Merge pull request #119 from icgc-argo/payload-gen-variant-calling@0.4.0

[release]

Author: junjun-zhang

payload-gen-variant-calling/.dockerignore

@@ -0,0 +1,5 @@
+.gitignore
+.nextflow*
+tests
+work
+outdir

payload-gen-variant-calling/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"]

payload-gen-variant-calling/main.nf

@@ -0,0 +1,98 @@
+#!/usr/bin/env nextflow
+
+/*
+ * Copyright (c) 2019-2021, Ontario Institute for Cancer Research (OICR).
+ *                                                                                                               
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published
+ * by the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ */
+
+/*
+ * 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 = '0.4.0'  // 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 = ""
+
+
+process payloadGenVariantCalling {
+  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 : ''}"
+
+  input:
+    path normal_analysis
+    path tumour_analysis
+    path files_to_upload
+    val wf_name
+    val wf_short_name
+    val wf_version
+
+  output:
+    path "*.payload.json", emit: payload
+    path "out/*{.tgz,.vcf.gz,.vcf.gz.tbi}", emit: files_to_upload
+
+  script:
+    args_tumour_analysis = !tumour_analysis.empty() ? "-t ${tumour_analysis}" : ""
+    """
+    main.py \
+         -f ${files_to_upload} \
+         -n ${normal_analysis} \
+         -r ${workflow.runName} \
+         -j ${workflow.sessionId} \
+         -w ${wf_name} \
+         -s ${wf_short_name} \
+         -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
+  )
+}