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08db860938
* initial commit to setup branch * workflow finished * Update nextflow.config * tumour to tumor, getpileup passed as nomral and tumor * paired_somatic renamed to tumor_normal_somatic * Apply suggestions from code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * updated index names in meta.yml * changed index file names in main script and test * Apply suggestions from code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Apply suggestions from code review * fixed bug from changes * Apply suggestions from code review * modified yml to allow new subworkflow testing * Update test.yml * Update test.yml * updated to follow the new mergebam syntax, also made unaligned input sample specific Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
16 lines
710 B
Text
16 lines
710 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_MERGEBAMALIGNMENT } from '../../../../modules/gatk4/mergebamalignment/main.nf'
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workflow test_gatk4_mergebamalignment {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
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GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
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}
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