all is good Merge branch 'main' of https://github.com/icgc-argo-qc-wg…

…/argo-qc-tools into main

README.md

@@ -1,3 +1,11 @@
-# Collection of ARGO QC Tools
+# Collection of ARGO QC Tools in WFPM Packages
 
-Update this to describe your awesome project.
+## QC packages and underlying software tools
+
+| wfpm package name | QC software tool name | tool version |
+|-------------------|-----------------------|--------------|
+| fastqc            | FastQC                |  0.11.9      |
+| cutadapt          | Cutadapt              |  2.10        |
+| samtools-stats    | Samtools:stats        |  1.12        |
+| picard-collect-rna-seq-metrics | Picard:CollectRnaSeqMetrics  | 2.25.6 |
+| picard-collect-hs-metrics  | Picard:CollectHsMetrics | 2.25.7 |

picard-collect-hs-metrics/.dockerignore

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

picard-collect-hs-metrics/Dockerfile

@@ -0,0 +1,22 @@
+FROM continuumio/miniconda3:4.9.2
+
+# filled by wfpm
+LABEL org.opencontainers.image.source https://github.com/icgc-argo-qc-wg/argo-qc-tools
+
+# add ps (required by nextflow)
+RUN apt-get -y update  && \
+    apt-get install -y procps && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+ENV PATH="//opt/conda/bin:${PATH}"
+
+# install java
+RUN conda install --yes -c conda-forge openjdk=11.0.9.1
+
+# Fetch Picard
+RUN wget https://github.com/broadinstitute/picard/releases/download/2.25.7/picard.jar
+
+ENTRYPOINT ["/usr/bin/env"]
+
+CMD ["/bin/bash"]

picard-collect-hs-metrics/main.nf

@@ -0,0 +1,89 @@
+#!/usr/bin/env nextflow
+
+/*
+  Copyright (c) 2021, ICGC ARGO
+
+  Permission is hereby granted, free of charge, to any person obtaining a copy
+  of this software and associated documentation files (the "Software"), to deal
+  in the Software without restriction, including without limitation the rights
+  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+  copies of the Software, and to permit persons to whom the Software is
+  furnished to do so, subject to the following conditions:
+
+  The above copyright notice and this permission notice shall be included in all
+  copies or substantial portions of the Software.
+
+  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+  SOFTWARE.
+
+  Authors:
+    Andrej Benjak
+*/
+
+/********************************************************************/
+/* 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 = '0.1.0'  // package version
+
+container = [
+    'ghcr.io': 'ghcr.io/icgc-argo-qc-wg/argo-qc-tools.picard-collect-hs-metrics'
+]
+default_container_registry = 'ghcr.io'
+/********************************************************************/
+
+
+// universal params go here
+params.container_registry = ""
+params.container_version = ""
+params.container = ""
+
+params.cpus = 1
+params.mem = 4  // GB
+params.publish_dir = "picard-collect-hs-metrics_outdir"  // set to empty string will disable publishDir
+
+
+// tool specific parmas go here, add / change as needed
+params.bam = ""
+params.target_intervals= ""
+params.bait_intervals= ""
+params.output_pattern = "*.hs_metrics.txt"  // output file name pattern
+
+
+process picardCollectHsMetrics {
+  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 "${params.mem} GB"
+
+  input:
+    path bam
+    path target_intervals
+    path bait_intervals
+
+  output:
+    path "${params.output_pattern}", emit: output_file
+
+  shell:
+
+    '''
+    java -jar /picard.jar CollectHsMetrics --INPUT !{bam} --TARGET_INTERVALS !{target_intervals} --BAIT_INTERVALS !{bait_intervals} --OUTPUT \$(basename !{bam} .bam).hs_metrics.txt
+    '''
+}
+
+
+// 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 {
+  picardCollectHsMetrics(
+    file(params.bam),
+    file(params.target_intervals),
+    file(params.bait_intervals)
+  )
+}

picard-collect-hs-metrics/main.py

@@ -0,0 +1,60 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+  Copyright (c) 2021, ICGC ARGO
+
+  Permission is hereby granted, free of charge, to any person obtaining a copy
+  of this software and associated documentation files (the "Software"), to deal
+  in the Software without restriction, including without limitation the rights
+  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+  copies of the Software, and to permit persons to whom the Software is
+  furnished to do so, subject to the following conditions:
+
+  The above copyright notice and this permission notice shall be included in all
+  copies or substantial portions of the Software.
+
+  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+  SOFTWARE.
+
+  Authors:
+    Andrej Benjak
+"""
+
+import os
+import sys
+import argparse
+import subprocess
+
+
+def main():
+    """
+    Python implementation of tool: picard-collect-hs-metrics
+
+    This is auto-generated Python code, please update as needed!
+    """
+
+    parser = argparse.ArgumentParser(description='Tool: picard-collect-hs-metrics')
+    parser.add_argument('-i', '--input-file', dest='input_file', type=str,
+                        help='Input file', required=True)
+    parser.add_argument('-o', '--output-dir', dest='output_dir', type=str,
+                        help='Output directory', required=True)
+    args = parser.parse_args()
+
+    if not os.path.isfile(args.input_file):
+        sys.exit('Error: specified input file %s does not exist or is not accessible!' % args.input_file)
+
+    if not os.path.isdir(args.output_dir):
+        sys.exit('Error: specified output dir %s does not exist or is not accessible!' % args.output_dir)
+
+    subprocess.run(f"cp {args.input_file} {args.output_dir}/", shell=True, check=True)
+
+
+if __name__ == "__main__":
+    main()
+

picard-collect-hs-metrics/nextflow.config

@@ -0,0 +1,4 @@
+docker {
+    enabled = true
+    runOptions = '-u \$(id -u):\$(id -g)'
+}

picard-collect-hs-metrics/pkg.json

@@ -0,0 +1,37 @@
+{
+    "name": "picard-collect-hs-metrics",
+    "version": "0.1.0",
+    "description": "Picard CollectHsMetrics",
+    "main": "main.nf",
+    "deprecated": false,
+    "keywords": [
+        "qc metrics",
+        "wes",
+        "exome"
+    ],
+    "repository": {
+        "type": "git",
+        "url": "https://github.com/icgc-argo-qc-wg/argo-qc-tools.git"
+    },
+    "container": {
+        "registries": [
+            {
+                "registry": "ghcr.io",
+                "type": "docker",
+                "org": "icgc-argo-qc-wg",
+                "default": true
+            }
+        ]
+    },
+    "dependencies": [],
+    "devDependencies": [],
+    "contributors": [
+        {
+            "name": "Andrej Benjak",
+            "email": "[email protected]"
+        }
+    ],
+    "license": "MIT",
+    "bugReport": "https://github.com/icgc-argo-qc-wg/argo-qc-tools/issues",
+    "homepage": "https://github.com/icgc-argo-qc-wg/argo-qc-tools#readme"
+}

picard-collect-hs-metrics/tests/checker.nf

@@ -0,0 +1,111 @@
+#!/usr/bin/env nextflow
+
+/*
+  Copyright (c) 2021, ICGC ARGO
+
+  Permission is hereby granted, free of charge, to any person obtaining a copy
+  of this software and associated documentation files (the "Software"), to deal
+  in the Software without restriction, including without limitation the rights
+  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+  copies of the Software, and to permit persons to whom the Software is
+  furnished to do so, subject to the following conditions:
+
+  The above copyright notice and this permission notice shall be included in all
+  copies or substantial portions of the Software.
+
+  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+  SOFTWARE.
+
+  Authors:
+    Andrej Benjak
+*/
+
+/*
+ This is an auto-generated checker workflow to test the generated main template workflow, it's
+ meant to illustrate how testing works. Please update to suit your own needs.
+*/
+
+/********************************************************************/
+/* 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 = '0.1.0'  // package version
+
+container = [
+    'ghcr.io': 'ghcr.io/icgc-argo-qc-wg/argo-qc-tools.picard-collect-hs-metrics'
+]
+default_container_registry = 'ghcr.io'
+/********************************************************************/
+
+// universal params
+params.container_registry = ""
+params.container_version = ""
+params.container = ""
+
+// tool specific parmas go here, add / change as needed
+params.bam = ""
+params.target_intervals= ""
+params.bait_intervals= ""
+params.expected_output = ""
+
+include { picardCollectHsMetrics } from '../main'
+
+
+process file_smart_diff {
+  container "${params.container ?: container[params.container_registry ?: default_container_registry]}:${params.container_version ?: version}"
+
+  input:
+    path output_file
+    path expected_file
+
+  output:
+    stdout()
+
+  script:
+    """
+    # we need to remove the date field from the files before comparison
+
+    grep -v 'Started on' ${output_file} > normalized_output
+
+    grep -v 'Started on' ${expected_file} > normalized_expected
+
+    diff normalized_output normalized_expected \
+      && ( echo "Test PASSED" && exit 0 ) || ( echo "Test FAILED, output file mismatch." && exit 1 )
+    """
+}
+
+
+workflow checker {
+  take:
+    bam
+    target_intervals
+    bait_intervals
+    expected_output
+
+  main:
+    picardCollectHsMetrics(
+      bam,
+      target_intervals,
+      bait_intervals
+    )
+
+    file_smart_diff(
+      picardCollectHsMetrics.out.output_file,
+      expected_output
+    )
+}
+
+
+workflow {
+  checker(
+    file(params.bam),
+    file(params.target_intervals),
+    file(params.bait_intervals),
+    file(params.expected_output)
+  )
+}