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f112e4d701
* New module added bamcmp Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
36 lines
1.2 KiB
Text
36 lines
1.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BWA_INDEX } from '../../../modules/bwa/index/main.nf'
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include { BWA_MEM } from '../../../modules/bwa/mem/main.nf'
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include { BWA_INDEX as BWA_INDEX_COV2 } from '../../../modules/bwa/index/main.nf'
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include { BWA_MEM as BWA_MEM_COV2 } from '../../../modules/bwa/mem/main.nf'
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include { SAMTOOLS_SORT } from '../../../modules/samtools/sort/main.nf'
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include { SAMTOOLS_SORT as SAMTOOLS_SORT_COV2 } from '../../../modules/samtools/sort/main.nf'
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include { BAMCMP } from '../../../modules/bamcmp/main.nf'
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workflow test_bamcmp {
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input = [
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[ id:'test'], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
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]
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fasta1 = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fasta2 = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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BWA_INDEX ( fasta1 )
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BWA_MEM ( input, BWA_INDEX.out.index, false )
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SAMTOOLS_SORT (BWA_MEM.out.bam)
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BWA_INDEX_COV2 ( fasta2 )
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BWA_MEM_COV2 ( input, BWA_INDEX_COV2.out.index, false )
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SAMTOOLS_SORT_COV2 (BWA_MEM_COV2.out.bam)
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BAMCMP (SAMTOOLS_SORT.out.bam.join(SAMTOOLS_SORT_COV2.out.bam, by: [0]))
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}
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