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03de60e6fa
* Bump checkM version and add support for pre-defined database * Add markfile output to checkm/lineagewf and add checkm/qa * Remove unnecessary BAM from tests * Fix channels to ensure single meta * Blah * Use secondary name evwyhere * Remove second incovcatiojn * Don't run module directrly for join * And for the other test * Correct module name * Fix name again * Try and fix out_format 9 not being picked up * Contains to matches to allow regex * Fix tests (finally) * Fix verisoning * [automated] Fix linting with Prettier * Update modules/checkm/qa/main.nf Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
44 lines
1.4 KiB
Text
44 lines
1.4 KiB
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'
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include { CHECKM_LINEAGEWF as CHECKM_LINEAGEWF_FASTA } from '../../../../modules/checkm/lineagewf/main.nf'
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include { CHECKM_QA } from '../../../../modules/checkm/qa/main.nf'
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include { CHECKM_QA as CHECKM_QA_FASTA } from '../../../../modules/checkm/qa/main.nf'
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workflow test_checkm_qa {
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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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ch_checkmqa_input = CHECKM_LINEAGEWF.out.checkm_output
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.join(CHECKM_LINEAGEWF.out.marker_file)
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.map{
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meta, dir, marker ->
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[ meta, dir, marker, []]
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}
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CHECKM_QA ( ch_checkmqa_input, [] )
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}
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workflow test_checkm_qa_fasta {
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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_FASTA ( input, fasta_ext, [] )
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ch_checkmqa_input = CHECKM_LINEAGEWF_FASTA.out.checkm_output
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.join(CHECKM_LINEAGEWF_FASTA.out.marker_file)
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.map{
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meta, dir, marker ->
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[ meta, dir, marker, []]
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}
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CHECKM_QA_FASTA ( ch_checkmqa_input, [] )
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}
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