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1d668eefa2
* Update seqwish to version 0.7.2 * seqwish can work with a comma-separated list of PAFs * level with nf-core/modules master branch * update seqwish/induce to v0.7.6 * add pangenome test data * test seqwish/induce v0.7.6 with pangenomics test data * we already have pointed to the pangenomics test data sets * update paths to test data * add path to bgzipped fa, gzi, fai * remove one tab * remove one tab * actually execute the 2nd test * try to fix versions.yml * pangenomic tests can be run in their own subworkflow * maybe the csv input is the problem * remove space as suggested by Rike * csv input was not the problem * update test.yml * typo * enable pangenome tests * add md5sum for pangenomic test * Update tests/modules/seqwish/induce/test.yml Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * PAF input is a list of files * beautify comment Co-authored-by: Michael L Heuer <heuermh@acm.org> Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
23 lines
808 B
Text
23 lines
808 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SEQWISH_INDUCE } from '../../../../modules/seqwish/induce/main.nf'
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workflow test_seqwish_induce_transcriptome {
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input = [ [ id:'test' ], // meta map
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[ file(params.test_data['sarscov2']['genome']['transcriptome_paf'], checkIfExists: true)],
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[ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
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]
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SEQWISH_INDUCE ( input )
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}
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workflow test_seqwish_induce_pangenome {
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input = [ [ id:'test' ], // meta map
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[ file(params.test_data['homo_sapiens']['pangenome']['pangenome_paf'], checkIfExists: true)],
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[ file(params.test_data['homo_sapiens']['pangenome']['pangenome_fa'], checkIfExists: true) ]
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]
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SEQWISH_INDUCE ( input )
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}
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