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240ee4328c
* fix: remove left-over unnecessary code * Make gzipping optional for DAS_Tool scaffolds2bin * Add optional unzipping * Make gunzip optional for DAS_Tool scaffolds2bin * Apply suggestions from code review Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Update modules/dastool/scaffolds2bin/meta.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
48 lines
2.1 KiB
Text
48 lines
2.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GUNZIP } from '../../../../modules/gunzip/main.nf'
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include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf'
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include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf'
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include { DASTOOL_SCAFFOLDS2BIN } from '../../../../modules/dastool/scaffolds2bin/main.nf'
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workflow test_dastool_scaffolds2bin {
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input_depth = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
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METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
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Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
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.map { it -> [[ id:'test', single_end:false ], it] }
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.join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
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.set { input_metabat2 }
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METABAT2_METABAT2 ( input_metabat2 )
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DASTOOL_SCAFFOLDS2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
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}
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workflow test_dastool_scaffolds2bin_ungzipped {
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input_depth = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
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METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
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Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
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.map { it -> [[ id:'test', single_end:false ], it] }
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.join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
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.set { input_metabat2 }
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METABAT2_METABAT2 ( input_metabat2 )
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// TODO test unzipped input files
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ch_input_2_scaffolds2bin = GUNZIP( METABAT2_METABAT2.out.fasta ).gunzip
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DASTOOL_SCAFFOLDS2BIN ( ch_input_2_scaffolds2bin, "fa")
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}
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