mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
Update filters paths
This commit is contained in:
drpatelh
parent
ff23473e82
commit
743ba37d4b
23 changed files with 34 additions and 1002 deletions
65
.github/filters.yml
vendored
65
.github/filters.yml
vendored
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@ -1,28 +1,28 @@
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bowtie2_align:
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- software/bowtie2/align/**
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- software/bowtie2/build/**
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- tests/software/bowtie2/**
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bowtie2_build:
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- software/bowtie2/build/**
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- tests/software/bowtie2/**
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bowtie_align:
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bowtie_align:
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- software/bowtie/align/**
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- software/bowtie/align/**
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- software/bowtie/build/**
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- software/bowtie/build/**
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- tests/software/bowtie/**
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- tests/software/bowtie/align/**
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bowtie_build:
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bowtie_build:
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- software/bowtie/build/**
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- software/bowtie/build/**
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- tests/software/bowtie/**
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- tests/software/bowtie/build/**
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bowtie2_align:
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- software/bowtie2/align/**
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- software/bowtie2/build/**
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- tests/software/bowtie2/align/**
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bowtie2_build:
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- software/bowtie2/build/**
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- tests/software/bowtie2/build/**
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bwa_index:
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bwa_index:
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- software/bwa/index/**
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- software/bwa/index/**
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- tests/software/bwa/**
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- tests/software/bwa/index/**
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bwa_mem:
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bwa_mem:
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- software/bwa/mem/**
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- software/bwa/mem/**
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- tests/software/bwa/**
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- tests/software/bwa/mem/**
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cutadapt:
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cutadapt:
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- software/cutadapt/**
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- software/cutadapt/**
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@ -30,11 +30,11 @@ cutadapt:
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dsh_filterbed:
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dsh_filterbed:
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- software/dsh/filterbed/**
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- software/dsh/filterbed/**
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- tests/software/dsh/**
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- tests/software/dsh/filterbed/**
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dsh_splitbed:
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dsh_splitbed:
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- software/dsh/splitbed/**
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- software/dsh/splitbed/**
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- tests/software/dsh/**
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- tests/software/dsh/splitbed/**
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fastp:
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fastp:
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- software/fastp/**
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- software/fastp/**
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@ -58,19 +58,19 @@ pangolin:
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picard_collectmultiplemetrics:
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picard_collectmultiplemetrics:
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- software/picard/collectmultiplemetrics/**
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- software/picard/collectmultiplemetrics/**
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- tests/software/picard/**
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- tests/software/picard/collectmultiplemetrics/**
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picard_markduplicates:
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picard_markduplicates:
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- software/picard/markduplicates/**
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- software/picard/markduplicates/**
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- tests/software/picard/**
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- tests/software/picard/markduplicates/**
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picard_mergesamfiles:
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picard_mergesamfiles:
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- software/picard/mergesamfiles/**
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- software/picard/mergesamfiles/**
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- tests/software/picard/**
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- tests/software/picard/mergesamfiles/**
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preseq_lcextrap:
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preseq_lcextrap:
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- software/preseq/lcextrap/**
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- software/preseq/lcextrap/**
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- tests/software/preseq/**
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- tests/software/preseq/lcextrap/**
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quast:
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quast:
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- software/quast/**
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- software/quast/**
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@ -78,52 +78,51 @@ quast:
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salmon_index:
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salmon_index:
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- software/salmon/index/**
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- software/salmon/index/**
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- tests/software/salmon/**
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- tests/software/salmon/index/**
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salmon_quant:
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salmon_quant:
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- software/salmon/quant/**
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- software/salmon/quant/**
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- tests/software/salmon/**
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- tests/software/salmon/quant/**
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samtools_flagstat:
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samtools_flagstat:
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- software/samtools/flagstat/**
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- software/samtools/flagstat/**
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- tests/software/samtools/**
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- tests/software/samtools/flagstat/**
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samtools_idxstats:
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samtools_idxstats:
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- software/samtools/idxstats/**
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- software/samtools/idxstats/**
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- tests/software/samtools/**
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- tests/software/samtools/idxstats/**
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samtools_index:
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samtools_index:
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- software/samtools/index/**
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- software/samtools/index/**
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- tests/software/samtools/**
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- tests/software/samtools/index/**
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samtools_mpileup:
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samtools_mpileup:
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- software/samtools/mpileup/**
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- software/samtools/mpileup/**
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- tests/software/samtools/**
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- tests/software/samtools/mpileup/**
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samtools_sort:
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samtools_sort:
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- software/samtools/sort/**
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- software/samtools/sort/**
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- tests/software/samtools/**
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- tests/software/samtools/sort/**
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samtools_stats:
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samtools_stats:
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- software/samtools/stats/**
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- software/samtools/stats/**
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- tests/software/samtools/**
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- tests/software/samtools/stats/**
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samtools_view:
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samtools_view:
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- software/samtools/view/**
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- software/samtools/view/**
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- tests/software/samtools/**
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- tests/software/samtools/view/**
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seacr_callpeak:
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seacr_callpeak:
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- software/seacr/callpeak/**
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- software/seacr/callpeak/**
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- tests/software/seacr/**
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- tests/software/seacr/callpeak/**
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star_align:
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star_align:
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- software/star/align/**
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- software/star/align/**
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- tests/software/star/**
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- tests/software/star/align/**
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star_genomegenerate:
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star_genomegenerate:
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- software/star/genomegenerate/**
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- software/star/genomegenerate/**
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- tests/software/star/**
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- tests/software/star/genomegenerate/**
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stringtie:
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stringtie:
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- software/stringtie/**
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- software/stringtie/**
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@ -135,4 +134,4 @@ trimgalore:
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ucsc_bedgraphtobigwig:
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ucsc_bedgraphtobigwig:
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- software/ucsc/bedgraphtobigwig/**
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- software/ucsc/bedgraphtobigwig/**
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- tests/software/ucsc/**
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- tests/software/ucsc/bedgraphtobigwig/**
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@ -1,33 +0,0 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BOWTIE_BUILD } from '../../../software/bowtie/build/main.nf' addParams( options: [:] )
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include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf' addParams( options: [:] )
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workflow test_bowtie_build {
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fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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BOWTIE_BUILD ( fasta )
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}
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workflow test_bowtie_alignment_single_end {
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fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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BOWTIE_BUILD ( fasta )
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
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BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
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}
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workflow test_bowtie_alignment_paired_end {
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fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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BOWTIE_BUILD ( fasta )
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
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BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
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}
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@ -1,64 +0,0 @@
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- name: Run bowtie build
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command: nextflow run ./tests/software/bowtie -entry test_bowtie_build -c tests/config/nextflow.config
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tags:
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- bowtie
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- bowtie_build
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files:
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- path: output/bowtie/bowtie/NC_010473.1.ebwt
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md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
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- path: output/bowtie/bowtie/NC_010473.2.ebwt
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md5sum: bfd10c5319c6a0dbc540fd789254a5dd
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- path: output/bowtie/bowtie/NC_010473.3.ebwt
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md5sum: cd201e81724f3099131aec16ef2cc53b
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- path: output/bowtie/bowtie/NC_010473.4.ebwt
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md5sum: bbb9d6d21ad765d135f95290204e8433
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- path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
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md5sum: 44f719c2fe42e1f35d54e798775846d1
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- path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
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md5sum: f3c398bba5158f4039334a932d79c051
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- name: Run bowtie build and align single-end
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command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
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tags:
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- bowtie
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- bowtie_align
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files:
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- path: output/bowtie/bowtie/NC_010473.1.ebwt
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md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
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- path: output/bowtie/bowtie/NC_010473.2.ebwt
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md5sum: bfd10c5319c6a0dbc540fd789254a5dd
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- path: output/bowtie/bowtie/NC_010473.3.ebwt
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md5sum: cd201e81724f3099131aec16ef2cc53b
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- path: output/bowtie/bowtie/NC_010473.4.ebwt
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md5sum: bbb9d6d21ad765d135f95290204e8433
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- path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
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md5sum: 44f719c2fe42e1f35d54e798775846d1
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- path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
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md5sum: f3c398bba5158f4039334a932d79c051
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- path: output/bowtie/test.out
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md5sum: a81cb18024616415a6cec3108a36fccd
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- path: output/bowtie/test.bam
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md5sum: 9feed8a55d4b5e600dcc577768ef07fc
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- name: Run bowtie index and align paired-end
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command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config
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tags:
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- bowtie
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- bowtie_align
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files:
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- path: output/bowtie/bowtie/NC_010473.1.ebwt
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md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
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- path: output/bowtie/bowtie/NC_010473.2.ebwt
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md5sum: bfd10c5319c6a0dbc540fd789254a5dd
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- path: output/bowtie/bowtie/NC_010473.3.ebwt
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md5sum: cd201e81724f3099131aec16ef2cc53b
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- path: output/bowtie/bowtie/NC_010473.4.ebwt
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md5sum: bbb9d6d21ad765d135f95290204e8433
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- path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
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md5sum: 44f719c2fe42e1f35d54e798775846d1
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- path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
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md5sum: f3c398bba5158f4039334a932d79c051
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- path: output/bowtie/test.out
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md5sum: a23e9a2a76e949aeb3693bcfae41a615
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- path: output/bowtie/test.bam
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md5sum: cf6a6381aa504e8342638ff3b509721e
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@ -1,33 +0,0 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BOWTIE2_BUILD } from '../../../software/bowtie2/build/main.nf' addParams( options: [:] )
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include { BOWTIE2_ALIGN } from '../../../software/bowtie2/align/main.nf' addParams( options: [:] )
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workflow test_bowtie2_build {
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fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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BOWTIE2_BUILD ( fasta )
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}
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workflow test_bowtie2_alignment_single_end {
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fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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BOWTIE2_BUILD ( fasta )
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
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BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
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}
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workflow test_bowtie2_alignment_paired_end {
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fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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BOWTIE2_BUILD ( fasta )
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
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BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
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}
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@ -1,64 +0,0 @@
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- name: Run bowtie2 build
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command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_build -c tests/config/nextflow.config
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tags:
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- bowtie2
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- bowtie2_build
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files:
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- path: output/bowtie2/bowtie2/NC_010473.1.bt2
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md5sum: 4db22d92e72111a5fbf609b3d9a43015
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- path: output/bowtie2/bowtie2/NC_010473.2.bt2
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md5sum: f4429ec74ee0064732c4bb26718a3eb1
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- path: output/bowtie2/bowtie2/NC_010473.3.bt2
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md5sum: cd201e81724f3099131aec16ef2cc53b
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- path: output/bowtie2/bowtie2/NC_010473.4.bt2
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md5sum: bbb9d6d21ad765d135f95290204e8433
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- path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
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md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
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- path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
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md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
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- name: Run bowtie2 index and align single-end
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command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_alignment_single_end -c tests/config/nextflow.config
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tags:
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- bowtie2
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- bowtie2_align
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files:
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- path: output/bowtie2/bowtie2/NC_010473.1.bt2
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md5sum: 4db22d92e72111a5fbf609b3d9a43015
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- path: output/bowtie2/bowtie2/NC_010473.2.bt2
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md5sum: f4429ec74ee0064732c4bb26718a3eb1
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- path: output/bowtie2/bowtie2/NC_010473.3.bt2
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md5sum: cd201e81724f3099131aec16ef2cc53b
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- path: output/bowtie2/bowtie2/NC_010473.4.bt2
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md5sum: bbb9d6d21ad765d135f95290204e8433
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- path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
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md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
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- path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
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|
||||||
md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
|
|
||||||
- path: output/bowtie2/test.bowtie2.log
|
|
||||||
md5sum: 90041c264231be535042adb93a279356
|
|
||||||
- path: output/bowtie2/test.bam
|
|
||||||
md5sum: 906102f401d8234b6473790988fb09cf
|
|
||||||
|
|
||||||
- name: Run bowtie2 index and align paired-end
|
|
||||||
command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_alignment_paired_end -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- bowtie2
|
|
||||||
- bowtie2_align
|
|
||||||
files:
|
|
||||||
- path: output/bowtie2/bowtie2/NC_010473.1.bt2
|
|
||||||
md5sum: 4db22d92e72111a5fbf609b3d9a43015
|
|
||||||
- path: output/bowtie2/bowtie2/NC_010473.2.bt2
|
|
||||||
md5sum: f4429ec74ee0064732c4bb26718a3eb1
|
|
||||||
- path: output/bowtie2/bowtie2/NC_010473.3.bt2
|
|
||||||
md5sum: cd201e81724f3099131aec16ef2cc53b
|
|
||||||
- path: output/bowtie2/bowtie2/NC_010473.4.bt2
|
|
||||||
md5sum: bbb9d6d21ad765d135f95290204e8433
|
|
||||||
- path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
|
|
||||||
md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
|
|
||||||
- path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
|
|
||||||
md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
|
|
||||||
- path: output/bowtie2/test.bowtie2.log
|
|
||||||
md5sum: 9f9eb40b5f57e0f2d5c874f2c1b5cfd5
|
|
||||||
- path: output/bowtie2/test.bam
|
|
||||||
md5sum: 732a33cd9816b38ea9b919c25eeb78f8
|
|
||||||
|
|
@ -1,44 +0,0 @@
|
||||||
#!/usr/bin/env nextflow
|
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
|
||||||
|
|
||||||
include { BWA_INDEX } from '../../../software/bwa/index/main.nf' addParams( options: [:] )
|
|
||||||
include { BWA_MEM as BWA_MEM_SE } from '../../../software/bwa/mem/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
|
|
||||||
include { BWA_MEM as BWA_MEM_PE } from '../../../software/bwa/mem/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
|
|
||||||
|
|
||||||
workflow test_bwa_index {
|
|
||||||
BWA_INDEX ( file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) )
|
|
||||||
}
|
|
||||||
|
|
||||||
/*
|
|
||||||
* Test with single-end data
|
|
||||||
*/
|
|
||||||
workflow test_bwa_mem_single_end {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:true ], // meta map
|
|
||||||
[ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
|
|
||||||
|
|
||||||
BWA_MEM_SE (
|
|
||||||
input,
|
|
||||||
file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
|
|
||||||
file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
|
|
||||||
)
|
|
||||||
}
|
|
||||||
|
|
||||||
/*
|
|
||||||
* Test with paired-end data
|
|
||||||
*/
|
|
||||||
workflow test_bwa_mem_paired_end {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
[ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
|
|
||||||
file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
|
|
||||||
|
|
||||||
BWA_MEM_PE (
|
|
||||||
input,
|
|
||||||
file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
|
|
||||||
file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
|
|
||||||
)
|
|
||||||
}
|
|
||||||
|
|
@ -1,32 +0,0 @@
|
||||||
- name: Run bwa index
|
|
||||||
command: nextflow run ./tests/software/bwa -entry test_bwa_index -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- bwa
|
|
||||||
- bwa_index
|
|
||||||
files:
|
|
||||||
- path: output/bwa/NC_010473.fa.amb
|
|
||||||
md5sum: 942a990ae872f1c0b8d72dda2db405d5
|
|
||||||
- path: output/bwa/NC_010473.fa.bwt
|
|
||||||
md5sum: 7301b52e2ecb893d429a49fa692447ae
|
|
||||||
- path: output/bwa/NC_010473.fa.pac
|
|
||||||
md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad
|
|
||||||
- path: output/bwa/NC_010473.fa.sa
|
|
||||||
md5sum: a47dcc92e750e2f16fbd979b8ff9538e
|
|
||||||
|
|
||||||
- name: Run bwa mem single-end
|
|
||||||
command: nextflow run ./tests/software/bwa -entry test_bwa_mem_single_end -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- bwa
|
|
||||||
- bwa_mem
|
|
||||||
files:
|
|
||||||
- path: output/test_single_end/test.bam
|
|
||||||
md5sum: 3ee21210bac387e0335008146e4728bc
|
|
||||||
|
|
||||||
- name: Run bwa mem paired-end
|
|
||||||
command: nextflow run ./tests/software/bwa -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- bwa
|
|
||||||
- bwa_mem
|
|
||||||
files:
|
|
||||||
- path: output/test_paired_end/test.bam
|
|
||||||
md5sum: 510d8acc6448c07cdacce8e64ec0904c
|
|
||||||
|
|
@ -1,24 +0,0 @@
|
||||||
#!/usr/bin/env nextflow
|
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
|
||||||
|
|
||||||
include { DSH_FILTERBED } from '../../../software/dsh/filterbed/main.nf' addParams( options: [suffix: '.filtered', args: '--range chr1:0-1000'] )
|
|
||||||
include { DSH_SPLITBED } from '../../../software/dsh/splitbed/main.nf' addParams( options: [suffix: '.', args: '--records 2'] )
|
|
||||||
|
|
||||||
workflow test_dsh_filterbed {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'A' ], // meta map
|
|
||||||
[ file("${launchDir}/tests/data/bed/A.bed.gz", checkIfExists: true) ] ]
|
|
||||||
|
|
||||||
DSH_FILTERBED ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow test_dsh_splitbed {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'A' ], // meta map
|
|
||||||
[ file("${launchDir}/tests/data/bed/A.bed.gz", checkIfExists: true) ] ]
|
|
||||||
|
|
||||||
DSH_SPLITBED ( input )
|
|
||||||
}
|
|
||||||
|
|
@ -1,19 +0,0 @@
|
||||||
- name: Run dsh filterbed
|
|
||||||
command: nextflow run ./tests/software/dsh -entry test_dsh_filterbed -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- dsh
|
|
||||||
- dsh_filterbed
|
|
||||||
files:
|
|
||||||
- path: output/dsh/A.filtered.bed.gz
|
|
||||||
md5sum: 91cee4392d6034793f99f6c53891d866
|
|
||||||
|
|
||||||
- name: Run dsh splitbed
|
|
||||||
command: nextflow run ./tests/software/dsh -entry test_dsh_splitbed -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- dsh
|
|
||||||
- dsh_splitbed
|
|
||||||
files:
|
|
||||||
- path: output/dsh/A.0.bed.gz
|
|
||||||
md5sum: 619e51c435d0e7138ca41b660ed07e3a
|
|
||||||
- path: output/dsh/A.1.bed.gz
|
|
||||||
md5sum: 223bba025a0bb859de9a1bf385550a7e
|
|
||||||
|
|
@ -1,48 +0,0 @@
|
||||||
#!/usr/bin/env nextflow
|
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
|
||||||
|
|
||||||
include { PICARD_MERGESAMFILES } from '../../../software/picard/mergesamfiles/main.nf' addParams( options: [:] )
|
|
||||||
include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../software/picard/collectmultiplemetrics/main.nf' addParams( options: [:] )
|
|
||||||
include { PICARD_MARKDUPLICATES } from '../../../software/picard/markduplicates/main.nf' addParams( options: [:] )
|
|
||||||
|
|
||||||
workflow test_picard_mergesamfiles {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
[ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
|
|
||||||
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true), ] ]
|
|
||||||
|
|
||||||
PICARD_MERGESAMFILES ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
workflow test_picard_collectmultiplemetrics {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
|
|
||||||
|
|
||||||
PICARD_COLLECTMULTIPLEMETRICS (
|
|
||||||
input,
|
|
||||||
file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
|
|
||||||
)
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow test_picard_markduplicates {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
|
|
||||||
|
|
||||||
PICARD_MARKDUPLICATES ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow test_picard_markduplicates_not_sorted {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
|
|
||||||
|
|
||||||
PICARD_MARKDUPLICATES ( input )
|
|
||||||
}
|
|
||||||
|
|
@ -1,43 +0,0 @@
|
||||||
- name: Run picard mergesamfiles
|
|
||||||
command: nextflow run ./tests/software/picard -entry test_picard_mergesamfiles -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- picard
|
|
||||||
- picard_mergesamfiles
|
|
||||||
files:
|
|
||||||
- path: output/picard/test.bam
|
|
||||||
md5sum: a9c8a28d1aac362df5973ba2d9923f86
|
|
||||||
|
|
||||||
- name: Run picard collectmultiplemetrics
|
|
||||||
command: nextflow run ./tests/software/picard -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- picard
|
|
||||||
- picard_collectmultiplemetrics
|
|
||||||
files:
|
|
||||||
# These can't be md5'd consistently
|
|
||||||
- path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
|
|
||||||
- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
|
|
||||||
- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
|
|
||||||
- path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
|
|
||||||
- path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
|
|
||||||
- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
|
|
||||||
- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
|
|
||||||
- path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
|
|
||||||
- path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
|
|
||||||
|
|
||||||
- name: Run picard MarkDuplicates
|
|
||||||
command: nextflow run ./tests/software/picard -entry test_picard_markduplicates -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- picard
|
|
||||||
- picard_markduplicates
|
|
||||||
files:
|
|
||||||
- path: output/picard/test.MarkDuplicates.metrics.txt
|
|
||||||
- path: output/picard/test.bam
|
|
||||||
md5sum: 0ed0bfc94069380334ccd595f6d8207c
|
|
||||||
|
|
||||||
- name: Run picard MarkDuplicates without a sorted bam file so it fails
|
|
||||||
command: nextflow run ./tests/software/picard -entry test_picard_markduplicates_not_sorted -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- picard
|
|
||||||
- picard_markduplicates
|
|
||||||
- should fail
|
|
||||||
exit_code: 1
|
|
||||||
|
|
@ -1,32 +0,0 @@
|
||||||
#!/usr/bin/env nextflow
|
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
|
||||||
|
|
||||||
include { PRESEQ_LCEXTRAP as PRESEQ_LCEXTRAP_SE } from '../../../software/preseq/lcextrap/main.nf' addParams( options: [ publish_dir:'test_preseq_single_end' ] )
|
|
||||||
include { PRESEQ_LCEXTRAP as PRESEQ_LCEXTRAP_PE } from '../../../software/preseq/lcextrap/main.nf' addParams( options: [ publish_dir:'test_preseq_paired_end' ] )
|
|
||||||
|
|
||||||
/*
|
|
||||||
* Test with single-end data
|
|
||||||
*/
|
|
||||||
|
|
||||||
workflow test_preseq_single_end {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:true ], // meta map
|
|
||||||
[ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true), ] ]
|
|
||||||
PRESEQ_LCEXTRAP_SE ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
/*
|
|
||||||
* Test with paired-end data
|
|
||||||
*/
|
|
||||||
|
|
||||||
workflow test_preseq_paired_end {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
[ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true), ] ]
|
|
||||||
|
|
||||||
PRESEQ_LCEXTRAP_PE ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
@ -1,21 +0,0 @@
|
||||||
- name: Run preseq single-end lcextrap
|
|
||||||
command: nextflow run ./tests/software/preseq -entry test_preseq_single_end -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- preseq
|
|
||||||
- preseq_lcextrap
|
|
||||||
|
|
||||||
files:
|
|
||||||
- path: output/test_preseq_single_end/test.ccurve.txt
|
|
||||||
md5sum: 76ae04c8eaf19c94e3210bb69da38498
|
|
||||||
- path: output/test_preseq_single_end/test.command.log
|
|
||||||
|
|
||||||
- name: Run preseq paired-end lcextrap
|
|
||||||
command: nextflow run ./tests/software/preseq -entry test_preseq_paired_end -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- preseq
|
|
||||||
- preseq_lcextrap
|
|
||||||
|
|
||||||
files:
|
|
||||||
- path: output/test_preseq_paired_end/test.ccurve.txt
|
|
||||||
md5sum: 2836d2fabd2213f097fd7063db550276
|
|
||||||
- path: output/test_preseq_paired_end/test.command.log
|
|
||||||
|
|
@ -1,35 +0,0 @@
|
||||||
#!/usr/bin/env nextflow
|
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
|
||||||
def quant_options = [args: '--minAssignedFrags 1']
|
|
||||||
include { SALMON_INDEX } from '../../../software/salmon/index/main.nf' addParams( options: [:] )
|
|
||||||
include { SALMON_QUANT } from '../../../software/salmon/quant/main.nf' addParams( options: quant_options )
|
|
||||||
|
|
||||||
workflow test_salmon_index {
|
|
||||||
genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
|
|
||||||
transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
|
|
||||||
SALMON_INDEX ( genome_fasta, transcript_fasta )
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow test_salmon_quant_pe {
|
|
||||||
genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
|
|
||||||
transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
|
|
||||||
gtf = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
[ file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz", checkIfExists: true),
|
|
||||||
file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_2.fastq.gz", checkIfExists: true) ] ]
|
|
||||||
|
|
||||||
SALMON_INDEX ( genome_fasta, transcript_fasta )
|
|
||||||
SALMON_QUANT( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false)
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow test_salmon_quant_se {
|
|
||||||
genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
|
|
||||||
transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
|
|
||||||
gtf = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
|
|
||||||
input = [ [ id:'test', single_end:true ], // meta map
|
|
||||||
file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz", checkIfExists: true) ]
|
|
||||||
|
|
||||||
SALMON_INDEX ( genome_fasta, transcript_fasta )
|
|
||||||
SALMON_QUANT( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false)
|
|
||||||
}
|
|
||||||
|
|
@ -1,139 +0,0 @@
|
||||||
- name: salmon index
|
|
||||||
command: nextflow run ./tests/software/salmon -entry test_salmon_index -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- salmon
|
|
||||||
- salmon_index
|
|
||||||
files:
|
|
||||||
- path: ./output/salmon/salmon/info.json
|
|
||||||
md5sum: 61ff4d3471134c280668355ddd39e99f
|
|
||||||
- path: ./output/salmon/salmon/mphf.bin
|
|
||||||
md5sum: 53669a47610e33e031faafd32703b714
|
|
||||||
- path: ./output/salmon/salmon/complete_ref_lens.bin
|
|
||||||
md5sum: f57562f1fca3ae7b133f895ae13c3d08
|
|
||||||
- path: ./output/salmon/salmon/ref_indexing.log
|
|
||||||
- path: ./output/salmon/salmon/versionInfo.json
|
|
||||||
md5sum: 204865f645102587c4953fccb256797c
|
|
||||||
- path: ./output/salmon/salmon/seq.bin
|
|
||||||
- path: ./output/salmon/salmon/pre_indexing.log
|
|
||||||
- path: ./output/salmon/salmon/rank.bin
|
|
||||||
md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
|
|
||||||
- path: ./output/salmon/salmon/reflengths.bin
|
|
||||||
md5sum: f57562f1fca3ae7b133f895ae13c3d08
|
|
||||||
- path: ./output/salmon/salmon/ctable.bin
|
|
||||||
- path: ./output/salmon/salmon/ctg_offsets.bin
|
|
||||||
md5sum: 27a76542337df436436e66017f66dd25
|
|
||||||
- path: ./output/salmon/salmon/pos.bin
|
|
||||||
- path: ./output/salmon/salmon/duplicate_clusters.tsv
|
|
||||||
md5sum: 51b5292e3a874119c0e1aa566e95d70c
|
|
||||||
- path: ./output/salmon/salmon/refAccumLengths.bin
|
|
||||||
md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
|
|
||||||
- path: ./output/salmon/salmon/refseq.bin
|
|
||||||
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
|
|
||||||
|
|
||||||
- name: salmon quant paired end
|
|
||||||
command: nextflow run ./tests/software/salmon -entry test_salmon_quant_pe -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- salmon
|
|
||||||
- salmon_quant
|
|
||||||
- salmon_quant_pe
|
|
||||||
files:
|
|
||||||
- path: ./output/salmon/salmon/pos.bin
|
|
||||||
- path: ./output/salmon/salmon/versionInfo.json
|
|
||||||
md5sum: 204865f645102587c4953fccb256797c
|
|
||||||
- path: ./output/salmon/salmon/complete_ref_lens.bin
|
|
||||||
md5sum: f57562f1fca3ae7b133f895ae13c3d08
|
|
||||||
- path: ./output/salmon/test/lib_format_counts.json
|
|
||||||
md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea
|
|
||||||
- path: ./output/salmon/test/aux_info/expected_bias.gz
|
|
||||||
md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
|
|
||||||
- path: ./output/salmon/test/libParams/flenDist.txt
|
|
||||||
md5sum: f90c7256c9b18d4131f4d4ecb69d0f55
|
|
||||||
- path: ./output/salmon/salmon/ref_indexing.log
|
|
||||||
- path: ./output/salmon/test/aux_info/observed_bias_3p.gz
|
|
||||||
md5sum: ef13c06a538e9c34ca9f84212c82f44e
|
|
||||||
- path: ./output/salmon/salmon/ctable.bin
|
|
||||||
- path: ./output/salmon/test/aux_info/meta_info.json
|
|
||||||
- path: ./output/salmon/test/aux_info/fld.gz
|
|
||||||
- path: ./output/salmon/salmon/refseq.bin
|
|
||||||
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
|
|
||||||
- path: ./output/salmon/salmon/info.json
|
|
||||||
md5sum: 61ff4d3471134c280668355ddd39e99f
|
|
||||||
- path: ./output/salmon/salmon/seq.bin
|
|
||||||
- path: ./output/salmon/test/cmd_info.json
|
|
||||||
md5sum: 007676e4d79de0809a03e0ea045ed4a1
|
|
||||||
- path: ./output/salmon/test/aux_info/observed_bias.gz
|
|
||||||
md5sum: ef13c06a538e9c34ca9f84212c82f44e
|
|
||||||
- path: ./output/salmon/salmon/duplicate_clusters.tsv
|
|
||||||
md5sum: 51b5292e3a874119c0e1aa566e95d70c
|
|
||||||
- path: ./output/salmon/test/quant.genes.sf
|
|
||||||
md5sum: eb3e7b44801a0b3af07c25963927e20d
|
|
||||||
- path: ./output/salmon/salmon/rank.bin
|
|
||||||
md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
|
|
||||||
- path: ./output/salmon/salmon/mphf.bin
|
|
||||||
md5sum: 53669a47610e33e031faafd32703b714
|
|
||||||
- path: ./output/salmon/test/aux_info/ambig_info.tsv
|
|
||||||
md5sum: 950001575c24fb6bc2c7a6848043b126
|
|
||||||
- path: ./output/salmon/test/logs/salmon_quant.log
|
|
||||||
- path: ./output/salmon/salmon/pre_indexing.log
|
|
||||||
- path: ./output/salmon/salmon/refAccumLengths.bin
|
|
||||||
md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
|
|
||||||
- path: ./output/salmon/test/quant.sf
|
|
||||||
md5sum: addb78e233f248b8f62cae3e217bf689
|
|
||||||
- path: ./output/salmon/salmon/reflengths.bin
|
|
||||||
md5sum: f57562f1fca3ae7b133f895ae13c3d08
|
|
||||||
- path: ./output/salmon/salmon/ctg_offsets.bin
|
|
||||||
md5sum: 27a76542337df436436e66017f66dd25
|
|
||||||
|
|
||||||
- name: salmon quant single-end
|
|
||||||
command: nextflow run ./tests/software/salmon -entry test_salmon_quant_se -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- salmon
|
|
||||||
- salmon_quant
|
|
||||||
- salmon_quant_se
|
|
||||||
files:
|
|
||||||
- path: ./output/salmon/salmon/versionInfo.json
|
|
||||||
md5sum: 204865f645102587c4953fccb256797c
|
|
||||||
- path: ./output/salmon/salmon/ctg_offsets.bin
|
|
||||||
md5sum: 27a76542337df436436e66017f66dd25
|
|
||||||
- path: ./output/salmon/test/aux_info/meta_info.json
|
|
||||||
- path: ./output/salmon/salmon/duplicate_clusters.tsv
|
|
||||||
md5sum: 51b5292e3a874119c0e1aa566e95d70c
|
|
||||||
- path: ./output/salmon/salmon/pre_indexing.log
|
|
||||||
- path: ./output/salmon/salmon/rank.bin
|
|
||||||
md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
|
|
||||||
- path: ./output/salmon/test/aux_info/observed_bias.gz
|
|
||||||
md5sum: ef13c06a538e9c34ca9f84212c82f44e
|
|
||||||
- path: ./output/salmon/test/aux_info/expected_bias.gz
|
|
||||||
md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
|
|
||||||
- path: ./output/salmon/test/aux_info/fld.gz
|
|
||||||
- path: ./output/salmon/salmon/ctable.bin
|
|
||||||
- path: ./output/salmon/salmon/info.json
|
|
||||||
md5sum: 61ff4d3471134c280668355ddd39e99f
|
|
||||||
- path: ./output/salmon/test/quant.genes.sf
|
|
||||||
md5sum: 5b39785b4d8da533c08ee4a6c8bc1211
|
|
||||||
- path: ./output/salmon/salmon/refseq.bin
|
|
||||||
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
|
|
||||||
- path: ./output/salmon/salmon/complete_ref_lens.bin
|
|
||||||
md5sum: f57562f1fca3ae7b133f895ae13c3d08
|
|
||||||
- path: ./output/salmon/test/logs/salmon_quant.log
|
|
||||||
- path: ./output/salmon/test/libParams/flenDist.txt
|
|
||||||
md5sum: 2de170bdc9f6fd237d286429b292bb28
|
|
||||||
- path: ./output/salmon/salmon/ref_indexing.log
|
|
||||||
- path: ./output/salmon/salmon/refAccumLengths.bin
|
|
||||||
md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
|
|
||||||
- path: ./output/salmon/salmon/seq.bin
|
|
||||||
- path: ./output/salmon/salmon/mphf.bin
|
|
||||||
md5sum: 53669a47610e33e031faafd32703b714
|
|
||||||
- path: ./output/salmon/test/aux_info/observed_bias_3p.gz
|
|
||||||
md5sum: ef13c06a538e9c34ca9f84212c82f44e
|
|
||||||
- path: ./output/salmon/test/lib_format_counts.json
|
|
||||||
md5sum: aca0a40187eb407b1b8fc85c01284583
|
|
||||||
- path: ./output/salmon/salmon/reflengths.bin
|
|
||||||
md5sum: f57562f1fca3ae7b133f895ae13c3d08
|
|
||||||
- path: ./output/salmon/salmon/pos.bin
|
|
||||||
- path: ./output/salmon/test/cmd_info.json
|
|
||||||
md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a
|
|
||||||
- path: ./output/salmon/test/aux_info/ambig_info.tsv
|
|
||||||
md5sum: c3306d26186ffe018ad4f19d52256180
|
|
||||||
- path: ./output/salmon/test/quant.sf
|
|
||||||
md5sum: b08095ac70f89efc3146cdf488d0eb73
|
|
||||||
|
|
@ -1,80 +0,0 @@
|
||||||
#!/usr/bin/env nextflow
|
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
|
||||||
|
|
||||||
include { SAMTOOLS_FLAGSTAT } from '../../../software/samtools/flagstat/main.nf' addParams( options: [:] )
|
|
||||||
include { SAMTOOLS_IDXSTATS } from '../../../software/samtools/idxstats/main.nf' addParams( options: [:] )
|
|
||||||
include { SAMTOOLS_INDEX } from '../../../software/samtools/index/main.nf' addParams( options: [:] )
|
|
||||||
include { SAMTOOLS_SORT } from '../../../software/samtools/sort/main.nf' addParams( options: [:] )
|
|
||||||
include { SAMTOOLS_STATS } from '../../../software/samtools/stats/main.nf' addParams( options: [:] )
|
|
||||||
include { SAMTOOLS_VIEW } from '../../../software/samtools/view/main.nf' addParams( options: [:] )
|
|
||||||
include { SAMTOOLS_MPILEUP } from '../../../software/samtools/mpileup/main.nf' addParams( options: [:] )
|
|
||||||
|
|
||||||
workflow test_samtools_flagstat {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
|
|
||||||
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
|
|
||||||
|
|
||||||
SAMTOOLS_FLAGSTAT ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow test_samtools_idxstats {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
|
|
||||||
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
|
|
||||||
|
|
||||||
SAMTOOLS_IDXSTATS ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow test_samtools_index {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
|
|
||||||
|
|
||||||
SAMTOOLS_INDEX ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
// FIXME Why is this passing it an already sorted bam?
|
|
||||||
workflow test_samtools_sort {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
|
|
||||||
|
|
||||||
SAMTOOLS_SORT ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow test_samtools_stats {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
|
|
||||||
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
|
|
||||||
|
|
||||||
SAMTOOLS_STATS ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow test_samtools_view {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
|
|
||||||
|
|
||||||
SAMTOOLS_VIEW ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow test_samtools_mpileup {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
def fasta = []
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
|
|
||||||
fasta = [ file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) ]
|
|
||||||
|
|
||||||
SAMTOOLS_MPILEUP ( input, fasta )
|
|
||||||
}
|
|
||||||
|
|
@ -1,62 +0,0 @@
|
||||||
- name: Run samtools flagstat test workflow
|
|
||||||
command: nextflow run ./tests/software/samtools/ -entry test_samtools_flagstat -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- samtools
|
|
||||||
- samtools_flagstat
|
|
||||||
files:
|
|
||||||
- path: output/samtools/test.paired_end.sorted.bam.flagstat
|
|
||||||
md5sum: 80590621c74f5ee43ada20d010a3837f
|
|
||||||
|
|
||||||
- name: Run samtools idxstats test workflow
|
|
||||||
command: nextflow run ./tests/software/samtools/ -entry test_samtools_idxstats -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- samtools
|
|
||||||
- samtools_idxstats
|
|
||||||
files:
|
|
||||||
- path: output/samtools/test.paired_end.sorted.bam.idxstats
|
|
||||||
md5sum: 3bee8b7d55e412da2b3816c5a18d60d5
|
|
||||||
|
|
||||||
- name: Run samtools index test workflow
|
|
||||||
command: nextflow run ./tests/software/samtools/ -entry test_samtools_index -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- samtools
|
|
||||||
- samtools_index
|
|
||||||
files:
|
|
||||||
- path: output/samtools/test.paired_end.sorted.bam.bai
|
|
||||||
md5sum: 67338c2995eae82c849830ca55aa7bd1
|
|
||||||
|
|
||||||
- name: Run samtools sort test workflow
|
|
||||||
command: nextflow run ./tests/software/samtools/ -entry test_samtools_sort -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- samtools
|
|
||||||
- samtools_sort
|
|
||||||
files:
|
|
||||||
- path: output/samtools/test.bam
|
|
||||||
md5sum: a41bfadacd2eeef1d31e05c135cc4f4e
|
|
||||||
|
|
||||||
- name: Run samtools stats test workflow
|
|
||||||
command: nextflow run ./tests/software/samtools/ -entry test_samtools_stats -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- samtools
|
|
||||||
- samtools_stats
|
|
||||||
files:
|
|
||||||
- path: output/samtools/test.paired_end.sorted.bam.stats
|
|
||||||
md5sum: 06c183864d6e47ab89b0650cae831a93
|
|
||||||
|
|
||||||
- name: Run samtools view test workflow
|
|
||||||
command: nextflow run ./tests/software/samtools/ -entry test_samtools_view -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- samtools
|
|
||||||
- samtools_view
|
|
||||||
files:
|
|
||||||
- path: output/samtools/test.bam
|
|
||||||
md5sum: 7ea2c325e2249ed7ef44e1d9fdc4f8ff
|
|
||||||
|
|
||||||
- name: Run samtools mpileup test workflow
|
|
||||||
command: nextflow run ./tests/software/samtools/ -entry test_samtools_mpileup -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- samtools
|
|
||||||
- samtools_mpileup
|
|
||||||
files:
|
|
||||||
- path: output/samtools/test.mpileup
|
|
||||||
md5sum: 95c2646fa7bd535207722008c581c81d
|
|
||||||
|
|
@ -1,20 +0,0 @@
|
||||||
#!/usr/bin/env nextflow
|
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
|
||||||
|
|
||||||
include { SEACR_CALLPEAK } from '../../../software/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] )
|
|
||||||
|
|
||||||
workflow test_seacr_callpeak {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [[ id:'test_1'],
|
|
||||||
file("${launchDir}/tests/data/bedgraph/K27me3_1_to_chr20.bedgraph", checkIfExists: true),
|
|
||||||
file("${launchDir}/tests/data/bedgraph/IgG_1_to_chr20.bedgraph", checkIfExists: true) ]
|
|
||||||
|
|
||||||
SEACR_CALLPEAK ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
// For local testing
|
|
||||||
workflow {
|
|
||||||
test_seacr_callpeak()
|
|
||||||
}
|
|
||||||
|
|
@ -1,8 +0,0 @@
|
||||||
- name: Run seacr call peak test workflow
|
|
||||||
command: nextflow run ./tests/software/seacr/ -entry test_seacr_callpeak -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- seacr
|
|
||||||
- seacr_callpeak
|
|
||||||
files:
|
|
||||||
- path: output/seacr/test_1.stringent.bed
|
|
||||||
md5sum: 3ac70475669eb6a7b8ca89e19a08a28e
|
|
||||||
|
|
@ -1,36 +0,0 @@
|
||||||
#!/usr/bin/env nextflow
|
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
|
||||||
def options_align = [args: '--readFilesCommand zcat']
|
|
||||||
def options_gg = [args: '--genomeSAindexNbases 9']
|
|
||||||
include { STAR_ALIGN } from '../../../software/star/align/main.nf' addParams( options: options_align )
|
|
||||||
include { STAR_GENOMEGENERATE } from '../../../software/star/genomegenerate/main.nf' addParams( options: options_gg )
|
|
||||||
|
|
||||||
workflow test_star_genomegenerate {
|
|
||||||
fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
|
|
||||||
gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
|
|
||||||
STAR_GENOMEGENERATE ( fasta, gtf )
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow test_star_alignment_single_end {
|
|
||||||
fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
|
|
||||||
gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
|
|
||||||
STAR_GENOMEGENERATE ( fasta, gtf )
|
|
||||||
|
|
||||||
input = [ [ id:'test', single_end:true ], // meta map
|
|
||||||
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
|
|
||||||
|
|
||||||
STAR_ALIGN( input, STAR_GENOMEGENERATE.out.index, gtf)
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow test_star_alignment_paired_end {
|
|
||||||
fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
|
|
||||||
gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
|
|
||||||
STAR_GENOMEGENERATE ( fasta, gtf )
|
|
||||||
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
|
|
||||||
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
|
|
||||||
|
|
||||||
STAR_ALIGN( input, STAR_GENOMEGENERATE.out.index, gtf)
|
|
||||||
}
|
|
||||||
|
|
@ -1,108 +0,0 @@
|
||||||
- name: Run star genomegenerate
|
|
||||||
command: nextflow run ./tests/software/star -entry test_star_genomegenerate -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- star
|
|
||||||
- star_genomegenerate
|
|
||||||
files:
|
|
||||||
- path: output/star/star/Genome
|
|
||||||
md5sum: 323c992bac354f93073ce0fc43f222f8
|
|
||||||
- path: output/star/star/SA
|
|
||||||
md5sum: 3e70e4fc6d031e1915bb510727f2c559
|
|
||||||
- path: output/star/star/SAindex
|
|
||||||
md5sum: a94198b95a245d4f64af2a7133b6ec7b
|
|
||||||
- path: output/star/star/chrLength.txt
|
|
||||||
md5sum: f2bea3725fe1c01420c57fb73bdeb31a
|
|
||||||
- path: output/star/star/chrNameLength.txt
|
|
||||||
md5sum: c7ceb0a8827b2ea91c386933bee48742
|
|
||||||
- path: output/star/star/chrStart.txt
|
|
||||||
md5sum: faf5c55020c99eceeef3e34188ac0d2f
|
|
||||||
- path: output/star/star/exonGeTrInfo.tab
|
|
||||||
md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6
|
|
||||||
- path: output/star/star/exonInfo.tab
|
|
||||||
md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343
|
|
||||||
- path: output/star/star/genomeParameters.txt
|
|
||||||
md5sum: ed47b8b034cae2fefcdb39321aea47cd
|
|
||||||
- path: output/star/star/sjdbInfo.txt
|
|
||||||
md5sum: 1082ab459363b3f2f7aabcef0979c1ed
|
|
||||||
- path: output/star/star/sjdbList.fromGTF.out.tab
|
|
||||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
|
||||||
- path: output/star/star/sjdbList.out.tab
|
|
||||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
|
||||||
- path: output/star/star/transcriptInfo.tab
|
|
||||||
md5sum: 8fbe69abbbef4f89da3854873984dbac
|
|
||||||
|
|
||||||
- name: Run star single-end alignment
|
|
||||||
command: nextflow run ./tests/software/star -entry test_star_alignment_single_end -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- star
|
|
||||||
- star_align
|
|
||||||
- star_alignment_single_end
|
|
||||||
files:
|
|
||||||
- path: output/star/star/Genome
|
|
||||||
md5sum: 323c992bac354f93073ce0fc43f222f8
|
|
||||||
- path: output/star/star/SA
|
|
||||||
md5sum: 3e70e4fc6d031e1915bb510727f2c559
|
|
||||||
- path: output/star/star/SAindex
|
|
||||||
md5sum: a94198b95a245d4f64af2a7133b6ec7b
|
|
||||||
- path: output/star/star/chrLength.txt
|
|
||||||
md5sum: f2bea3725fe1c01420c57fb73bdeb31a
|
|
||||||
- path: output/star/star/chrNameLength.txt
|
|
||||||
md5sum: c7ceb0a8827b2ea91c386933bee48742
|
|
||||||
- path: output/star/star/chrStart.txt
|
|
||||||
md5sum: faf5c55020c99eceeef3e34188ac0d2f
|
|
||||||
- path: output/star/star/exonGeTrInfo.tab
|
|
||||||
md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6
|
|
||||||
- path: output/star/star/exonInfo.tab
|
|
||||||
md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343
|
|
||||||
- path: output/star/star/genomeParameters.txt
|
|
||||||
md5sum: ed47b8b034cae2fefcdb39321aea47cd
|
|
||||||
- path: output/star/star/sjdbInfo.txt
|
|
||||||
md5sum: 1082ab459363b3f2f7aabcef0979c1ed
|
|
||||||
- path: output/star/star/sjdbList.fromGTF.out.tab
|
|
||||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
|
||||||
- path: output/star/star/sjdbList.out.tab
|
|
||||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
|
||||||
- path: output/star/star/transcriptInfo.tab
|
|
||||||
md5sum: 8fbe69abbbef4f89da3854873984dbac
|
|
||||||
- path: output/star/test.Aligned.out.bam
|
|
||||||
md5sum: d7f59c1728482e76a18e3f6eb9c66c25
|
|
||||||
- path: output/star/test.SJ.out.tab
|
|
||||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
|
||||||
|
|
||||||
- name: Run star paired-end alignment
|
|
||||||
command: nextflow run ./tests/software/star -entry test_star_alignment_paired_end -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- star
|
|
||||||
- star_align
|
|
||||||
- star_alignment_paired_end
|
|
||||||
files:
|
|
||||||
- path: output/star/star/Genome
|
|
||||||
md5sum: 323c992bac354f93073ce0fc43f222f8
|
|
||||||
- path: output/star/star/SA
|
|
||||||
md5sum: 3e70e4fc6d031e1915bb510727f2c559
|
|
||||||
- path: output/star/star/SAindex
|
|
||||||
md5sum: a94198b95a245d4f64af2a7133b6ec7b
|
|
||||||
- path: output/star/star/chrLength.txt
|
|
||||||
md5sum: f2bea3725fe1c01420c57fb73bdeb31a
|
|
||||||
- path: output/star/star/chrNameLength.txt
|
|
||||||
md5sum: c7ceb0a8827b2ea91c386933bee48742
|
|
||||||
- path: output/star/star/chrStart.txt
|
|
||||||
md5sum: faf5c55020c99eceeef3e34188ac0d2f
|
|
||||||
- path: output/star/star/exonGeTrInfo.tab
|
|
||||||
md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6
|
|
||||||
- path: output/star/star/exonInfo.tab
|
|
||||||
md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343
|
|
||||||
- path: output/star/star/genomeParameters.txt
|
|
||||||
md5sum: ed47b8b034cae2fefcdb39321aea47cd
|
|
||||||
- path: output/star/star/sjdbInfo.txt
|
|
||||||
md5sum: 1082ab459363b3f2f7aabcef0979c1ed
|
|
||||||
- path: output/star/star/sjdbList.fromGTF.out.tab
|
|
||||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
|
||||||
- path: output/star/star/sjdbList.out.tab
|
|
||||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
|
||||||
- path: output/star/star/transcriptInfo.tab
|
|
||||||
md5sum: 8fbe69abbbef4f89da3854873984dbac
|
|
||||||
- path: output/star/test.Aligned.out.bam
|
|
||||||
md5sum: 5c52bcaa15e86914ad6b895638235166
|
|
||||||
- path: output/star/test.SJ.out.tab
|
|
||||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
|
||||||
|
|
@ -1,15 +0,0 @@
|
||||||
#!/usr/bin/env nextflow
|
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
|
||||||
|
|
||||||
include { UCSC_BEDGRAPHTOBIGWIG } from '../../../software/ucsc/bedgraphtobigwig/main.nf' addParams( options: [:] )
|
|
||||||
|
|
||||||
workflow test_ucsc_bedgraphtobigwig {
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test' ], // meta map
|
|
||||||
[ file('https://raw.githubusercontent.com/igvteam/igv.js/master/test/data/wig/bedgraph-example-uscs.bedgraph', checkIfExists: true) ] ]
|
|
||||||
UCSC_BEDGRAPHTOBIGWIG (
|
|
||||||
input,
|
|
||||||
file('https://raw.githubusercontent.com/igvteam/igv.js/master/test/data/wig/chrom.sizes', checkIfExists: true)
|
|
||||||
)
|
|
||||||
}
|
|
||||||
|
|
@ -1,7 +0,0 @@
|
||||||
- name: Run bedgraphtobigwig test workflow
|
|
||||||
command: nextflow run ./tests/software/ucsc/ -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- ucsc_bedgraphtobigwig
|
|
||||||
files:
|
|
||||||
- path: output/ucsc/test.bigWig
|
|
||||||
md5sum: 5346de25b01ecbff91b63178b3bfbeec
|
|
||||||
Loading…
Reference in a new issue