Kevin Menden 4566525da2 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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bandage/image	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
bcftools	Adding arguments to make md5 hashes stable	2021-02-23 19:39:24 +01:00
bedtools	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
bismark	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
blast	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
bowtie	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
bowtie2	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
bwa	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
bwamem2	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
bwameth	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
cat/fastq	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
cutadapt	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
dsh	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
fastp	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
fastqc	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
gatk/createsequencedictionary	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
gatk4	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
gffread	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
gunzip	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
ivar	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
methyldackel	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
minimap2/align	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
mosdepth	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
multiqc	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
pangolin	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
picard	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
preseq/lcextrap	Fix preseq tests	2021-02-03 17:28:44 +00:00
qualimap/bamqc	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
quast	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
salmon	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
samtools	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
seacr/callpeak	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
seqkit/split2	Add all tests back in	2021-02-24 09:57:23 +01:00
seqwish/induce	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
star	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
stringtie	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
tabix	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
tiddit/sv	Check only for vcf file to exists (includes cmd)	2021-02-26 07:14:29 +01:00
TOOL/SUBTOOL	fix: update checksum or filename	2021-02-17 01:34:50 +01:00
trimgalore	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
ucsc/bedgraphtobigwig	Change path to tests	2021-02-03 16:44:56 +00:00
untar	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00