2021-03-22 17:16:04 +00:00
|
|
|
adapterremoval:
|
|
|
|
|
- software/adapterremoval/**
|
|
|
|
|
- tests/software/adapterremoval/**
|
|
|
|
|
|
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/**
|
|
|
|
|
|
2021-03-22 12:38:08 +00:00
|
|
|
bismark_align:
|
|
|
|
|
- software/bismark/align/**
|
2021-03-22 16:46:11 +00:00
|
|
|
- software/bismark/genomepreparation/**
|
2021-03-22 12:38:08 +00:00
|
|
|
- tests/software/bismark/align/**
|
|
|
|
|
|
2021-02-23 17:02:16 +00:00
|
|
|
bismark_deduplicate:
|
|
|
|
|
- software/bismark/deduplicate/**
|
|
|
|
|
- tests/software/bismark/deduplicate/**
|
|
|
|
|
|
2021-03-22 16:46:11 +00:00
|
|
|
bismark_genomepreparation:
|
|
|
|
|
- software/bismark/genomepreparation/**
|
|
|
|
|
- tests/software/bismark/genomepreparation/**
|
2021-02-18 09:56:36 +00:00
|
|
|
|
2021-03-22 16:46:11 +00:00
|
|
|
bismark_methylationextractor:
|
|
|
|
|
- software/bismark/methylationextractor/**
|
|
|
|
|
- software/bismark/genomepreparation/**
|
|
|
|
|
- tests/software/bismark/methylationextractor/**
|
2021-03-20 23:54:42 +00:00
|
|
|
|
2021-03-22 12:38:08 +00:00
|
|
|
bismark_report:
|
2021-03-22 16:46:11 +00:00
|
|
|
- software/bismark/genomepreparation/**
|
2021-03-22 12:38:08 +00:00
|
|
|
- software/bismark/align/**
|
|
|
|
|
- software/bismark/deduplicate/**
|
2021-03-22 16:46:11 +00:00
|
|
|
- software/bismark/methylationextractor/**
|
2021-03-22 12:38:08 +00:00
|
|
|
- software/bismark/report/**
|
|
|
|
|
- tests/software/bismark/report/**
|
|
|
|
|
|
2021-03-22 13:58:54 +00:00
|
|
|
bismark_summary:
|
2021-03-22 16:46:11 +00:00
|
|
|
- software/bismark/genomepreparation/**
|
2021-03-22 13:58:54 +00:00
|
|
|
- software/bismark/align/**
|
|
|
|
|
- software/bismark/deduplicate/**
|
2021-03-22 16:46:11 +00:00
|
|
|
- software/bismark/methylationextractor/**
|
2021-03-22 13:58:54 +00:00
|
|
|
- software/bismark/summary/**
|
|
|
|
|
- tests/software/bismark/summary/**
|
|
|
|
|
|
2021-03-22 17:16:04 +00:00
|
|
|
blast_blastn:
|
|
|
|
|
- software/blast/blastn/**
|
|
|
|
|
- tests/software/blast/blastn/**
|
|
|
|
|
|
2021-03-20 23:54:42 +00:00
|
|
|
blast_makeblastdb:
|
|
|
|
|
- software/blast/makeblastdb/**
|
|
|
|
|
- tests/software/blast/makeblastdb/**
|
|
|
|
|
|
2021-03-22 16:05:59 +00:00
|
|
|
bowtie2_align:
|
|
|
|
|
- software/bowtie2/align/**
|
|
|
|
|
- software/bowtie2/build/**
|
|
|
|
|
- tests/software/bowtie2/align/**
|
2021-02-09 14:47:53 +00:00
|
|
|
|
2021-03-22 16:05:59 +00:00
|
|
|
bowtie2_build:
|
|
|
|
|
- software/bowtie2/build/**
|
|
|
|
|
- tests/software/bowtie2/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
|
|
|
|
2021-03-22 16:05:59 +00:00
|
|
|
bowtie_build:
|
|
|
|
|
- software/bowtie/build/**
|
|
|
|
|
- tests/software/bowtie/build_test/**
|
2021-02-03 16:04:43 +00:00
|
|
|
|
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
|
|
|
|
2021-03-22 16:05:59 +00:00
|
|
|
picard_collectwgsmetrics:
|
|
|
|
|
- software/picard/collectwgsmetrics/**
|
|
|
|
|
- tests/software/picard/collectwgsmetrics/**
|
|
|
|
|
|
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:
|
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- software/salmon/index/**
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2021-02-03 16:04:43 +00:00
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- tests/software/salmon/index/**
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2021-02-02 21:27:45 +00:00
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salmon_quant:
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- software/salmon/quant/**
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2021-02-03 16:04:43 +00:00
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- tests/software/salmon/quant/**
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2021-02-02 21:27:45 +00:00
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2021-02-17 16:01:22 +00:00
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samtools_faidx:
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- software/samtools/faidx/**
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- tests/software/samtools/faidx/**
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2021-01-24 05:50:20 +00:00
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samtools_flagstat:
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- software/samtools/flagstat/**
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2021-02-03 16:04:43 +00:00
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- tests/software/samtools/flagstat/**
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2021-01-24 05:50:20 +00:00
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samtools_idxstats:
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- software/samtools/idxstats/**
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2021-02-03 16:04:43 +00:00
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- tests/software/samtools/idxstats/**
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2021-01-24 05:50:20 +00:00
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samtools_index:
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- software/samtools/index/**
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2021-02-03 16:04:43 +00:00
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- tests/software/samtools/index/**
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2021-01-24 05:50:20 +00:00
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2021-02-02 21:27:45 +00:00
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samtools_mpileup:
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- software/samtools/mpileup/**
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2021-02-03 16:04:43 +00:00
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- tests/software/samtools/mpileup/**
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2021-02-02 21:27:45 +00:00
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|
2021-03-22 12:48:23 +00:00
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samtools_merge:
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- software/samtools/merge/**
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- tests/software/samtools/merge/**
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2021-01-24 05:50:20 +00:00
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samtools_sort:
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- software/samtools/sort/**
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2021-02-03 16:04:43 +00:00
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- tests/software/samtools/sort/**
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2021-01-24 05:50:20 +00:00
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samtools_stats:
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- software/samtools/stats/**
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2021-02-03 16:04:43 +00:00
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- tests/software/samtools/stats/**
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2021-01-24 05:50:20 +00:00
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|
2021-02-02 21:27:45 +00:00
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samtools_view:
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- software/samtools/view/**
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2021-02-03 16:04:43 +00:00
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- tests/software/samtools/view/**
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2021-02-02 21:27:45 +00:00
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seacr_callpeak:
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- software/seacr/callpeak/**
|
2021-02-03 16:04:43 +00:00
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- tests/software/seacr/callpeak/**
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2021-02-02 21:27:45 +00:00
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|
2021-02-23 11:43:30 +00:00
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|
seqkit_split2:
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- software/seqkit/split2/**
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- tests/software/seqkit/split2/**
|
2021-02-24 09:29:13 +00:00
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|
2021-02-17 17:19:47 +00:00
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|
|
seqwish_induce:
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- software/seqwish/induce/**
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- tests/software/seqwish/induce/**
|
2021-02-23 11:43:30 +00:00
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|
|
|
2021-03-18 13:48:38 +00:00
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|
|
spades:
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- software/spades/**
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- tests/software/spades/**
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|
2021-02-02 21:27:45 +00:00
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|
star_align:
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- software/star/align/**
|
2021-02-03 16:04:43 +00:00
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|
- tests/software/star/align/**
|
2021-02-02 21:27:45 +00:00
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|
star_genomegenerate:
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|
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|
- software/star/genomegenerate/**
|
2021-02-03 16:04:43 +00:00
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|
- tests/software/star/genomegenerate/**
|
2021-02-02 21:27:45 +00:00
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|
|
|
2021-01-24 05:50:20 +00:00
|
|
|
stringtie:
|
2021-02-03 16:04:43 +00:00
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|
|
- software/stringtie/**
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|
- tests/software/stringtie/**
|
2021-01-24 05:50:20 +00:00
|
|
|
|
2021-02-16 18:11:36 +00:00
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|
|
tabix_bgzip:
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|
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|
|
- software/tabix/bgzip/**
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|
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|
- tests/software/tabix/bgzip/**
|
|
|
|
|
|
2021-02-19 09:56:04 +00:00
|
|
|
tabix_tabix:
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|
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- software/tabix/tabix/**
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|
- tests/software/tabix/tabix/**
|
|
|
|
|
|
2021-02-24 14:59:10 +00:00
|
|
|
tiddit_sv:
|
|
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|
|
- software/tiddit/sv/**
|
|
|
|
|
- tests/software/tiddit/sv/**
|
|
|
|
|
|
2021-01-24 05:50:20 +00:00
|
|
|
trimgalore:
|
|
|
|
|
- software/trimgalore/**
|
|
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|
|
- tests/software/trimgalore/**
|
|
|
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|
|
|
|
|
|
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
|
|
|
|
2021-03-22 17:14:24 +00:00
|
|
|
unicycler:
|
|
|
|
|
- software/unicycler/**
|
|
|
|
|
- tests/software/unicycler/**
|
|
|
|
|
|
2021-03-17 11:54:15 +00:00
|
|
|
untar:
|
|
|
|
|
- software/untar/**
|
|
|
|
|
- tests/software/untar/**
|
