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* new module: samtools/fastq * solve conflict: pytest_software.yml * solve linting conflicts * solved EditorConfig linting problem * Module samtools/fastq: * output compressed fastq.gz file(s) * add if conditionals for single/paired reads * samtools/fastq: modified test.yml * samtools/fastq: modified main.nf to avoid duplicated part of the script section * fix README.md * modify test path gatk4 * fix config * Add new module gatk4/haplotypecaller * solve check issues * fix test.yml file * fix test.yml gz.tbi * Update software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: suzannejin <suzanne.jin@crg.eu> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
17 lines
729 B
Text
17 lines
729 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_SPLITNCIGARREADS } from '../../../../software/gatk4/splitncigarreads/main.nf' addParams( options: [:] )
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workflow test_gatk4_splitncigarreads {
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input = [ [ id:'test' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_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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file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
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]
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GATK4_SPLITNCIGARREADS ( input, fasta )
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}
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