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![Kevin Menden](/assets/img/avatar_default.png)
* initial data restructuing * fixed bedtools_complement * fixed bedtools_genomecov * fixed bedtools_getfasta * fixed bedtools_intersect * fixed bedtools maskfasta * fixed bedtools_merge * fixed bedtools_slop * fixed bedtools_sort * fixed bismark_genome_preparation * fixed blast * fixed bowtie data * fixed bowtie2 data * fixed bwa data * fixed bwamem2 data usage * fixed cat_fastq data * fixed cutadapt data * fixed dsh data * fixed fastp data * fixed fastqc; fixed bug with wrong fastq format * fixed gatk * fixed data for gffread, gunzip * fixed ivar paths * fixed data paths for minimap2 * fixed mosdepth * fixed multiqc, pangolin * fixed picard data paths * fixed data paths for qualimap, quast * fixed salmon data paths * fixed samtools paths * fixed seqwish, stringtie paths * fixed tabix, trimgalore paths * cleaned up data * added first description to README * changed test data naming again; everything up to bwa fixed * everything up to gatk4 * fixed everything up to ivar * fixed everything up to picard * everything up to quast * everything fixed up to stringtie * switched everyting to 'test' naming scheme * fixed samtools and ivar tests * cleaned up README a bit * add (simulated) methylation test data based on SARS-CoV-2 genome; simulated with Sherman --non_dir --genome sarscov2/fasta/ --paired -n 10000 -l 100 --CG 20 --CH 90 * bwameth/align: update data paths and checksums also, build index on the go * bwameth/index: update data paths and checksums * methyldackel/extract: update data paths and checksums * methyldackel/mbias: update data paths and checksums * bismark/deduplicate: update data paths and checksums * remove obsolete testdata * remove empty 'dummy_file.txt' * update data/README.md * methyldackel: fix test * Revert "methyldackel: fix test" This reverts commit f175a32d144b1b0bfa0c6885da80c51e3cfe038a. * methyldackel: fix test for real * move test.genome.sizes * changed test names * switched genomic to genome and transcriptome * fix bedtools, blast * fix gtf, tabix, .paf * fix bowtie,bwa,bwameth * fixed: bwa, bwamem, gatk, gffread, quast * fixed bismark and blast * fixed remaining tests * delete bam file Co-authored-by: phue <patrick.huether@gmail.com>
39 lines
1.2 KiB
Text
39 lines
1.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BWAMEM2_INDEX } from '../../../../software/bwamem2/index/main.nf' addParams( options: [:] )
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include { BWAMEM2_MEM } from '../../../../software/bwamem2/mem/main.nf' addParams( options: [:] )
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/*
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* Test with single-end data
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*/
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workflow test_bwamem2_mem_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("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] ]
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BWAMEM2_INDEX ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
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BWAMEM2_MEM (
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input,
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BWAMEM2_INDEX.out.index
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)
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}
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/*
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* Test with paired-end data
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*/
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workflow test_bwamem2_mem_paired_end {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true) ] ]
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BWAMEM2_INDEX ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
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BWAMEM2_MEM (
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input,
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BWAMEM2_INDEX.out.index
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)
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}
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