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* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Added but test failing due to null on output channel * fix prefix variable * Complete checkm_lineagewf * Remove TODOs * Add description of fasta_ext parameter * Improve meta map for this context * Update meta.yml * Update modules/checkm/lineagewf/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
24 lines
793 B
Text
24 lines
793 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { CHECKM_LINEAGEWF } from '../../../../modules/checkm/lineagewf/main.nf' addParams( options: [:] )
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workflow test_checkm_lineagewf {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) ]
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fasta_ext = 'fasta'
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CHECKM_LINEAGEWF ( input, fasta_ext )
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}
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workflow test_checkm_lineagewf_multi {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] ]
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fasta_ext = 'fasta'
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CHECKM_LINEAGEWF ( input, fasta_ext )
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}
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