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313241749c
* Add kraken2 run module * Add kraken2 run module * Add coronavirus kraken2 db * Adding kraken2 run tests * Update software/kraken2/run/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Fixing files commited by mistake * Remove params for meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
25 lines
865 B
Text
25 lines
865 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { KRAKEN2_RUN } from '../../../../software/kraken2/run/main.nf' addParams( options: [:] )
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workflow test_kraken2_run_single_end {
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ]
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db = [ file("${launchDir}/tests/data/genomics/sarscov2/db/kraken2", checkIfExists: true) ]
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KRAKEN2_RUN ( input, db )
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}
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workflow test_kraken2_run_paired_end {
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def input, db = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_*.fastq.gz", checkIfExists: true) ]
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db = [ file("${launchDir}/tests/data/genomics/sarscov2/db/kraken2", checkIfExists: true) ]
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KRAKEN2_RUN ( input, db )
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}
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