mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +00:00
3c4d9466f4
* initial 'modules create' of minia * fixed tests * finished meta.yml * fixed filters.yml * resolved issues in pytest_software.yml * add newline * Update software/minia/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
326 lines
6.8 KiB
YAML
326 lines
6.8 KiB
YAML
bandage_image:
|
|
- software/bandage/image/**
|
|
- tests/software/bandage/image/**
|
|
|
|
bcftools_consensus:
|
|
- software/bcftools/consensus/**
|
|
- tests/software/bcftools/consensus/**
|
|
|
|
bcftools_filter:
|
|
- software/bcftools/filter/**
|
|
- tests/software/bcftools/filter/**
|
|
|
|
bcftools_isec:
|
|
- software/bcftools/isec/**
|
|
- tests/software/bcftools/isec/**
|
|
|
|
bcftools_merge:
|
|
- software/bcftools/merge/**
|
|
- tests/software/bcftools/merge/**
|
|
|
|
bcftools_mpileup:
|
|
- software/bcftools/mpileup/**
|
|
- tests/software/bcftools/mpileup/**
|
|
|
|
bcftools_stats:
|
|
- software/bcftools/stats/**
|
|
- tests/software/bcftools/stats/**
|
|
|
|
bedtools_complement:
|
|
- software/bedtools/complement/**
|
|
- tests/software/bedtools/complement/**
|
|
|
|
bedtools_genomecov:
|
|
- software/bedtools/genomecov/**
|
|
- tests/software/bedtools/genomecov/**
|
|
|
|
bedtools_getfasta:
|
|
- software/bedtools/getfasta/**
|
|
- tests/software/bedtools/getfasta/**
|
|
|
|
bedtools_intersect:
|
|
- software/bedtools/intersect/**
|
|
- tests/software/bedtools/intersect/**
|
|
|
|
bedtools_maskfasta:
|
|
- software/bedtools/maskfasta/**
|
|
- tests/software/bedtools/maskfasta/**
|
|
|
|
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_deduplicate:
|
|
- software/bismark/deduplicate/**
|
|
- tests/software/bismark/deduplicate/**
|
|
|
|
bismark_genome_preparation:
|
|
- software/bismark/genome_preparation/**
|
|
- tests/software/bismark/genome_preparation/**
|
|
|
|
blast_blastn:
|
|
- software/blast/blastn/**
|
|
- tests/software/blast/blastn/**
|
|
|
|
bowtie_build:
|
|
- software/bowtie/build/**
|
|
- tests/software/bowtie/build_test/**
|
|
|
|
bowtie_align:
|
|
- software/bowtie/align/**
|
|
- software/bowtie/build/**
|
|
- tests/software/bowtie/align/**
|
|
|
|
bowtie2_build:
|
|
- software/bowtie2/build/**
|
|
- tests/software/bowtie2/build_test/**
|
|
|
|
bowtie2_align:
|
|
- software/bowtie2/align/**
|
|
- software/bowtie2/build/**
|
|
- tests/software/bowtie2/align/**
|
|
|
|
bwa_index:
|
|
- software/bwa/index/**
|
|
- tests/software/bwa/index/**
|
|
|
|
bwa_mem:
|
|
- software/bwa/mem/**
|
|
- tests/software/bwa/mem/**
|
|
|
|
bwamem2_index:
|
|
- software/bwamem2/index/**
|
|
- tests/software/bwamem2/index/**
|
|
|
|
bwamem2_mem:
|
|
- software/bwamem2/mem/**
|
|
- tests/software/bwamem2/mem/**
|
|
|
|
bwameth_align:
|
|
- software/bwameth/align/**
|
|
- tests/software/bwameth/align/**
|
|
|
|
bwameth_index:
|
|
- software/bwameth/index/**
|
|
- tests/software/bwameth/index/**
|
|
|
|
cat_fastq:
|
|
- software/cat/fastq/**
|
|
- tests/software/cat/fastq/**
|
|
|
|
cutadapt:
|
|
- software/cutadapt/**
|
|
- tests/software/cutadapt/**
|
|
|
|
dsh_filterbed:
|
|
- software/dsh/filterbed/**
|
|
- tests/software/dsh/filterbed/**
|
|
|
|
dsh_splitbed:
|
|
- software/dsh/splitbed/**
|
|
- 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_mergevcfs:
|
|
- software/gatk4/mergevcfs/**
|
|
- tests/software/gatk4/mergevcfs/**
|
|
|
|
gatk4_revertsam:
|
|
- software/gatk4/revertsam/**
|
|
- tests/software/gatk4/revertsam/**
|
|
|
|
gatk4_samtofastq:
|
|
- software/gatk4/samtofastq/**
|
|
- tests/software/gatk4/samtofastq/**
|
|
|
|
gatk4_splitncigarreads:
|
|
- software/gatk4/splitncigarreads/**
|
|
- tests/software/gatk4/splitncigarreads/**
|
|
|
|
gffread:
|
|
- software/gffread/**
|
|
- tests/software/gffread/**
|
|
|
|
gunzip:
|
|
- software/gunzip/**
|
|
- tests/software/gunzip/**
|
|
|
|
ivar_consensus:
|
|
- software/ivar/consensus/**
|
|
- tests/software/ivar/consensus/**
|
|
|
|
ivar_trim:
|
|
- software/ivar/trim/**
|
|
- tests/software/ivar/trim/**
|
|
|
|
ivar_variants:
|
|
- software/ivar/variants/**
|
|
- tests/software/ivar/variants/**
|
|
|
|
methyldackel_extract:
|
|
- software/methyldackel/extract/**
|
|
- tests/software/methyldackel/extract/**
|
|
|
|
methyldackel_mbias:
|
|
- software/methyldackel/mbias/**
|
|
- tests/software/methyldackel/mbias/**
|
|
|
|
minia:
|
|
- software/minia/**
|
|
- tests/software/minia/**
|
|
|
|
minimap2_align:
|
|
- software/minimap2/align/**
|
|
- tests/software/minimap2/align/**
|
|
|
|
mosdepth:
|
|
- software/mosdepth/**
|
|
- tests/software/mosdepth/**
|
|
|
|
multiqc:
|
|
- software/fastqc/**
|
|
- software/multiqc/**
|
|
- tests/software/multiqc/**
|
|
|
|
pangolin:
|
|
- software/pangolin/**
|
|
- tests/software/pangolin/**
|
|
|
|
picard_collectmultiplemetrics:
|
|
- software/picard/collectmultiplemetrics/**
|
|
- tests/software/picard/collectmultiplemetrics/**
|
|
|
|
picard_markduplicates:
|
|
- software/picard/markduplicates/**
|
|
- tests/software/picard/markduplicates/**
|
|
|
|
picard_mergesamfiles:
|
|
- software/picard/mergesamfiles/**
|
|
- tests/software/picard/mergesamfiles/**
|
|
|
|
preseq_lcextrap:
|
|
- software/preseq/lcextrap/**
|
|
- tests/software/preseq/lcextrap/**
|
|
|
|
qualimap_bamqc:
|
|
- software/qualimap/bamqc/**
|
|
- tests/software/qualimap/bamqc/**
|
|
|
|
quast:
|
|
- software/quast/**
|
|
- tests/software/quast/**
|
|
|
|
salmon_index:
|
|
- software/salmon/index/**
|
|
- tests/software/salmon/index/**
|
|
|
|
salmon_quant:
|
|
- software/salmon/quant/**
|
|
- tests/software/salmon/quant/**
|
|
|
|
samtools_faidx:
|
|
- software/samtools/faidx/**
|
|
- tests/software/samtools/faidx/**
|
|
|
|
samtools_flagstat:
|
|
- software/samtools/flagstat/**
|
|
- tests/software/samtools/flagstat/**
|
|
|
|
samtools_idxstats:
|
|
- software/samtools/idxstats/**
|
|
- tests/software/samtools/idxstats/**
|
|
|
|
samtools_index:
|
|
- software/samtools/index/**
|
|
- tests/software/samtools/index/**
|
|
|
|
samtools_mpileup:
|
|
- software/samtools/mpileup/**
|
|
- tests/software/samtools/mpileup/**
|
|
|
|
samtools_sort:
|
|
- software/samtools/sort/**
|
|
- tests/software/samtools/sort/**
|
|
|
|
samtools_stats:
|
|
- software/samtools/stats/**
|
|
- tests/software/samtools/stats/**
|
|
|
|
samtools_view:
|
|
- software/samtools/view/**
|
|
- tests/software/samtools/view/**
|
|
|
|
seacr_callpeak:
|
|
- software/seacr/callpeak/**
|
|
- tests/software/seacr/callpeak/**
|
|
|
|
seqkit_split2:
|
|
- software/seqkit/split2/**
|
|
- tests/software/seqkit/split2/**
|
|
|
|
seqwish_induce:
|
|
- software/seqwish/induce/**
|
|
- tests/software/seqwish/induce/**
|
|
|
|
star_align:
|
|
- software/star/align/**
|
|
- tests/software/star/align/**
|
|
|
|
star_genomegenerate:
|
|
- software/star/genomegenerate/**
|
|
- tests/software/star/genomegenerate/**
|
|
|
|
stringtie:
|
|
- software/stringtie/**
|
|
- tests/software/stringtie/**
|
|
|
|
tabix_bgzip:
|
|
- software/tabix/bgzip/**
|
|
- tests/software/tabix/bgzip/**
|
|
|
|
tabix_tabix:
|
|
- software/tabix/tabix/**
|
|
- tests/software/tabix/tabix/**
|
|
|
|
tiddit_sv:
|
|
- software/tiddit/sv/**
|
|
- tests/software/tiddit/sv/**
|
|
|
|
trimgalore:
|
|
- software/trimgalore/**
|
|
- tests/software/trimgalore/**
|
|
|
|
ucsc_bedgraphtobigwig:
|
|
- software/ucsc/bedgraphtobigwig/**
|
|
- tests/software/ucsc/bedgraphtobigwig/**
|
|
|
|
untar:
|
|
- software/untar/**
|
|
- tests/software/untar/**
|
|
|
|
gatk4_variantfiltration:
|
|
- software/gatk4/variantfiltration/**
|
|
- tests/software/gatk4/variantfiltration/**
|