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f5d5926516
* Match target bed to input files * Intervals in getpileupsumamries * more interval updates * change targets in strelka * remove leftover channel * fix checksums * add new test vcfs * add new test vcfs * Update modules/freebayes/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
45 lines
2.5 KiB
Text
45 lines
2.5 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { STRELKA_SOMATIC } from '../../../../modules/strelka/somatic/main.nf'
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workflow test_strelka_somatic {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
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[],[],
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file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true)
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
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STRELKA_SOMATIC (input, fasta, fai )
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}
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workflow test_strelka_best_practices_somatic {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_genome21_indels_vcf_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_genome21_indels_vcf_gz_tbi'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true)
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
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STRELKA_SOMATIC ( input, fasta, fai )
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}
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