mirror of
https://github.com/MillironX/nf-core_modules.git
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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>
16 lines
725 B
YAML
16 lines
725 B
YAML
- name: bwamem2 index
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command: nextflow run ./tests/software/bwamem2/index -entry test_bwamem2_index -c tests/config/nextflow.config
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tags:
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- bwamem2
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- bwamem2_index
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files:
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- path: ./output/bwamem2/bwamem2/test_genome.fasta.amb
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md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
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- path: ./output/bwamem2/bwamem2/test_genome.fasta.pac
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md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
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- path: ./output/bwamem2/bwamem2/test_genome.fasta.0123
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md5sum: b02870de80106104abcb03cd9463e7d8
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- path: ./output/bwamem2/bwamem2/test_genome.fasta.bwt.2bit.64
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md5sum: d097a1b82dee375d41a1ea69895a9216
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- path: ./output/bwamem2/bwamem2/test_genome.fasta.ann
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md5sum: c32e11f6c859f166c7525a9c1d583567
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