
@@ -38,8 +38,9 @@ process Kraken {
 }
 
 process Krona {
-    tag "$meta.lib"
 
+    tag "$meta.lib"
+	errorStrategy 'ignore'
     publishDir "${params.resultsdir}/${meta.id}/${meta.casename}/${meta.lib}/qc/kraken", mode: 'copy'
 
     input:
@@ -261,7 +262,7 @@ process Genotyping_Sample {
      sed -i 's/.bwa//g' ${meta.id}.genotyping.txt
      sed -i 's/.star//g' ${meta.id}.genotyping.txt
 
-     sh tsv2html.sh --name ${meta.id} --diagnosis '${meta.diagnosis}' --head ${meta.id}.genotyping.txt  > genotyping.html
+     sh tsv2html.sh --name ${meta.id} --diagnosis '${meta.diagnosis}' --pipeline ${Pipeline_version} --head ${meta.id}.genotyping.txt  > genotyping.html
      """
 
 }

diff --git a/nextflow.config b/nextflow.config
@@ -33,11 +33,11 @@ plugins {
 prov {
   formats {
     bco {
-      file = 'log/bco_${timestamp}.json'
+      file = "log/bco_${timestamp}.json"
       overwrite = true
     }
     legacy {
-      file = 'log/manifest_${timestamp}.json'
+      file = "log/manifest_${timestamp}.json"
       overwrite = true
     }
   }