2021-02-04 18:10:54 +00:00
|
|
|
bandage_image:
|
|
|
|
|
- software/bandage/image/**
|
|
|
|
|
- tests/software/bandage/image/**
|
|
|
|
|
|
2021-02-08 17:10:50 +00:00
|
|
|
bcftools_consensus:
|
2021-02-08 21:48:21 +00:00
|
|
|
- software/bcftools/consensus/**
|
2021-02-09 17:16:16 +00:00
|
|
|
- tests/software/bcftools/consensus/**
|
2021-02-08 17:10:50 +00:00
|
|
|
|
|
|
|
|
bcftools_filter:
|
2021-02-08 20:57:31 +00:00
|
|
|
- software/bcftools/filter/**
|
2021-02-09 17:16:16 +00:00
|
|
|
- tests/software/bcftools/filter/**
|
2021-02-08 17:10:50 +00:00
|
|
|
|
|
|
|
|
bcftools_isec:
|
2021-02-08 20:57:31 +00:00
|
|
|
- software/bcftools/isec/**
|
2021-02-09 17:16:16 +00:00
|
|
|
- tests/software/bcftools/isec/**
|
2021-02-08 17:10:50 +00:00
|
|
|
|
2021-02-12 23:08:57 +00:00
|
|
|
bcftools_merge:
|
|
|
|
|
- software/bcftools/merge/**
|
|
|
|
|
- tests/software/bcftools/merge/**
|
|
|
|
|
|
2021-02-23 18:05:57 +00:00
|
|
|
bcftools_mpileup:
|
|
|
|
|
- software/bcftools/mpileup/**
|
|
|
|
|
- tests/software/bcftools/mpileup/**
|
|
|
|
|
|
2021-02-08 17:10:50 +00:00
|
|
|
bcftools_stats:
|
2021-02-08 20:57:31 +00:00
|
|
|
- software/bcftools/stats/**
|
2021-02-09 17:16:16 +00:00
|
|
|
- tests/software/bcftools/stats/**
|
2021-02-08 17:10:50 +00:00
|
|
|
|
2021-02-07 23:20:53 +00:00
|
|
|
bedtools_complement:
|
|
|
|
|
- software/bedtools/complement/**
|
|
|
|
|
- tests/software/bedtools/complement/**
|
|
|
|
|
|
|
|
|
|
bedtools_genomecov:
|
|
|
|
|
- software/bedtools/genomecov/**
|
|
|
|
|
- tests/software/bedtools/genomecov/**
|
|
|
|
|
|
2021-02-09 16:56:51 +00:00
|
|
|
bedtools_getfasta:
|
|
|
|
|
- software/bedtools/getfasta/**
|
|
|
|
|
- tests/software/bedtools/getfasta/**
|
|
|
|
|
|
2021-02-07 23:20:53 +00:00
|
|
|
bedtools_intersect:
|
|
|
|
|
- software/bedtools/intersect/**
|
|
|
|
|
- tests/software/bedtools/intersect/**
|
|
|
|
|
|
2021-02-08 22:41:10 +00:00
|
|
|
bedtools_maskfasta:
|
|
|
|
|
- software/bedtools/maskfasta/**
|
|
|
|
|
- tests/software/bedtools/maskfasta/**
|
|
|
|
|
|
2021-02-07 23:20:53 +00:00
|
|
|
bedtools_merge:
|
|
|
|
|
- software/bedtools/merge/**
|
|
|
|
|
- tests/software/bedtools/merge/**
|
|
|
|
|
|
|
|
|
|
bedtools_slop:
|
|
|
|
|
- software/bedtools/slop/**
|
|
|
|
|
- tests/software/bedtools/slop/**
|
|
|
|
|
|
|
|
|
|
bedtools_sort:
|
|
|
|
|
- software/bedtools/sort/**
|
|
|
|
|
- tests/software/bedtools/sort/**
|
|
|
|
|
|
2021-02-23 17:02:16 +00:00
|
|
|
bismark_deduplicate:
|
|
|
|
|
- software/bismark/deduplicate/**
|
|
|
|
|
- tests/software/bismark/deduplicate/**
|
|
|
|
|
|
2021-02-18 09:56:36 +00:00
|
|
|
bismark_genome_preparation:
|
|
|
|
|
- software/bismark/genome_preparation/**
|
|
|
|
|
- tests/software/bismark/genome_preparation/**
|
|
|
|
|
|
2021-02-09 16:07:23 +00:00
|
|
|
blast_blastn:
|
2021-02-09 15:58:36 +00:00
|
|
|
- software/blast/blastn/**
|
2021-02-09 17:16:16 +00:00
|
|
|
- tests/software/blast/blastn/**
|
2021-02-09 14:47:53 +00:00
|
|
|
|
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
|
|
|
bowtie_build:
|
2021-02-07 23:20:53 +00:00
|
|
|
- software/bowtie/build/**
|
2021-03-15 14:39:42 +00:00
|
|
|
- tests/software/bowtie/build_test/**
|
2021-02-07 23:20:53 +00:00
|
|
|
|
2021-01-24 05:50:20 +00:00
|
|
|
bowtie_align:
|
|
|
|
|
- software/bowtie/align/**
|
2021-02-02 21:27:45 +00:00
|
|
|
- software/bowtie/build/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/bowtie/align/**
|
2021-01-24 05:50:20 +00:00
|
|
|
|
2021-03-15 14:39:42 +00:00
|
|
|
bowtie2_build:
|
2021-02-07 23:20:53 +00:00
|
|
|
- software/bowtie2/build/**
|
2021-03-15 14:39:42 +00:00
|
|
|
- tests/software/bowtie2/build_test/**
|
2021-02-03 16:04:43 +00:00
|
|
|
|
|
|
|
|
bowtie2_align:
|
|
|
|
|
- software/bowtie2/align/**
|
|
|
|
|
- software/bowtie2/build/**
|
|
|
|
|
- tests/software/bowtie2/align/**
|
|
|
|
|
|
2021-01-24 05:50:20 +00:00
|
|
|
bwa_index:
|
|
|
|
|
- software/bwa/index/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/bwa/index/**
|
2021-01-24 05:50:20 +00:00
|
|
|
|
|
|
|
|
bwa_mem:
|
|
|
|
|
- software/bwa/mem/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/bwa/mem/**
|
2021-01-24 05:50:20 +00:00
|
|
|
|
2021-02-12 12:53:49 +00:00
|
|
|
bwamem2_index:
|
|
|
|
|
- software/bwamem2/index/**
|
|
|
|
|
- tests/software/bwamem2/index/**
|
|
|
|
|
|
|
|
|
|
bwamem2_mem:
|
|
|
|
|
- software/bwamem2/mem/**
|
|
|
|
|
- tests/software/bwamem2/mem/**
|
|
|
|
|
|
2021-02-17 17:23:11 +00:00
|
|
|
bwameth_align:
|
|
|
|
|
- software/bwameth/align/**
|
|
|
|
|
- tests/software/bwameth/align/**
|
|
|
|
|
|
2021-02-17 17:03:48 +00:00
|
|
|
bwameth_index:
|
|
|
|
|
- software/bwameth/index/**
|
|
|
|
|
- tests/software/bwameth/index/**
|
|
|
|
|
|
2021-02-12 16:22:07 +00:00
|
|
|
cat_fastq:
|
|
|
|
|
- software/cat/fastq/**
|
|
|
|
|
- tests/software/cat/fastq/**
|
|
|
|
|
|
2021-02-02 21:27:45 +00:00
|
|
|
cutadapt:
|
|
|
|
|
- software/cutadapt/**
|
|
|
|
|
- tests/software/cutadapt/**
|
|
|
|
|
|
|
|
|
|
dsh_filterbed:
|
|
|
|
|
- software/dsh/filterbed/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/dsh/filterbed/**
|
2021-02-02 21:27:45 +00:00
|
|
|
|
|
|
|
|
dsh_splitbed:
|
|
|
|
|
- software/dsh/splitbed/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/dsh/splitbed/**
|
2021-02-02 21:27:45 +00:00
|
|
|
|
|
|
|
|
fastp:
|
|
|
|
|
- software/fastp/**
|
|
|
|
|
- tests/software/fastp/**
|
|
|
|
|
|
2021-01-24 04:55:07 +00:00
|
|
|
fastqc:
|
|
|
|
|
- software/fastqc/**
|
|
|
|
|
- tests/software/fastqc/**
|
2021-01-24 05:50:20 +00:00
|
|
|
|
2021-03-08 13:45:46 +00:00
|
|
|
gatk4_bedtointervallist:
|
|
|
|
|
- software/gatk4/bedtointervallist/**
|
|
|
|
|
- tests/software/gatk4/bedtointervallist/**
|
|
|
|
|
|
|
|
|
|
gatk4_createsequencedictionary:
|
|
|
|
|
- software/gatk4/createsequencedictionary/**
|
|
|
|
|
- tests/software/gatk4/createsequencedictionary/**
|
2021-02-16 12:40:06 +00:00
|
|
|
|
2021-03-18 13:48:38 +00:00
|
|
|
gatk4_mergebamalignment:
|
|
|
|
|
- software/gatk4/mergebamalignment/**
|
|
|
|
|
- tests/software/gatk4/mergebamalignment/**
|
|
|
|
|
|
2021-02-19 12:36:42 +00:00
|
|
|
gatk4_mergevcfs:
|
|
|
|
|
- software/gatk4/mergevcfs/**
|
|
|
|
|
- tests/software/gatk4/mergevcfs/**
|
|
|
|
|
|
2021-02-22 14:21:39 +00:00
|
|
|
gatk4_revertsam:
|
|
|
|
|
- software/gatk4/revertsam/**
|
|
|
|
|
- tests/software/gatk4/revertsam/**
|
|
|
|
|
|
2021-02-19 11:41:29 +00:00
|
|
|
gatk4_samtofastq:
|
|
|
|
|
- software/gatk4/samtofastq/**
|
|
|
|
|
- tests/software/gatk4/samtofastq/**
|
2021-02-19 10:26:31 +00:00
|
|
|
|
2021-02-22 12:36:49 +00:00
|
|
|
gatk4_splitncigarreads:
|
|
|
|
|
- software/gatk4/splitncigarreads/**
|
|
|
|
|
- tests/software/gatk4/splitncigarreads/**
|
|
|
|
|
|
2021-03-18 13:48:38 +00:00
|
|
|
gatk4_variantfiltration:
|
|
|
|
|
- software/gatk4/variantfiltration/**
|
|
|
|
|
- tests/software/gatk4/variantfiltration/**
|
|
|
|
|
|
2021-01-24 05:50:20 +00:00
|
|
|
gffread:
|
|
|
|
|
- software/gffread/**
|
|
|
|
|
- tests/software/gffread/**
|
|
|
|
|
|
2021-02-09 09:05:55 +00:00
|
|
|
gunzip:
|
|
|
|
|
- software/gunzip/**
|
|
|
|
|
- tests/software/gunzip/**
|
|
|
|
|
|
2021-02-12 18:59:46 +00:00
|
|
|
ivar_consensus:
|
|
|
|
|
- software/ivar/consensus/**
|
|
|
|
|
- tests/software/ivar/consensus/**
|
|
|
|
|
|
2021-02-13 00:02:10 +00:00
|
|
|
ivar_trim:
|
|
|
|
|
- software/ivar/trim/**
|
|
|
|
|
- tests/software/ivar/trim/**
|
|
|
|
|
|
2021-02-15 17:28:10 +00:00
|
|
|
ivar_variants:
|
|
|
|
|
- software/ivar/variants/**
|
|
|
|
|
- tests/software/ivar/variants/**
|
|
|
|
|
|
2021-03-18 13:08:06 +00:00
|
|
|
kraken2_run:
|
|
|
|
|
- software/kraken2/run/**
|
|
|
|
|
- tests/software/kraken2/run/**
|
|
|
|
|
|
2021-02-17 18:18:55 +00:00
|
|
|
methyldackel_extract:
|
|
|
|
|
- software/methyldackel/extract/**
|
|
|
|
|
- tests/software/methyldackel/extract/**
|
|
|
|
|
|
2021-02-17 18:27:57 +00:00
|
|
|
methyldackel_mbias:
|
|
|
|
|
- software/methyldackel/mbias/**
|
|
|
|
|
- tests/software/methyldackel/mbias/**
|
|
|
|
|
|
2021-03-17 11:54:15 +00:00
|
|
|
minia:
|
|
|
|
|
- software/minia/**
|
|
|
|
|
- tests/software/minia/**
|
|
|
|
|
|
2021-02-04 19:42:08 +00:00
|
|
|
minimap2_align:
|
|
|
|
|
- software/minimap2/align/**
|
|
|
|
|
- tests/software/minimap2/align/**
|
|
|
|
|
|
2021-02-15 13:33:44 +00:00
|
|
|
mosdepth:
|
|
|
|
|
- software/mosdepth/**
|
|
|
|
|
- tests/software/mosdepth/**
|
|
|
|
|
|
2021-01-24 05:50:20 +00:00
|
|
|
multiqc:
|
2021-02-03 17:43:14 +00:00
|
|
|
- software/fastqc/**
|
2021-01-24 05:50:20 +00:00
|
|
|
- software/multiqc/**
|
|
|
|
|
- tests/software/multiqc/**
|
|
|
|
|
|
2021-02-02 21:27:45 +00:00
|
|
|
pangolin:
|
|
|
|
|
- software/pangolin/**
|
|
|
|
|
- tests/software/pangolin/**
|
|
|
|
|
|
2021-01-24 05:50:20 +00:00
|
|
|
picard_collectmultiplemetrics:
|
|
|
|
|
- software/picard/collectmultiplemetrics/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/picard/collectmultiplemetrics/**
|
2021-01-24 05:50:20 +00:00
|
|
|
|
|
|
|
|
picard_markduplicates:
|
|
|
|
|
- software/picard/markduplicates/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/picard/markduplicates/**
|
2021-01-24 05:50:20 +00:00
|
|
|
|
|
|
|
|
picard_mergesamfiles:
|
|
|
|
|
- software/picard/mergesamfiles/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/picard/mergesamfiles/**
|
2021-01-24 05:50:20 +00:00
|
|
|
|
|
|
|
|
preseq_lcextrap:
|
|
|
|
|
- software/preseq/lcextrap/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/preseq/lcextrap/**
|
2021-01-24 05:50:20 +00:00
|
|
|
|
2021-02-17 16:34:51 +00:00
|
|
|
qualimap_bamqc:
|
|
|
|
|
- software/qualimap/bamqc/**
|
|
|
|
|
- tests/software/qualimap/bamqc/**
|
|
|
|
|
|
2021-02-02 21:27:45 +00:00
|
|
|
quast:
|
|
|
|
|
- software/quast/**
|
|
|
|
|
- tests/software/quast/**
|
|
|
|
|
|
|
|
|
|
salmon_index:
|
|
|
|
|
- software/salmon/index/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/salmon/index/**
|
2021-02-02 21:27:45 +00:00
|
|
|
|
|
|
|
|
salmon_quant:
|
|
|
|
|
- software/salmon/quant/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/salmon/quant/**
|
2021-02-02 21:27:45 +00:00
|
|
|
|
2021-02-17 16:01:22 +00:00
|
|
|
samtools_faidx:
|
|
|
|
|
- software/samtools/faidx/**
|
|
|
|
|
- tests/software/samtools/faidx/**
|
|
|
|
|
|
2021-01-24 05:50:20 +00:00
|
|
|
samtools_flagstat:
|
|
|
|
|
- software/samtools/flagstat/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/samtools/flagstat/**
|
2021-01-24 05:50:20 +00:00
|
|
|
|
|
|
|
|
samtools_idxstats:
|
|
|
|
|
- software/samtools/idxstats/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/samtools/idxstats/**
|
2021-01-24 05:50:20 +00:00
|
|
|
|
|
|
|
|
samtools_index:
|
|
|
|
|
- software/samtools/index/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/samtools/index/**
|
2021-01-24 05:50:20 +00:00
|
|
|
|
2021-02-02 21:27:45 +00:00
|
|
|
samtools_mpileup:
|
|
|
|
|
- software/samtools/mpileup/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/samtools/mpileup/**
|
2021-02-02 21:27:45 +00:00
|
|
|
|
2021-01-24 05:50:20 +00:00
|
|
|
samtools_sort:
|
|
|
|
|
- software/samtools/sort/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/samtools/sort/**
|
2021-01-24 05:50:20 +00:00
|
|
|
|
|
|
|
|
samtools_stats:
|
|
|
|
|
- software/samtools/stats/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/samtools/stats/**
|
2021-01-24 05:50:20 +00:00
|
|
|
|
2021-02-02 21:27:45 +00:00
|
|
|
samtools_view:
|
|
|
|
|
- software/samtools/view/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/samtools/view/**
|
2021-02-02 21:27:45 +00:00
|
|
|
|
|
|
|
|
seacr_callpeak:
|
|
|
|
|
- software/seacr/callpeak/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/seacr/callpeak/**
|
2021-02-02 21:27:45 +00:00
|
|
|
|
2021-02-23 11:43:30 +00:00
|
|
|
seqkit_split2:
|
|
|
|
|
- software/seqkit/split2/**
|
|
|
|
|
- tests/software/seqkit/split2/**
|
2021-02-24 09:29:13 +00:00
|
|
|
|
2021-02-17 17:19:47 +00:00
|
|
|
seqwish_induce:
|
|
|
|
|
- software/seqwish/induce/**
|
|
|
|
|
- tests/software/seqwish/induce/**
|
2021-02-23 11:43:30 +00:00
|
|
|
|
2021-03-18 13:48:38 +00:00
|
|
|
spades:
|
|
|
|
|
- software/spades/**
|
|
|
|
|
- tests/software/spades/**
|
|
|
|
|
|
2021-02-02 21:27:45 +00:00
|
|
|
star_align:
|
|
|
|
|
- software/star/align/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/star/align/**
|
2021-02-02 21:27:45 +00:00
|
|
|
|
|
|
|
|
star_genomegenerate:
|
|
|
|
|
- software/star/genomegenerate/**
|
2021-02-03 16:04:43 +00:00
|
|
|
- tests/software/star/genomegenerate/**
|
2021-02-02 21:27:45 +00:00
|
|
|
|
2021-01-24 05:50:20 +00:00
|
|
|
stringtie:
|
2021-02-03 16:04:43 +00:00
|
|
|
- software/stringtie/**
|
|
|
|
|
- tests/software/stringtie/**
|
2021-01-24 05:50:20 +00:00
|
|
|
|
2021-02-16 18:11:36 +00:00
|
|
|
tabix_bgzip:
|
|
|
|
|
- software/tabix/bgzip/**
|
|
|
|
|
- tests/software/tabix/bgzip/**
|
|
|
|
|
|
2021-02-19 09:56:04 +00:00
|
|
|
tabix_tabix:
|
|
|
|
|
- software/tabix/tabix/**
|
|
|
|
|
- tests/software/tabix/tabix/**
|
|
|
|
|
|
2021-02-24 14:59:10 +00:00
|
|
|
tiddit_sv:
|
|
|
|
|
- software/tiddit/sv/**
|
|
|
|
|
- tests/software/tiddit/sv/**
|
|
|
|
|
|
2021-01-24 05:50:20 +00:00
|
|
|
trimgalore:
|
|
|
|
|
- software/trimgalore/**
|
|
|
|
|
- tests/software/trimgalore/**
|
|
|
|
|
|
|
|
|
|
ucsc_bedgraphtobigwig:
|
|
|
|
|
- software/ucsc/bedgraphtobigwig/**
|
2021-02-08 00:57:06 +00:00
|
|
|
- tests/software/ucsc/bedgraphtobigwig/**
|
2021-03-17 08:42:35 +00:00
|
|
|
|
2021-03-17 11:54:15 +00:00
|
|
|
untar:
|
|
|
|
|
- software/untar/**
|
|
|
|
|
- tests/software/untar/**
|
|
|
|
|
|