Add verifybamid2

CHANGELOG.md

@@ -1,5 +1,10 @@
 # CHANGELOG
 
+### 3.11.1
+* Add a process to get contamination values from verifybamid2 software.
+* Update configs/nextflow.hopper.config with a specific verifybamid2 container.
+* Update configs/nextflow.hopper.config with specific SVDPrefix files for panel and wgs.
+
 ### 3.10.4
 * Added --format vcf to `vep_sv` to fix for cases where vcf file carries no variants. 
 

configs/nextflow.hopper.config

@@ -87,10 +87,11 @@ params {
   queue             = 'normal'
 
   // CONTAINERS //
-  container_vep       = "/fs1/resources/containers/ensembl-vep_release_111.0.sif"
-  container_fastp     = '/fs1/resources/containers/fastp_0.23.4.sif'
-  container_sentieon  = '/fs1/resources/containers/sentieon_202308.sif'
-  container_d4tools   = "/fs1/resources/containers/d4tools_0.3.8.sif"
+  container_vep            = "/fs1/resources/containers/ensembl-vep_release_111.0.sif"
+  container_fastp          = '/fs1/resources/containers/fastp_0.23.4.sif'
+  container_sentieon       = '/fs1/resources/containers/sentieon_202308.sif'
+  container_d4tools        = "/fs1/resources/containers/d4tools_0.3.8.sif"
+  container_verifybamid2   = "/fs1/resources/containers/verifybamid2_2.0.1.sif"
 
   run_chanjo2       = true
   reanalyze         = false
@@ -147,6 +148,7 @@ profiles {
     params.gatkreffolders = "${params.refpath}/gatk_cnv/cnvref/masked_hg38/gatk_ref"
     params.gens_accessdir = "/access/wgs/plot_data"
     params.accessdir = params.loaddir + "/wgs/"
+    params.verifybamid2_svdprefix = "/fs1/resources/ref/hg38/VerifyBamID/resource/no_chr/1000g.phase3.100k.b38.vcf.gz.dat"
   }
 
   oncov1 {
@@ -193,6 +195,7 @@ profiles {
     params.gatkreffolders = "${params.refpath}/annotation_dbs/onco-solid/gatk_ref/gatk_ref_oncov1-0"
     params.gens_accessdir = "/access/twist-onco/plot_data"
     params.accessdir = params.loaddir + "/twist-onco/"
+    params.verifybamid2_svdprefix = "/fs1/resources/ref/hg38/VerifyBamID/resource/exome/no_chr/1000g.phase3.10k.b38.exome.vcf.gz.dat"
   }
 
   onco {
@@ -237,6 +240,7 @@ profiles {
     params.gatkreffolders = "${params.refpath}/annotation_dbs/onco-solid/gatk_ref/gatk_ref_oncov2-0"
     params.gens_accessdir = "/access/twist-onco/plot_data"
     params.accessdir = "/access/twist-onco/"
+    params.verifybamid2_svdprefix = "/fs1/resources/ref/hg38/VerifyBamID/resource/exome/no_chr/1000g.phase3.10k.b38.exome.vcf.gz.dat"
   } 
 
 exome {
@@ -276,6 +280,7 @@ exome {
     params.gatkreffolders = "/fs1/viktor/gatk_ref/gatk_ref"
     params.gens_accessdir = "/access/wgs/plot_data"
     params.accessdir = "/access/exome/"
+    params.verifybamid2_svdprefix = "/fs1/resources/ref/hg38/VerifyBamID/resource/exome/no_chr/1000g.phase3.10k.b38.exome.vcf.gz.dat"
   } 
 
 myeloid {
@@ -316,6 +321,7 @@ myeloid {
     params.gatkreffolders = "${params.refpath}/gatk_cnv/onco/cnvref/gatk_ref"
     params.gens_accessdir = "/access/myeloid_const/plot_data"
     params.accessdir = "/access/myeloid_const/"
+    params.verifybamid2_svdprefix = "/fs1/resources/ref/hg38/VerifyBamID/resource/exome/no_chr/1000g.phase3.10k.b38.exome.vcf.gz.dat"
   } 
 
 modycf {
@@ -360,6 +366,7 @@ modycf {
     params.gatkreffolders = "${params.refpath}/annotation_dbs/modycf/gatk_ref/masked/gatk_ref_modycf_masked"
     params.gens_accessdir = "/access/wgs/plot_data"
     params.accessdir = "/access/modycf/"
+    params.verifybamid2_svdprefix = "/fs1/resources/ref/hg38/VerifyBamID/resource/exome/no_chr/1000g.phase3.10k.b38.exome.vcf.gz.dat"
   }
 
 }

docs/list_of_all_used_software.md

@@ -36,4 +36,3 @@
 | vcflib                 | 1.0.9        | Open-Source | https://github.com/vcflib/vcflib                       | https://github.com/vcflib/vcflib/issues                | Alexander Koc         | Parse and manipulate VCF files with python and zig bindings                               |
 | vep                    | 111.0        | Open-Source | https://www.ensembl.org/info/docs/tools/vep/index.html | https://github.com/Ensembl/ensembl-vep/issues          | Ram Sai Nanduri       | Predict functional effects of genomic variants                                            |
 | verifybamid2           | 2.0.1        | Open-Source | https://github.com/Griffan/VerifyBamID                 | https://github.com/Griffan/VerifyBamID/issues          | Paul Piccinelli       | Detecting and estimating inter-sample DNA contamination                                 |
-

main.nf

@@ -107,7 +107,8 @@ bam_choice.into{
 	bam_qc_choice;
 	dedup_dummy_choice;
 	bam_bqsr_choice;
-	bam_gatk_choice }
+	bam_gatk_choice;
+        verifybamid2_bam_choice }
 
 // bqsr expects sample_id to come first, instead of group_id
 bam_bqsr_choice.map {
@@ -399,7 +400,7 @@ process markdup {
 		set id, group, file(bam), file(bai) from bam_markdup.mix(merged_bam_dedup)
 
 	output:
-		set group, id, file("${id}_dedup.bam"), file("${id}_dedup.bam.bai") into complete_bam, chanjo_bam, d4_bam, expansionhunter_bam, yaml_bam, cov_bam, bam_manta, bam_nator, bam_tiddit, bam_manta_panel, bam_delly_panel, bam_cnvkit_panel, bam_freebayes, bam_mito, smncnc_bam, bam_gatk, depth_onco
+		set group, id, file("${id}_dedup.bam"), file("${id}_dedup.bam.bai") into complete_bam, chanjo_bam, d4_bam, verifybamid2_bam, expansionhunter_bam, yaml_bam, cov_bam, bam_manta, bam_nator, bam_tiddit, bam_manta_panel, bam_delly_panel, bam_cnvkit_panel, bam_freebayes, bam_mito, smncnc_bam, bam_gatk, depth_onco
 		set id, group, file("${id}_dedup.bam"), file("${id}_dedup.bam.bai") into qc_bam, bam_melt, bam_bqsr
 		set val(id), file("dedup_metrics.txt") into dedupmet_sentieonqc
 		set group, file("${group}_bam.INFO") into bam_INFO
@@ -646,6 +647,67 @@ def d4_coverage_version(task) {
 	"""
 }
 
+process verifybamid2 {
+        cpus 16
+        memory '10 GB'
+        // publishDir "${OUTDIR}/contamination", mode: 'copy', overwrite: 'true', pattern: '*.selfSM'
+        tag "$id"
+        container = "${params.container_verifybamid2}"
+
+        input:
+                set group, id, file(bam), file(bai) from verifybamid2_bam
+
+        output:
+                file("${id}.result.selfSM")
+                file("${id}.result.Ancestry")
+                set group, file("*versions.yml") into ch_verifybamid2_versions
+
+        script:
+
+                if ( params.antype == "wgs") {
+                         """
+                         verifybamid2 \
+                         --SVDPrefix ${params.verifybamid2_svdprefix} \
+                         --Reference ${genome_file} \
+                         --BamFile ${bam}
+
+                         mv result.selfSM ${id}.result.selfSM
+                         mv result.Ancestry ${id}.result.Ancestry
+                         ${verifybamid2_version(task)}
+                         """
+                }
+                else {
+                         """
+                         verifybamid2 \
+                         --DisableSanityCheck \
+                         --SVDPrefix ${params.verifybamid2_svdprefix} \
+                         --Reference ${genome_file} \
+                         --BamFile ${bam}
+
+                         mv result.selfSM ${id}.result.selfSM
+                         mv result.Ancestry ${id}.result.Ancestry
+                         ${verifybamid2_version(task)}
+                         """
+                }
+
+
+        stub:
+                """
+                touch "${id}.result.selfSM"
+                touch "${id}.result.Ancestry"
+
+                ${verifybamid2_version(task)}
+                """
+}
+def verifybamid2_version(task) {
+        """
+        cat <<-END_VERSIONS > ${task.process}_versions.yml
+        ${task.process}:
+            VerifyBamID2: \$( echo \$( verifybamid2 --help 2>&1 | grep Version ) | sed "s/^.*Version://" )
+        END_VERSIONS
+        """
+}
+
 // Calculate coverage for paneldepth
 process depth_onco {
 	cpus 2
@@ -3931,6 +3993,7 @@ process combine_versions {
 			ch_bqsr_versions.first(),
 			ch_sentieon_qc_versions.first(),
 			ch_d4_coverage_versions.first(),
+                        ch_verifybamid2_versions.first(),
 			ch_smn_copy_number_caller_versions.first(),
 			ch_expansionhunter_versions.first(),
 			ch_stranger_versions.first(),