Merge pull request #29 from ICGC-ARGO-Structural-Variation-CN-WG/argo…

…-sv-cnv-calling@0.1.0

draft first [release]

argo-sv-cnv-calling/local_modules/demo-copy-file.nf

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+#!/usr/bin/env nextflow
+
+/*
+ This is an example process as a local module. Using local module is optional, in general
+ is discouraged. A process can pentially be reused in different workflows should be developed
+ in an independent package, so that it can be imported by anyone into any workflow.
+*/
+
+nextflow.enable.dsl = 2
+
+params.input_file = ""
+params.publish_dir = ""
+
+
+process demoCopyFile {
+  publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir
+
+  input:
+    path input_file
+
+  output:
+    path "output_dir/*", emit: output_file
+
+  script:
+    """
+    mkdir output_dir
+    cp ${input_file} output_dir/
+    """
+}

argo-sv-cnv-calling/main.nf

@@ -0,0 +1,293 @@
+#!/usr/bin/env nextflow
+
+/*
+  Copyright (c) 2021, ICGC-ARGO-Structural-Variation-CN-WG
+
+  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:
+    Junjun Zhang
+*/
+
+nextflow.enable.dsl = 2
+version = '0.1.0'  // package version
+
+// universal params go here, change default value as needed
+params.container = ""
+params.container_registry = ""
+params.container_version = ""
+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.cleanup = true
+
+params.study_id = ""
+params.tumour_aln_analysis_id = ""
+params.normal_aln_analysis_id = ""
+
+params.ref_genome_build = 'hg38'  // GRCh38
+params.ref_genome_fa = ""
+params.tumour_aln_seq = ""
+params.normal_aln_seq = ""
+params.tumour_id = ""
+
+params.donor_sex = "female"  // or "male"
+params.gcwiggle = ""
+params.dbsnp_file = ""
+params.is_test = false  // must be explictly set to true when run as test
+
+// song/score download/upload
+params.max_retries = 3
+params.first_retry_wait_time = 10
+params.song_url = ""
+params.score_url = ""
+params.api_token = ""
+
+params.download = [:]
+params.cram2bam = [
+  'cpus': 2,
+  'mem': 2
+]
+
+// song/score download
+download_params = [
+    'cpus': params.cpus,
+    'mem': params.mem,
+    'max_retries': params.max_retries,
+    'first_retry_wait_time': params.first_retry_wait_time,
+    'song_url': params.song_url,
+    'score_url': params.score_url,
+    'api_token': params.api_token,
+    *:(params.download ?: [:])
+]
+
+cram2bam_params = [
+  'cpus': params.cpus,
+  'mem': params.mem,
+  *:(params.cram2bam ?: [:])
+]
+
+// seqzPreproces
+seqzPreprocess_params = [
+  'cpus': params.cpus,
+  'mem': params.mem,
+  'publish_dir': params.publish_dir,
+  'tumor_bam': params.tumour_aln_seq,
+  'normal_bam': params.normal_aln_seq,
+  'gcwiggle': params.gcwiggle,
+  'fasta': params.ref_genome_fa
+]
+
+// seqzMain
+seqzMain_params = [
+  'cpus': params.cpus,
+  'mem': params.mem,
+  'publish_dir': params.publish_dir
+]
+
+// svaba
+svaba_params = [
+  'cpus': params.cpus,
+  'mem': params.mem,
+  'publish_dir': params.publish_dir,
+  'sample_id': params.tumour_id,
+  'input_tumour_bam': params.tumour_aln_seq,
+  'input_normal_bam': params.normal_aln_seq,
+  'ref_genome_gz': params.ref_genome_fa,
+  'dbsnp_file': params.dbsnp_file
+]
+
+// facets
+facets_params = [
+  'cpus': params.cpus,
+  'mem': params.mem,
+  'publish_dir': params.publish_dir,
+  'pileup': 'NO_FILE',
+  'tumor_id': params.tumour_id,
+  'genome': params.ref_genome_build
+]
+
+// battenberg
+battenberg_params = [
+  'cpus': params.cpus,
+  'mem': params.mem,
+  'publish_dir': params.publish_dir,
+  'tumour_bam': params.tumour_aln_seq,
+  'normal_bam': params.normal_aln_seq,
+  'sex': params.donor_sex,
+  'battenberg_ref_dir': 'input/battenberg_references',  // can't really use path as input
+  'test': params.is_test
+]
+
+// snpPileup
+snpPileup_params = [
+  'cpus': params.cpus,
+  'mem': params.mem,
+  'publish_dir': params.publish_dir,
+  'tumor': params.tumour_aln_seq,
+  'normal': params.normal_aln_seq,
+  'ref': params.ref_genome_fa + '.gz',
+  'dbsnp': params.dbsnp_file
+]
+
+// manta
+manta_params = [
+  'cpus': params.cpus,
+  'mem': params.mem,
+  'publish_dir': params.publish_dir,
+  'normalBam': params.tumour_aln_seq,
+  'tumorBam': params.normal_aln_seq,
+  'referenceFasta': params.ref_genome_fa
+]
+
+
+include { cram2bam as cram2bamN; cram2bam as cram2bamT } from './wfpr_modules/github.com/icgc-argo-workflows/dna-seq-processing-tools/cram2bam@0.1.0/main.nf' params(cram2bam_params)
+include { SongScoreDownload as dnldT; SongScoreDownload as dnldN } from './wfpr_modules/github.com/icgc-argo/nextflow-data-processing-utility-tools/song-score-download@2.6.2/main.nf' params(download_params)
+include { getSecondaryFiles; getBwaSecondaryFiles } from './wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/helper-functions@1.0.1.1/main.nf' params([*:params, 'cleanup': false])
+include { seqzPreprocess } from './wfpr_modules/github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/seqz-preprocess@0.2.5/main.nf' params([*:seqzPreprocess_params, 'cleanup': false])
+include { svaba } from './wfpr_modules/github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/svaba@0.2.0/main.nf' params([*:svaba_params, 'cleanup': false])
+include { facets } from './wfpr_modules/github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/facets@0.3.0/main.nf' params([*:facets_params, 'cleanup': false])
+include { battenberg } from './wfpr_modules/github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/battenberg@0.1.0/main.nf' params([*:battenberg_params, 'cleanup': false])
+include { snpPileup } from './wfpr_modules/github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/snp-pileup@0.3.1/main.nf' params([*:snpPileup_params, 'cleanup': false])
+include { manta } from './wfpr_modules/github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/manta@0.2.0/main.nf' params([*:manta_params, 'cleanup': false])
+include { seqzMain } from './wfpr_modules/github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/seqz-main@0.2.5/main.nf' params([*:seqzMain_params, 'cleanup': false])
+
+
+// please update workflow code as needed
+workflow ArgoSvCnvCalling {
+  take:  // update as needed
+    study_id
+    tumour_aln_analysis_id
+    normal_aln_analysis_id
+    ref_genome_fa
+    ref_genome_gz_secondary_files
+    tumour_aln_seq
+    tumour_aln_seq_idx
+    normal_aln_seq
+    normal_aln_seq_idx
+    gcwiggle
+    dbsnp_file
+
+
+  main:  // update as needed
+    if (tumour_aln_analysis_id && normal_aln_analysis_id) {
+      // download tumour aligned seq and metadata from song/score (analysis type: sequencing_alignment)
+      dnldT(study_id, tumour_aln_analysis_id)
+      tumour_aln_seq = dnldT.out.files.flatten().first()
+      tumour_aln_seq_idx = dnldT.out.files.flatten().last()
+      tumour_aln_meta = dnldT.out.analysis_json
+
+      // download normal aligned seq and metadata from song/score (analysis type: sequencing_alignment)
+      dnldN(study_id, normal_aln_analysis_id)
+      normal_aln_seq = dnldN.out.files.flatten().first()
+      normal_aln_seq_idx = dnldN.out.files.flatten().last()
+      normal_aln_meta = dnldN.out.analysis_json
+    }
+
+    // some tools seem have trouble take CRAM as input, temporary solution here to convert CRAM to BAM
+    cram2bamT(
+      tumour_aln_seq,
+      ref_genome_fa,
+      ref_genome_gz_secondary_files
+    )
+
+    cram2bamN(
+      normal_aln_seq,
+      ref_genome_fa,
+      ref_genome_gz_secondary_files
+    )
+
+    seqzPreprocess(
+      cram2bamT.out.output_bam,
+      cram2bamN.out.output_bam,
+      ref_genome_fa,
+      gcwiggle
+    )
+
+    seqzMain(
+      seqzPreprocess.out.seqz
+    )
+
+    svaba(
+      cram2bamT.out.output_bam,
+      cram2bamN.out.output_bam,
+      cram2bamT.out.output_bai,
+      cram2bamN.out.output_bai,
+      ref_genome_fa,
+      ref_genome_gz_secondary_files,
+      dbsnp_file
+    )
+
+    battenberg(
+      tumour_aln_seq,
+      tumour_aln_seq_idx,
+      normal_aln_seq,
+      normal_aln_seq_idx,
+      file(params.battenberg_ref_dir)  // shouldn't use folder as input, temp for now
+    )
+
+    snpPileup(
+      tumour_aln_seq,
+      normal_aln_seq,
+      dbsnp_file,
+      ref_genome_fa,
+      ref_genome_gz_secondary_files
+    )
+
+    facets(
+      snpPileup.out.output_file
+    )
+
+    manta(
+      normal_aln_seq,
+      tumour_aln_seq,
+      ref_genome_fa,
+      normal_aln_seq_idx,
+      tumour_aln_seq_idx,
+      ref_genome_gz_secondary_files
+    )
+
+
+  emit:  // TODO: update as needed
+    cncf = facets.out.output_cncf
+
+}
+
+
+// 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 {
+  ArgoSvCnvCalling(
+    params.study_id,
+    params.tumour_aln_analysis_id,
+    params.normal_aln_analysis_id,
+    file(params.ref_genome_fa),
+    Channel.fromPath(getSecondaryFiles(params.ref_genome_fa, ['gzi'])).concat(
+      Channel.fromPath(getBwaSecondaryFiles(params.ref_genome_fa))
+    ).collect(),
+    file(params.tumour_aln_seq),
+    Channel.fromPath(getSecondaryFiles(params.tumour_aln_seq, ['bai', 'crai'])).collect(),
+    file(params.normal_aln_seq),
+    Channel.fromPath(getSecondaryFiles(params.normal_aln_seq, ['bai', 'crai'])).collect(),
+    file(params.gcwiggle),
+    file(params.dbsnp_file)
+  )
+}

argo-sv-cnv-calling/nextflow.config

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+docker {
+    enabled = true
+    runOptions = '-u \$(id -u):\$(id -g)'
+}

argo-sv-cnv-calling/pkg.json

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+{
+    "name": "argo-sv-cnv-calling",
+    "version": "0.1.0",
+    "description": "ARGO structure and copy number variation calling workflow",
+    "main": "main.nf",
+    "deprecated": false,
+    "keywords": [
+        "bioinformatics",
+        "ngs",
+        "variation calling",
+        "sv",
+        "cnv",
+        "cancer genomics"
+    ],
+    "repository": {
+        "type": "git",
+        "url": "https://github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number.git"
+    },
+    "dependencies": [
+        "github.com/icgc-argo-workflows/data-processing-utility-tools/helper-functions@1.0.1.1",
+        "github.com/icgc-argo-workflows/dna-seq-processing-tools/cram2bam@0.1.0",
+        "github.com/icgc-argo/nextflow-data-processing-utility-tools/song-score-download@2.6.2",
+        "github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/manta@0.2.0",
+        "github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/snp-pileup@0.3.1",
+        "github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/battenberg@0.1.0",
+        "github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/facets@0.3.0",
+        "github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/seqz-main@0.2.5",
+        "github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/seqz-preprocess@0.2.5",
+        "github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/svaba@0.2.0"
+    ],
+    "devDependencies": [],
+    "contributors": [
+        {
+            "name": "Junjun Zhang",
+            "email": "junjun.ca@gmail.com"
+        }
+    ],
+    "license": "MIT",
+    "bugReport": "https://github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/issues",
+    "homepage": "https://github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number#readme"
+}