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1455498152
* Make targets.bed optional when running in wgs mode * added test for cram * Update test_data_config with new reference.cnn * Update main.nf to allow tumor-only running Still need a unit-test for this. Almost ready, but needs this file as input https://github.com/nf-core/test-datasets/blob/modules/data/generic/cnn/reference.cnn * re-writing previous changes, but now it wont crash the entire CI-setup * fixing overlooked merge conflict * last overlooked merge-conflict * move all files to batch subfolder * adding an optional input for a reference file (needed when running germline and tumoronly) * minor typo * update meta.yml * aligning code, renaming cnvkit to cnvkit_batch, renaming tumorbam to tumor, normalbam to normal * Update pytest_modules.yml Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal> Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
64 lines
2.6 KiB
Text
Executable file
64 lines
2.6 KiB
Text
Executable file
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { CNVKIT_BATCH as CNVKIT_HYBRID } from '../../../../modules/cnvkit/batch/main.nf' addParams( options: [ 'args': '--output-reference reference.cnn' ] )
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include { CNVKIT_BATCH as CNVKIT_WGS } from '../../../../modules/cnvkit/batch/main.nf' addParams( options: [ 'args': '--output-reference reference.cnn --method wgs' ] )
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include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../modules/cnvkit/batch/main.nf' addParams( options: [ 'args': '--method wgs' ] )
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workflow test_cnvkit_hybrid {
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tumor = file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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normal = file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
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input = [ [ id:'test' ], // meta map
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tumor,
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normal
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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targets = file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
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CNVKIT_HYBRID ( input, fasta, targets, [] )
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}
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workflow test_cnvkit_wgs {
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tumor = file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
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normal = file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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input = [ [ id:'test'], // meta map
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tumor,
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normal
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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CNVKIT_WGS ( input, fasta, [], [] )
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}
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workflow test_cnvkit_cram {
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tumor = file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
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normal = file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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input = [ [ id:'test'], // meta map
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tumor,
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normal
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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CNVKIT_WGS ( input, fasta, [], [] )
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}
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workflow test_cnvkit_tumoronly {
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tumor = file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
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input = [ [ id:'test'], // meta map
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tumor,
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[ ]
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
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CNVKIT_TUMORONLY ( input, [], [], reference )
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}
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