diff --git a/bin/tsv2html.sh b/bin/tsv2html.sh
index 4bf8014..ee6a512 100755
--- 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 "
Hello,
- ngs-pipeline version v5.1 finished successfully on biowulf.nih.gov
+ ngs-pipeline version $pipeline finished successfully on biowulf.nih.gov
Please check the genotyping result on $diagnosis patient \"$name\"; a cell with red color indicate that corresponding library might not belong to the patient $name.
"
diff --git a/config/biowulf_small_test_params.config b/config/biowulf_small_test_params.config
index 030064c..c5d35f8 100755
--- a/config/biowulf_small_test_params.config
+++ b/config/biowulf_small_test_params.config
@@ -1,5 +1,5 @@
params {
- Pipeline_version = "5.1.1"
+ Pipeline_version = "5.1.2"
genome_version = "19"
genome_version_tcellextrect = "hg19"
genome_version_fusion_annotation = "v37lift37"
@@ -38,8 +38,8 @@ params {
access_hotspot = "/data/Clinomics/Ref/khanlab/hotspot/hg19_Hotspot.08.08.16_merged.bed"
hg19_hotspot_pos = "/data/Clinomics/Ref/khanlab/annotation/hg19_hotspot_pos.txt"
Biowulf_snpEff_config = "/data/Clinomics/Tools/ngs_pipeline_4.2/Tools_config/Biowulf_snpEff.config"
- dbNSFP2_4 = "/fdb/dbNSFP2/dbNSFP2.4.txt.gz"
- dbNSFP2_4_tbi = "/fdb/dbNSFP2/dbNSFP2.4.txt.gz.tbi"
+ dbNSFP2_4 = "/vf/users/khanlab/projects/Nextflow_dev/dev/dbNSFP/dbNSFP2.4.txt.gz"
+ dbNSFP2_4_tbi = "/vf/users/khanlab/projects/Nextflow_dev/dev/dbNSFP/dbNSFP2.4.txt.gz.tbi"
strelka_config = "/data/Clinomics/Tools/ngs_pipeline_4.3/Tools_config/Biowulf_Strelka.config.ini"
recode_vcf = "/data/Clinomics/Ref/khanlab/verifyBamID/Clinical_Research_Exome.recode.vcf"
cosmic_v67_hg19_vcf = "/data/khanlab/projects/ngs_pipeline_testing/References_4.0/New_GRCh37/cosmic_v67.hg19.vcf"
diff --git a/modules/qc/qc.nf b/modules/qc/qc.nf
index d5674c1..42c314c 100755
--- a/modules/qc/qc.nf
+++ b/modules/qc/qc.nf
@@ -38,8 +38,9 @@ process Kraken {
}
process Krona {
- tag "$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 ${meta.id}.genotyping.txt > genotyping.html
"""
}
diff --git a/nextflow.config b/nextflow.config
index 4a00a60..b21029f 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -33,11 +33,11 @@ plugins {
prov {
formats {
bco {
- file = 'log/bco_${timestamp}.json'
+ file = "log/bco_${timestamp}.json"
overwrite = true
}
legacy {
- file = 'log/manifest_${timestamp}.json'
+ file = "log/manifest_${timestamp}.json"
overwrite = true
}
}