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61 lines
1.8 KiB
Text
61 lines
1.8 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { LIMA } from '../../../modules/lima/main.nf' addParams( options: [args: '--isoseq --peek-guess', suffix: ".fl"] )
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workflow test_lima_bam {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['ccs'], checkIfExists: true),
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]
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primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
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LIMA ( input, primers )
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}
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workflow test_lima_fa {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['ccs_fa'], checkIfExists: true),
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]
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primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
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LIMA ( input, primers )
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}
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workflow test_lima_fa_gz {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['ccs_fa_gz'], checkIfExists: true),
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]
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primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
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LIMA ( input, primers )
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}
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workflow test_lima_fq {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['ccs_fq'], checkIfExists: true),
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]
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primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
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LIMA ( input, primers )
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}
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workflow test_lima_fq_gz {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['ccs_fq_gz'], checkIfExists: true),
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]
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primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
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LIMA ( input, primers )
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}
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