From 907754b46ce55341bd4c7fdbc23f0bfe28914d2f Mon Sep 17 00:00:00 2001
From: melferink <m.elferink@umcutrecht.nl>
Date: Mon, 20 Dec 2021 10:52:02 +0100
Subject: [PATCH 1/3] updated to SSv7 calling and bait targets

---
 WES.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/WES.config b/WES.config
index 578bd11..0ecb62c 100644
--- a/WES.config
+++ b/WES.config
@@ -6,7 +6,7 @@ params {
 
     gatk_rtc_options = '--known /hpc/diaggen/data/databases/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf.gz --known /hpc/diaggen/data/databases/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz'
 
-    gatk_hc_interval_list = 'Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_100bpflank.interval_list'
+    gatk_hc_interval_list = 'Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_100bpflank.interval_list'
     gatk_hc_options = '-stand_call_conf 10 --dbsnp /hpc/diaggen/data/databases/GATK_resource_bundle/b37/dbsnp_137.b37.vcf.gz'
 
     gatk_snp_filter = "-filter 'QD < 2.0' -filterName SNP_LowQualityDepth -filter 'MQ < 40.0' -filterName SNP_MappingQuality -filter 'FS > 60.0' -filterName SNP_StrandBias -filter 'HaplotypeScore > 13.0' -filterName SNP_HaplotypeScoreHigh -filter 'MQRankSum < -12.5' -filterName SNP_MQRankSumLow -filter 'ReadPosRankSum < -8.0' -filterName SNP_ReadPosRankSumLow"
@@ -22,7 +22,7 @@ params {
 
     exomedepth_path= '/hpc/diaggen/software/production/Dx_resources/ExomeDepth/'
 
-    picard_bait = 'Tracks/SureSelect_CREv2_elidS30409818_Covered.list'
+    picard_bait = 'Tracks/SureSelect_v7_elidS31285117_Covered.list'
     picard_target = 'Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_20bpflank.list'
 
     // following resources are inside the VerifyBamID2 container (quay.io/biocontainers/verifybamid2:2.0.1--h32f71e1_2).

From 322f7413d78c874c0312fd22bd156544fe9714a2 Mon Sep 17 00:00:00 2001
From: melferink <m.elferink@umcutrecht.nl>
Date: Mon, 20 Dec 2021 10:53:19 +0100
Subject: [PATCH 2/3] removed SSv7 option

---
 run_nextflow_wes.sh | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/run_nextflow_wes.sh b/run_nextflow_wes.sh
index eb84b49..4f5857e 100755
--- a/run_nextflow_wes.sh
+++ b/run_nextflow_wes.sh
@@ -8,13 +8,6 @@ input=`realpath -e $1`
 output=`realpath $2`
 email=$3
 
-design=${4-default}
-if [ $design == "SSv7" ]; then
-    echo " #### SSv7 design target files are used for the analysis ####"
-    gatk_hc_interval_list='--gatk_hc_interval_list Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_100bpflank.interval_list'
-    picard_bait='--picard_bait Tracks/SureSelect_v7_elidS31285117_Covered.list'
-fi
-
 mkdir -p $output && cd $output
 mkdir -p log
 
@@ -42,8 +35,6 @@ module load Java/1.8.0_60
 --fastq_path $input \
 --outdir $output \
 --email $email \
-${gatk_hc_interval_list:-""} \
-${picard_bait:-""} \
 -profile slurm \
 -resume -ansi-log false
 

From 82a1d27bb56a2f865224acf32f2c7a70a3d20833 Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Tue, 21 Dec 2021 08:58:37 +0100
Subject: [PATCH 3/3] change multiqc config 5% to 1%

---
 assets/multiqc_config.yaml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml
index 91f7f29..6f2f5c9 100644
--- a/assets/multiqc_config.yaml
+++ b/assets/multiqc_config.yaml
@@ -101,16 +101,16 @@ table_cond_formatting_rules:
             - lt: 95
     mqc-generalstats-verifybamid-FREEMIX:
         pass:
-            - lt: 5
-            - eq: 5
+            - lt: 1
+            - eq: 1
         fail:
-            - gt: 5
+            - gt: 1
     FREEMIX:
         pass:
-            - lt: 5
-            - eq: 5
+            - lt: 1
+            - eq: 1
         fail:
-            - gt: 5
+            - gt: 1
 
 custom_data:
     exoncov: