nf-core_modules/tests/config/pytest_software.yml

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bandage_image:
- software/bandage/image/**
- tests/software/bandage/image/**
bcftools_consensus:
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- software/bcftools/consensus/**
- tests/software/bcftools/consensus/**
bcftools_filter:
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- software/bcftools/filter/**
- tests/software/bcftools/filter/**
bcftools_isec:
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- software/bcftools/isec/**
- tests/software/bcftools/isec/**
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bcftools_merge:
- software/bcftools/merge/**
- tests/software/bcftools/merge/**
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bcftools_mpileup:
- software/bcftools/mpileup/**
- tests/software/bcftools/mpileup/**
bcftools_stats:
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- software/bcftools/stats/**
- tests/software/bcftools/stats/**
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bedtools_complement:
- software/bedtools/complement/**
- tests/software/bedtools/complement/**
bedtools_genomecov:
- software/bedtools/genomecov/**
- tests/software/bedtools/genomecov/**
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bedtools_getfasta:
- software/bedtools/getfasta/**
- tests/software/bedtools/getfasta/**
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bedtools_intersect:
- software/bedtools/intersect/**
- tests/software/bedtools/intersect/**
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bedtools_maskfasta:
- software/bedtools/maskfasta/**
- tests/software/bedtools/maskfasta/**
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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/**
bismark_align:
- software/bismark/align/**
- software/bismark/genome_preparation/**
- tests/software/bismark/align/**
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bismark_deduplicate:
- software/bismark/deduplicate/**
- tests/software/bismark/deduplicate/**
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bismark_genome_preparation:
- software/bismark/genome_preparation/**
- tests/software/bismark/genome_preparation/**
bismark_methylation_extractor:
- software/bismark/methylation_extractor/**
- software/bismark/genome_preparation/**
- tests/software/bismark/methylation_extractor/**
bismark_report:
- software/bismark/genome_preparation/**
- software/bismark/align/**
- software/bismark/deduplicate/**
- software/bismark/methylation_extractor/**
- software/bismark/report/**
- tests/software/bismark/report/**
blast_makeblastdb:
- software/blast/makeblastdb/**
- tests/software/blast/makeblastdb/**
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blast_blastn:
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- software/blast/blastn/**
- tests/software/blast/blastn/**
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>
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bowtie_build:
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- software/bowtie/build/**
- tests/software/bowtie/build_test/**
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bowtie_align:
- software/bowtie/align/**
- software/bowtie/build/**
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- tests/software/bowtie/align/**
bowtie2_build:
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- software/bowtie2/build/**
- tests/software/bowtie2/build_test/**
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bowtie2_align:
- software/bowtie2/align/**
- software/bowtie2/build/**
- tests/software/bowtie2/align/**
bwa_index:
- software/bwa/index/**
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- tests/software/bwa/index/**
bwa_mem:
- software/bwa/mem/**
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- tests/software/bwa/mem/**
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bwamem2_index:
- software/bwamem2/index/**
- tests/software/bwamem2/index/**
bwamem2_mem:
- software/bwamem2/mem/**
- tests/software/bwamem2/mem/**
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bwameth_align:
- software/bwameth/align/**
- tests/software/bwameth/align/**
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bwameth_index:
- software/bwameth/index/**
- tests/software/bwameth/index/**
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cat_fastq:
- software/cat/fastq/**
- tests/software/cat/fastq/**
cutadapt:
- software/cutadapt/**
- tests/software/cutadapt/**
dsh_filterbed:
- software/dsh/filterbed/**
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- tests/software/dsh/filterbed/**
dsh_splitbed:
- software/dsh/splitbed/**
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- tests/software/dsh/splitbed/**
fastp:
- software/fastp/**
- tests/software/fastp/**
fastqc:
- software/fastqc/**
- tests/software/fastqc/**
gatk4_bedtointervallist:
- software/gatk4/bedtointervallist/**
- tests/software/gatk4/bedtointervallist/**
gatk4_createsequencedictionary:
- software/gatk4/createsequencedictionary/**
- tests/software/gatk4/createsequencedictionary/**
gatk4_mergebamalignment:
- software/gatk4/mergebamalignment/**
- tests/software/gatk4/mergebamalignment/**
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gatk4_mergevcfs:
- software/gatk4/mergevcfs/**
- tests/software/gatk4/mergevcfs/**
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gatk4_revertsam:
- software/gatk4/revertsam/**
- tests/software/gatk4/revertsam/**
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gatk4_samtofastq:
- software/gatk4/samtofastq/**
- tests/software/gatk4/samtofastq/**
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gatk4_splitncigarreads:
- software/gatk4/splitncigarreads/**
- tests/software/gatk4/splitncigarreads/**
gatk4_variantfiltration:
- software/gatk4/variantfiltration/**
- tests/software/gatk4/variantfiltration/**
gffread:
- software/gffread/**
- tests/software/gffread/**
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gunzip:
- software/gunzip/**
- tests/software/gunzip/**
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ivar_consensus:
- software/ivar/consensus/**
- tests/software/ivar/consensus/**
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ivar_trim:
- software/ivar/trim/**
- tests/software/ivar/trim/**
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ivar_variants:
- software/ivar/variants/**
- tests/software/ivar/variants/**
kraken2_run:
- software/kraken2/run/**
- tests/software/kraken2/run/**
methyldackel_extract:
- software/methyldackel/extract/**
- tests/software/methyldackel/extract/**
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methyldackel_mbias:
- software/methyldackel/mbias/**
- tests/software/methyldackel/mbias/**
minia:
- software/minia/**
- tests/software/minia/**
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minimap2_align:
- software/minimap2/align/**
- tests/software/minimap2/align/**
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mosdepth:
- software/mosdepth/**
- tests/software/mosdepth/**
multiqc:
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- software/fastqc/**
- software/multiqc/**
- tests/software/multiqc/**
pangolin:
- software/pangolin/**
- tests/software/pangolin/**
picard_collectmultiplemetrics:
- software/picard/collectmultiplemetrics/**
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- tests/software/picard/collectmultiplemetrics/**
picard_markduplicates:
- software/picard/markduplicates/**
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- tests/software/picard/markduplicates/**
picard_mergesamfiles:
- software/picard/mergesamfiles/**
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- tests/software/picard/mergesamfiles/**
preseq_lcextrap:
- software/preseq/lcextrap/**
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- tests/software/preseq/lcextrap/**
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qualimap_bamqc:
- software/qualimap/bamqc/**
- tests/software/qualimap/bamqc/**
quast:
- software/quast/**
- tests/software/quast/**
salmon_index:
- software/salmon/index/**
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- tests/software/salmon/index/**
salmon_quant:
- software/salmon/quant/**
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- tests/software/salmon/quant/**
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samtools_faidx:
- software/samtools/faidx/**
- tests/software/samtools/faidx/**
samtools_flagstat:
- software/samtools/flagstat/**
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- tests/software/samtools/flagstat/**
samtools_idxstats:
- software/samtools/idxstats/**
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- tests/software/samtools/idxstats/**
samtools_index:
- software/samtools/index/**
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- tests/software/samtools/index/**
samtools_mpileup:
- software/samtools/mpileup/**
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- tests/software/samtools/mpileup/**
samtools_merge:
- software/samtools/merge/**
- tests/software/samtools/merge/**
samtools_sort:
- software/samtools/sort/**
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- tests/software/samtools/sort/**
samtools_stats:
- software/samtools/stats/**
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- tests/software/samtools/stats/**
samtools_view:
- software/samtools/view/**
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- tests/software/samtools/view/**
seacr_callpeak:
- software/seacr/callpeak/**
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- tests/software/seacr/callpeak/**
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seqkit_split2:
- software/seqkit/split2/**
- tests/software/seqkit/split2/**
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seqwish_induce:
- software/seqwish/induce/**
- tests/software/seqwish/induce/**
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spades:
- software/spades/**
- tests/software/spades/**
star_align:
- software/star/align/**
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- tests/software/star/align/**
star_genomegenerate:
- software/star/genomegenerate/**
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- tests/software/star/genomegenerate/**
stringtie:
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- software/stringtie/**
- tests/software/stringtie/**
tabix_bgzip:
- software/tabix/bgzip/**
- tests/software/tabix/bgzip/**
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tabix_tabix:
- software/tabix/tabix/**
- tests/software/tabix/tabix/**
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tiddit_sv:
- software/tiddit/sv/**
- tests/software/tiddit/sv/**
trimgalore:
- software/trimgalore/**
- tests/software/trimgalore/**
ucsc_bedgraphtobigwig:
- software/ucsc/bedgraphtobigwig/**
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- tests/software/ucsc/bedgraphtobigwig/**
untar:
- software/untar/**
- tests/software/untar/**