Merge pull request #105 from icgc-argo/payload-gen-seq-experiment@0.3.0

[release]

Author: junjun-zhang

payload-gen-seq-experiment/.dockerignore

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+.gitignore
+.nextflow*
+tests
+work
+outdir

payload-gen-seq-experiment/.gitignore

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+*.py[cod]
+
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+.eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+venv*/
+pyvenv*/
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+.coverage.*
+nosetests.xml
+coverage.xml
+htmlcov
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+.idea
+*.iml
+*.komodoproject
+
+# Complexity
+output/*.html
+output/*/index.html
+
+# Sphinx
+docs/_build
+
+.DS_Store
+*~
+.*.sw[po]
+.build
+.ve
+.env
+.cache
+.pytest
+.bootstrap
+.appveyor.token
+*.bak
+*.log
+.vscode
+.python-version
+.nextflow*
+work
+outdir

payload-gen-seq-experiment/Dockerfile

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+FROM python:3.7.5-slim-buster
+
+LABEL org.opencontainers.image.source https://github.com/icgc-argo/data-processing-utility-tools
+
+ENV PATH="/tools:${PATH}"
+
+COPY *.py /tools/
+
+CMD ["/bin/bash"]

payload-gen-seq-experiment/main.nf

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+#!/usr/bin/env nextflow
+
+/*
+  Copyright (C) 2021,  Ontario Institute for Cancer Research
+  
+  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 <http://www.gnu.org/licenses/>.
+
+  Authors:
+    Linda Xiang
+    Junjun Zhang
+*/
+
+/********************************************************************/
+/* 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 = '0.3.0'  // package version
+
+container = [
+    'ghcr.io': 'ghcr.io/icgc-argo/data-processing-utility-tools.payload-gen-seq-experiment'
+]
+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.metadata_json = "NO_FILE1"
+params.experiment_info_tsv = "NO_FILE2"
+params.read_group_info_tsv = "NO_FILE3"
+params.file_info_tsv = "NO_FILE4"
+
+
+process payloadGenSeqExperiment {
+  container "${params.container ?: container[params.container_registry ?: default_container_registry]}:${params.container_version ?: version}"
+  publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir
+
+  cpus params.cpus
+  memory "${params.mem} GB"
+
+  input:
+    path metadata_json
+    path experiment_info_tsv
+    path read_group_info_tsv
+    path file_info_tsv
+
+  output:
+    path "*.sequencing_experiment.payload.json", emit: payload
+
+  script:
+    args_metadata_json = !metadata_json.name.startsWith("NO_FILE") ? "-m ${metadata_json}" : ""
+    args_experiment_info_tsv = !experiment_info_tsv.name.startsWith("NO_FILE") ? "-x ${experiment_info_tsv}" : ""
+    args_read_group_info_tsv = !read_group_info_tsv.name.startsWith("NO_FILE") ? "-r ${read_group_info_tsv}" : ""
+    args_file_info_tsv = !file_info_tsv.name.startsWith("NO_FILE") ? "-f ${file_info_tsv}" : ""
+
+    """
+    main.py \
+         ${args_metadata_json} \
+         ${args_experiment_info_tsv} \
+         ${args_read_group_info_tsv} \
+         ${args_file_info_tsv}
+    """
+}
+
+
+// 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 {
+  payloadGenSeqExperiment(
+    file(params.metadata_json),
+    file(params.experiment_info_tsv),
+    file(params.read_group_info_tsv),
+    file(params.file_info_tsv)
+  )
+}