2020-11-25 00:16:56 +00:00
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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Converge test data usage (#249)
* 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>
2021-03-04 10:10:57 +00:00
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include { BWA_INDEX } from '../../../../software/bwa/index/main.nf' addParams( options: [:] )
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2021-02-03 16:20:02 +00:00
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include { BWA_MEM } from '../../../../software/bwa/mem/main.nf' addParams( options: [:] )
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2020-11-25 00:16:56 +00:00
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/*
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* Test with single-end data
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*/
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workflow test_bwa_mem_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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2021-03-24 09:53:41 +00:00
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[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
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]
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fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
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2020-11-25 00:16:56 +00:00
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2021-03-24 09:53:41 +00:00
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BWA_INDEX ( fasta )
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BWA_MEM ( input, BWA_INDEX.out.index )
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2020-11-25 00:16:56 +00:00
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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_bwa_mem_paired_end {
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input = [ [ id:'test', single_end:false ], // meta map
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2021-03-24 09:53:41 +00:00
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[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ]
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]
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fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
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2020-11-25 00:16:56 +00:00
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2021-03-24 09:53:41 +00:00
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BWA_INDEX ( fasta )
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BWA_MEM ( input, BWA_INDEX.out.index )
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2020-11-25 00:16:56 +00:00
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}
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