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e526eae472
* initial commit hisat2/build * initial commit hisat2/build * changed names for hisat2 * fixed directory structure and args * added splice site test data * added splice site inputs * replaced list with individual args * fixed removed commas * added test yml file * updated hisat2 conda version * added meta.yml * added meta.yml description * added meta.yml inputs * added meta.yml outputs * update conda version for hisat2 * removed trailing whitespace meta.yml * fixed version number for containers * added test data to test config * updated for new test logic * fix pytest issue? * fix pytest issue * fixed wrong tool in meta.yaml * updated tets.yaml name * handle build bug for testing * handle build bug for testing in yaml * moved test folder to fix build bug * use old hisat2 version to avoid conda giving inconsistent md5sum * initial commit * removed temp file * added meta yaml * add to pytest * added tests * added test yml * add align meta yaml * add hisat2 align to pytest * remove need for splice data by calling process * add hisat2 align se test * add hisat2 align pe test * update names hisat2 align * update software pytest for using mutiple modules * remove splice site test data since using module instead * remove splice site from config since using module instead * fixed extra brace * added hisat2 align test.yml * removed md5sum for bam files * updated build md5sums * Apply suggestions from code review Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
32 lines
1.6 KiB
Text
32 lines
1.6 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { HISAT2_EXTRACTSPLICESITES } from '../../../../software/hisat2/extractsplicesites/main.nf' addParams( options: [:] )
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include { HISAT2_BUILD } from '../../../../software/hisat2/build/main.nf' addParams( options: [:] )
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include { HISAT2_ALIGN } from '../../../../software/hisat2/align/main.nf' addParams( options: [:] )
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workflow test_hisat2_align_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
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HISAT2_EXTRACTSPLICESITES ( gtf )
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HISAT2_BUILD ( fasta, gtf, HISAT2_EXTRACTSPLICESITES.out.txt )
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HISAT2_ALIGN ( input, HISAT2_BUILD.out.index, HISAT2_EXTRACTSPLICESITES.out.txt )
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}
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workflow test_hisat2_align_paired_end {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
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HISAT2_EXTRACTSPLICESITES ( gtf )
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HISAT2_BUILD ( fasta, gtf, HISAT2_EXTRACTSPLICESITES.out.txt )
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HISAT2_ALIGN ( input, HISAT2_BUILD.out.index, HISAT2_EXTRACTSPLICESITES.out.txt )
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}
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