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Merge pull request #57 from UMCUGenetics/release/v1.8.0
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v1.8.0
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@melferink
melferink authored Sep 14, 2022
2 parents e7c8029 + cef5d19 commit 4cc3380
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Showing 5 changed files with 314 additions and 38 deletions.
2 changes: 1 addition & 1 deletion NextflowModules
Submodule NextflowModules updated 7 files
+63 −0 GATK/4.2.1.0/GenotypeGvcfs.nf
+65 −0 GATK/4.2.1.0/HaplotypeCaller.nf
+44 −0 GATK/4.2.1.0/MergeVcfs.nf
+30 −0 GATK/4.2.1.0/SelectVariants.nf
+48 −0 GATK/4.2.1.0/VariantFiltration.nf
+1 −1 SortMeRNA/4.2.0/SortMeRNA.nf
+1 −1 SortMeRNA/4.3.3/SortMeRNA.nf
148 changes: 116 additions & 32 deletions WES.config
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ 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_SSv7_100bpflank.interval_list'
gatk_hc_interval_list_snparray = 'SNPArray/InfiniumOmni5-4v1-2.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"
Expand All @@ -18,18 +19,20 @@ params {
exoncov_path = '/hpc/diaggen/software/production/ExonCov'
exoncov_bed = 'Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_20bpflank.bed'

clarity_epp_path = '/hpc/diaggen/software/production/clarity_epp'
exomedepth_path = '/hpc/diaggen/software/production/Dx_resources/ExomeDepth/'
baf_path = '/hpc/diaggen/software/production/Dx_BAF/'
upd_path = '/hpc/diaggen/software/production/Dx_UPD/'

exomedepth_path= '/hpc/diaggen/software/production/Dx_resources/ExomeDepth/'
clarity_epp_path = '/hpc/diaggen/software/production/clarity_epp'

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).
contamination_path_prefix='/usr/local/share/verifybamid2-2.0.1-2/resource/exome/1000g.phase3.10k.b37.exome.vcf.gz.dat'
contamination_sites_ud='/usr/local/share/verifybamid2-2.0.1-2/resource/exome/1000g.phase3.10k.b37.exome.vcf.gz.dat.UD'
contamination_sites_mu='/usr/local/share/verifybamid2-2.0.1-2/resource/exome/1000g.phase3.10k.b37.exome.vcf.gz.dat.mu'
contamination_sites_bed='/usr/local/share/verifybamid2-2.0.1-2/resource/exome/1000g.phase3.10k.b37.exome.vcf.gz.dat.bed'
contamination_path_prefix = '/usr/local/share/verifybamid2-2.0.1-2/resource/exome/1000g.phase3.10k.b37.exome.vcf.gz.dat'
contamination_sites_ud = '/usr/local/share/verifybamid2-2.0.1-2/resource/exome/1000g.phase3.10k.b37.exome.vcf.gz.dat.UD'
contamination_sites_mu = '/usr/local/share/verifybamid2-2.0.1-2/resource/exome/1000g.phase3.10k.b37.exome.vcf.gz.dat.mu'
contamination_sites_bed = '/usr/local/share/verifybamid2-2.0.1-2/resource/exome/1000g.phase3.10k.b37.exome.vcf.gz.dat.bed'

vcftools_path = '/hpc/local/CentOS7/cog_bioinf/vcftools-0.1.14/bin'
plink_path = '/hpc/local/CentOS7/cog_bioinf/plink_1.9b3/'
Expand All @@ -51,7 +54,7 @@ process {

publishDir {
path = "$params.outdir/QC/FastQC"
mode = 'copy'
mode = 'link'
}
}

Expand Down Expand Up @@ -95,17 +98,24 @@ process {

publishDir {
path = "$params.outdir/bam_files"
mode = 'copy'
mode = 'link'
}
}

withLabel: PICARD_2_22_0_IntervalListTools {
withName: PICARD_IntervalListTools {
cpus = 2
memory = '5G'
time = '5m'
clusterOptions = "$params.cluster_options --gres=tmpspace:10G"
}

withName: PICARD_IntervalListToolsSNP {
cpus = 2
memory = '16G'
time = '30m'
clusterOptions = "$params.cluster_options --gres=tmpspace:10G"
}

withLabel: GATK_3_8_1_0_gf15c1c3ef_HaplotypeCaller {
cpus = 2
memory = '20G'
Expand All @@ -125,7 +135,7 @@ process {

publishDir {
path = "$params.outdir"
mode = 'copy'
mode = 'link'
}
}

Expand All @@ -136,7 +146,7 @@ process {

publishDir {
path = "$params.outdir/single_sample_vcf"
mode = 'copy'
mode = 'link'
}
}

Expand All @@ -147,7 +157,7 @@ process {

publishDir {
path = "$params.outdir/fingerprint"
mode = 'copy'
mode = 'link'
}
}

Expand All @@ -164,7 +174,7 @@ process {

publishDir {
path = "$params.outdir/QC/ExonCov"
mode = 'copy'
mode = 'link'
}
}

Expand All @@ -175,16 +185,15 @@ process {
}

withLabel: ExomeDepth {
cpus = 2
cpus = 4
memory = '20G'
time = '2h'

publishDir = [
[path: "$params.outdir/exomedepth/UMCU", mode: 'copy', pattern: 'UMCU*.vcf'],
[path: "$params.outdir/exomedepth/HC", mode: 'copy', pattern: 'HC*.vcf'],
[path: "$params.outdir/exomedepth/", mode: 'copy', pattern: '*.xml'],
[path: "$params.outdir/exomedepth/logs", mode: 'copy', pattern: '*.log'],
[path: "$params.outdir/exomedepth/igv_tracks", mode: 'copy', pattern: '*.igv']
[path: "$params.outdir/exomedepth/UMCU", mode: 'link', pattern: 'UMCU*.vcf'],
[path: "$params.outdir/exomedepth/HC", mode: 'link', pattern: 'HC*.vcf'],
[path: "$params.outdir/exomedepth/logs", mode: 'link', pattern: '*.log'],
[path: "$params.outdir/exomedepth/igv_tracks", mode: 'link', pattern: '*.igv']
]
}

Expand All @@ -195,7 +204,7 @@ process {

publishDir {
path = "$params.outdir/QC/CNV"
mode = 'copy'
mode = 'link'
}
}

Expand All @@ -206,7 +215,7 @@ process {

publishDir {
path = "$params.outdir/QC/Kinship"
mode = 'copy'
mode = 'link'
}
}

Expand All @@ -218,7 +227,7 @@ process {

publishDir {
path = "$params.outdir/QC/Picard"
mode = 'copy'
mode = 'link'
}
}

Expand All @@ -230,7 +239,7 @@ process {

publishDir {
path = "$params.outdir/QC/Picard"
mode = 'copy'
mode = 'link'
}
}

Expand All @@ -241,7 +250,7 @@ process {

publishDir {
path = "$params.outdir/QC/Picard"
mode = 'copy'
mode = 'link'
}
}

Expand All @@ -253,7 +262,7 @@ process {

publishDir {
path = "$params.outdir/QC/Picard"
mode = 'copy'
mode = 'link'
}
}

Expand All @@ -264,7 +273,7 @@ process {

publishDir {
path = "$params.outdir/QC"
mode = 'copy'
mode = 'link'
}
}

Expand All @@ -275,7 +284,7 @@ process {

publishDir {
path = "$params.outdir/QC/Flagstat"
mode = 'copy'
mode = 'link'
}
}

Expand All @@ -286,7 +295,7 @@ process {

publishDir {
path = "$params.outdir/QC/Flagstat"
mode = 'copy'
mode = 'link'
}
}

Expand All @@ -303,7 +312,7 @@ process {

publishDir {
path = "$params.outdir/QC/Kinship"
mode = 'copy'
mode = 'link'
}
}

Expand All @@ -314,7 +323,7 @@ process {

publishDir {
path = "$params.outdir/log"
mode = 'copy'
mode = 'link'
}
}

Expand All @@ -325,18 +334,93 @@ process {

publishDir {
path = "$params.outdir/QC/VerifyBamID2"
mode = 'copy'
mode = 'link'
}
}

withLabel: GATK_4_2_1_0_HaplotypeCallerGVCF {
cpus = 2
memory = '20G'
time = '2h'
}

withLabel: GATK_4_2_1_0_GenotypeGVCF {
cpus = 2
memory = '10G'
time = '20m'
}

withLabel: GATK_4_2_1_0_MergeVcfs {
cpus = 2
memory = '10G'
time = '10m'
publishDir {
path = "$params.outdir/baf/"
mode = 'link'
}
}

withLabel: BAF_IGV {
cpus = 2
memory = '10G'
time = '10m'

publishDir {
path = "$params.outdir/baf/"
mode = 'link'
}
}

withLabel: UPD_IGV {
cpus = 2
memory = '10G'
time = '30m'

publishDir = [
[path: "$params.outdir/upd/", mode: 'link', pattern: '*.igv']
]
}

withLabel: ParseChildFromFullTrio {
cpus = 2
memory = '5G'
time = '5m'
}

withLabel: GetRefset {
cpus = 2
memory = '5G'
time = '5m'
}

withLabel: Single_IGV {
cpus = 2
memory = '5G'
time = '5m'

publishDir = [
[path: "$params.outdir/exomedepth/", mode: 'link', pattern: '*.xml']
]
}

withLabel: Family_IGV {
cpus = 2
memory = '5G'
time = '5m'

publishDir = [
[path: "$params.outdir/exomedepth/", mode: 'link', pattern: '*.xml']
]
}

withLabel: Workflow_Export_Params {
cpus = 2
memory = '5G'
time = '10m'

publishDir {
path = "$params.outdir/log"
mode = 'copy'
mode = 'link'
}
}
}
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