mirror of
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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>
24 lines
949 B
Text
24 lines
949 B
Text
##fileformat=VCFv4.2
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##reference=file://some/path/human_g1k_v37.fasta
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##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
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##INFO=<ID=MinDP,Number=1,Type=Integer,Description="Dummy">
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##ALT=<ID=DEL,Description="Deletion">
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##contig=<ID=1,assembly=b37,length=249250621>
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##contig=<ID=2,assembly=b37,length=249250621>
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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA001
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1 5 . C A . PASS . GT 0/1
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1 5 . C T . PASS . GT 0/1
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1 7 . T A . PASS . GT .
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1 10 . G A . PASS . GT 0/1
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1 12 . GACA GA . PASS . GT 0/1
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1 16 . T TAAA . PASS . GT 1/1
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1 19 . A C . PASS . GT 0/1
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1 61 . C A . PASS . GT 0/1
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2 61 . agag aa . PASS . GT 0/1
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2 119 . aaa t . PASS . GT 0/1
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2 179 . g gacgtacgt . PASS . GT 0/1
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2 200 . a <DEL> . PASS END=210 GT 1/0
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2 300 . a . . PASS END=310;MinDP=10 GT 0/1
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2 320 . a <*> . PASS END=330;MinDP=20 GT 0/1
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2 481 . t c,a . PASS . GT 0/2
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