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46 lines
2.1 KiB
Text
46 lines
2.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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def options_align = [args: '--readFilesCommand zcat --outSAMtype BAM Unsorted SortedByCoordinate']
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def options_gg = [args: '--genomeSAindexNbases 9']
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include { STAR_ALIGN } from '../../../software/star/align/main.nf' addParams( options: options_align )
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include { STAR_GENOMEGENERATE } from '../../../software/star/genomegenerate/main.nf' addParams( options: options_gg )
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workflow test_star_genomegenerate {
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fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
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gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
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STAR_GENOMEGENERATE ( fasta, gtf )
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}
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workflow test_star_alignment_single_end {
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fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
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gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
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STAR_GENOMEGENERATE ( fasta, gtf )
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
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STAR_ALIGN( input, STAR_GENOMEGENERATE.out.index, gtf)
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}
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// workflow test_star_alignment_single_end {
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// fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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// BOWTIE_INDEX ( fasta )
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// def input = []
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// input = [ [ id:'test', single_end:true ], // meta map
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// [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
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// BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
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// }
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// workflow test_star_alignment_paired_end {
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// fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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// BOWTIE_INDEX ( fasta )
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// def input = []
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// input = [ [ id:'test', single_end:false ], // meta map
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// [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
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// file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
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// BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
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// }
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