Merge pull request #14 from icgc-argo/sanger-wxs-variant-calling@3.1.…

…6-3.4.0 [release]
icgc-argo-workflows · Apr 16, 2021 · ab7b010 · ab7b010
2 parents edb52a6 + 1e7c75c
commit ab7b010
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Showing 12 changed files with 509 additions and 12 deletions.
diff --git a/example-params.json b/example-params.json
@@ -0,0 +1,59 @@
+{
+  "study_id": "TEST-PR",
+  "tumour_aln_analysis_id": "03905962-f1e1-41e8-9059-62f1e1c1e8fc",
+  "normal_aln_analysis_id": "9940db0f-c100-496a-80db-0fc100d96ac1",
+  "max_retries": 3,
+  "first_retry_wait_time": 5,
+  "cleanup": true,
+  "song_url": "https://song.rdpc-qa.cancercollaboratory.org",
+  "score_url": "https://score.rdpc-qa.cancercollaboratory.org",
+  "download": {
+    "song_url": "https://song.rdpc-qa.cancercollaboratory.org",
+    "song_cpus": 2,
+    "song_mem": 2,
+    "score_url": "https://score.rdpc-qa.cancercollaboratory.org",
+    "score_cpus": 3,
+    "score_mem": 8
+  },
+  "sangerWxsVariantCaller": {
+    "cpus": 4,
+    "mem": 10,
+    "exclude": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr22,chrX,chrY,chrUn%,HLA%,%_alt,%_random,chrM,chrEBV",
+    "vagrent_annot": "/nfs-dev-1-vol-qa-1/reference/sanger-variant-calling/VAGrENT_ref_GRCh38_hla_decoy_ebv_ensembl_91.tar.gz",
+    "ref_genome_tar": "/nfs-dev-1-vol-qa-1/reference/sanger-variant-calling/core_ref_GRCh38_hla_decoy_ebv.tar.gz",
+    "ref_snv_indel_tar": "/nfs-dev-1-vol-qa-1/reference/sanger-variant-calling/SNV_INDEL_ref_GRCh38_hla_decoy_ebv-fragment.tar.gz"  
+  },
+  "generateBas": {
+    "cpus":2,
+    "mem":8,
+    "ref_genome_fa": "/nfs-dev-1-vol-qa-1/reference/GRCh38_hla_decoy_ebv/GRCh38_hla_decoy_ebv.fa"
+  },
+  "repackSangerResults": {
+    "cpus": 2,
+    "mem": 4
+  },
+  "cavemanVcfFix": {
+    "cpus": 2,
+    "mem": 4
+  },
+  "prepSangerSupplement": {
+    "cpus": 2,
+    "mem": 4
+  },
+  "prepSangerQc": {
+    "cpus": 2,
+    "mem": 4
+  },
+  "extractSangerCall": {
+    "cpus": 2,
+    "mem": 4
+  },
+  "payloadGenVariantCall": {
+    "cpus": 2,
+    "mem": 4
+  },
+  "uploadVariant": {
+    "cpus": 2,
+    "mem": 4
+  }
+}
diff --git a/....0/tools/prep-sanger-qc/prep-sanger-qc.nf → ....0/tools/prep-sanger-qc/prep-sanger-qc.nf b/....0/tools/prep-sanger-qc/prep-sanger-qc.nf → ....0/tools/prep-sanger-qc/prep-sanger-qc.nf
@@ -23,16 +23,20 @@
  */
 
 nextflow.preview.dsl = 2
-version = '0.1.2.0'
+version = '0.1.3.0'
 
 params.qc_files = ""
+params.publish_dir = ""
+
 params.container_version = ""
 params.cpus = 1
 params.mem = 2  // in GB
 
 
 process prepSangerQc {
   container "quay.io/icgc-argo/prep-sanger-qc:prep-sanger-qc.${params.container_version ?: version}"
+  publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir
+
   cpus params.cpus
   memory "${params.mem} GB"
 

diff --git a/sanger-wxs-variant-calling/main.nf b/sanger-wxs-variant-calling/main.nf
@@ -2,7 +2,7 @@
 nextflow.enable.dsl = 2
 name = 'sanger-wxs-variant-calling'
 short_name = 'sanger-wxs'
-version = '3.1.6-3.3.0'
+version = '3.1.6-3.4.0'
 
 
 /*
@@ -224,9 +224,9 @@ include { sangerWxsVariantCaller as sangerWxs } from './modules/raw.githubuserco
 include { repackSangerResults as repack } from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/repack-sanger-results.0.2.0.0/tools/repack-sanger-results/repack-sanger-results' params(repackSangerResults_params)
 include { cavemanVcfFix as cavemanFix } from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/caveman-vcf-fix.0.1.0.0/tools/caveman-vcf-fix/caveman-vcf-fix' params(cavemanVcfFix_params)
 include { prepSangerSupplement as prepSupp } from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/prep-sanger-supplement.0.1.2.0/tools/prep-sanger-supplement/prep-sanger-supplement' params(prepSangerSupplement_params)
-include { prepSangerQc as prepQc } from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/prep-sanger-qc.0.1.2.0/tools/prep-sanger-qc/prep-sanger-qc' params(prepSangerQc_params)
+include { prepSangerQc as prepQc } from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/prep-sanger-qc.0.1.3.0/tools/prep-sanger-qc/prep-sanger-qc' params(prepSangerQc_params)
 include { extractFilesFromTarball as extractVarSnv; extractFilesFromTarball as extractVarIndel; extractFilesFromTarball as extractQC } from './modules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/extract-files-from-tarball.0.2.0.0/tools/extract-files-from-tarball/extract-files-from-tarball' params(extractSangerCall_params)
-include { payloadGenVariantCalling as pGenVarSnv; payloadGenVariantCalling as pGenVarIndel; payloadGenVariantCalling as pGenVarSupp; payloadGenVariantCalling as pGenQc } from "./modules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling.0.3.6.0/tools/payload-gen-variant-calling/payload-gen-variant-calling" params(payloadGenVariantCall_params)
+include { payloadGenVariantCalling as pGenVarSnv; payloadGenVariantCalling as pGenVarIndel; payloadGenVariantCalling as pGenVarSupp; payloadGenVariantCalling as pGenQc } from "./wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/main" params(payloadGenVariantCall_params)
 include { SongScoreUpload as upSnv; SongScoreUpload as upIndel; SongScoreUpload as upQc; SongScoreUpload as upSupp} from './wfpr_modules/github.com/icgc-argo/nextflow-data-processing-utility-tools/song-score-upload@2.6.1/main.nf' params(upload_params)
 include { cleanupWorkdir as cleanup } from './wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/cleanup-workdir@1.0.0/main'
 include { getSecondaryFiles } from './wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.0/main'

diff --git a/sanger-wxs-variant-calling/pkg.json b/sanger-wxs-variant-calling/pkg.json
@@ -1,6 +1,6 @@
 {
     "name": "sanger-wxs-variant-calling",
-    "version": "3.1.6-3.3.0",
+    "version": "3.1.6-3.4.0",
     "description": "ICGC ARGO Sanger WXS Variant Calling Workflow",
     "main": "main.nf",
     "deprecated": false,
@@ -14,6 +14,7 @@
         "url": "https://github.com/icgc-argo/sanger-wxs-variant-calling.git"
     },
     "dependencies": [
+        "github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0",
         "github.com/icgc-argo/data-processing-utility-tools/payload-add-uniform-ids@0.1.1",
         "github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.0",
         "github.com/icgc-argo/data-processing-utility-tools/cleanup-workdir@1.0.0",

diff --git a/sanger-wxs-variant-calling/tests/local-test-qa.nf.json b/sanger-wxs-variant-calling/tests/local-test-qa.nf.json
@@ -0,0 +1 @@
+../../example-params.json
diff --git a/...m/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/.dockerignore b/...m/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/.dockerignore
@@ -0,0 +1,5 @@
+.gitignore
+.nextflow*
+tests
+work
+outdir
diff --git a/....com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/Dockerfile b/....com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/Dockerfile
@@ -0,0 +1,18 @@
+FROM python:3.7.9
+
+LABEL org.opencontainers.image.source https://github.com/icgc-argo/data-processing-utility-tools
+
+RUN groupadd -g 1000 ubuntu && \
+    useradd -l -u 1000 -g ubuntu ubuntu && \
+    install -d -m 0755 -o ubuntu -g ubuntu /home/ubuntu
+
+ENV PATH="/tools:${PATH}"
+
+COPY *.py /tools/
+
+WORKDIR /tools
+
+USER ubuntu
+
+ENTRYPOINT ["/usr/bin/env"]
+CMD ["/bin/bash"]
diff --git a/...nt-calling/payload-gen-variant-calling.nf → ...payload-gen-variant-calling@0.4.0/main.nf b/...nt-calling/payload-gen-variant-calling.nf → ...payload-gen-variant-calling@0.4.0/main.nf
@@ -21,22 +21,39 @@
  * Author Junjun Zhang <junjun.zhang@oicr.on.ca>
  */
 
+/********************************************************************/
+/* this block is auto-generated based on info from pkg.json where   */
+/* changes can be made if needed, do NOT modify this block manually */
 nextflow.enable.dsl = 2
-version = '0.3.6.0'
+version = '0.4.0'  // package version
 
+container = [
+    'ghcr.io': 'ghcr.io/icgc-argo/data-processing-utility-tools.payload-gen-variant-calling'
+]
+default_container_registry = 'ghcr.io'
+/********************************************************************/
+
+
+// universal params go here
+params.container_registry = ""
+params.container_version = ""
+params.container = ""
+
+params.cpus = 1
+params.mem = 1  // GB
+params.publish_dir = ""  // set to empty string will disable publishDir
+
+// tool specific parmas go here, add / change as needed
 params.normal_analysis = ""
 params.tumour_analysis = ""
 params.files_to_upload = []
 params.wf_name = ""
 params.wf_short_name = ""
 params.wf_version = ""
-params.container_version = ''
-params.cpus = 1
-params.mem = 1  // GB
-params.publish_dir = ""
+
 
 process payloadGenVariantCalling {
-  container "quay.io/icgc-argo/payload-gen-variant-calling:payload-gen-variant-calling.${params.container_version ?: version}"
+  container "${params.container ?: container[params.container_registry ?: default_container_registry]}:${params.container_version ?: version}"
   cpus params.cpus
   memory "${params.mem} GB"
   publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: "${params.publish_dir ? true : ''}"
@@ -56,7 +73,7 @@ process payloadGenVariantCalling {
   script:
     args_tumour_analysis = !tumour_analysis.empty() ? "-t ${tumour_analysis}" : ""
     """
-    payload-gen-variant-calling.py \
+    main.py \
          -f ${files_to_upload} \
          -n ${normal_analysis} \
          -r ${workflow.runName} \
@@ -66,3 +83,16 @@ process payloadGenVariantCalling {
          -v ${wf_version} ${args_tumour_analysis}
     """
 }
+
+// this provides an entry point for this main script, so it can be run directly without clone the repo
+// using this command: nextflow run <git_acc>/<repo>/<pkg_name>/<main_script>.nf -r <pkg_name>.v<pkg_version> --params-file xxx
+workflow {
+  payloadGenVariantCalling(
+    file(params.normal_analysis),
+    file(params.tumour_analysis),
+    Channel.fromPath(params.files_to_upload).collect(),
+    params.wf_name,
+    params.wf_short_name,
+    params.wf_version
+  )
+}