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4566525da2
* 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>
29 lines
1.5 KiB
Text
29 lines
1.5 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { STAR_GENOMEGENERATE } from '../../../../software/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] )
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include { STAR_ALIGN } from '../../../../software/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat'] )
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workflow test_star_alignment_single_end {
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def fasta = file("${launchDir}/tests/data/generic/fasta/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
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def gtf = file("${launchDir}/tests/data/generic/gtf/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("${launchDir}/tests/data/generic/fastq/test_single_end.fastq.gz", checkIfExists: true) ] ]
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STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
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}
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workflow test_star_alignment_paired_end {
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def fasta = file("${launchDir}/tests/data/generic/fasta/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
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def gtf = file("${launchDir}/tests/data/generic/gtf/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
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STAR_GENOMEGENERATE ( fasta, gtf )
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ] ]
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STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
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}
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