millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2025-01-18 02:46:13 -05:00
Code Issues Releases Packages Activity

test(bedtools): Remove old style tests

Browse source 
AKA how the tests were done last week.
This commit is contained in:
Edmund Miller 2021-02-05 21:54:57 -06:00 • committed by sruthipsuresh
parent 7d52907d1c
commit 2b0d51ca9c
2 changed files with 0 additions and 120 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

64
tests/software/bedtools/main.nf
View file

@ -1,64 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BEDTOOLS_COMPLEMENT } from '../../../software/bedtools/complement/main.nf' addParams( options: [:] )
include { BEDTOOLS_GENOMECOV } from '../../../software/bedtools/genomecov/main.nf' addParams( options: [:] )
include { BEDTOOLS_INTERSECT } from '../../../software/bedtools/intersect/main.nf' addParams( options: [:] )
include { BEDTOOLS_MERGE } from '../../../software/bedtools/merge/main.nf' addParams( options: [:] )
include { BEDTOOLS_SLOP} from '../../../software/bedtools/slop/main.nf' addParams( options: [args: '-l 15 -r 30'] )
include { BEDTOOLS_SORT } from '../../../software/bedtools/sort/main.nf' addParams( options: [:] )
workflow test_bedtools_complement {
def input = []
input = [ [ id:'test'],
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
BEDTOOLS_COMPLEMENT( input )
}
workflow test_bedtools_genomecov {
def input = []
input = [ [ id:'test'],
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
BEDTOOLS_GENOMECOV( input )
}
workflow test_bedtools_intersect {
def input = []
input = [ [ id:'test'],
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
file("${launchDir}/tests/data/bed/B.bed", checkIfExists: true) ] //metamap
BEDTOOLS_INTERSECT( input )
}
workflow test_bedtools_merge {
def input = []
input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
BEDTOOLS_MERGE(input)
}
workflow test_bedtools_slop {
def input = []
input = [ [ id:'test'],
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
BEDTOOLS_SLOP ( input )
}
workflow test_bedtools_sort {
def input = []
input = [ [ id:'test'],
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
BEDTOOLS_SORT( input )
}

56
tests/software/bedtools/test.yml
View file

@ -1,56 +0,0 @@
- name: Run bedtools complement test workflow
command: nextflow run ./tests/software/bedtools/ -profile docker -entry test_bedtools_complement -c tests/config/nextflow.config
tags:
- bedtools
- bedtools_complement
files:
- path: output/bedtools/test.complement.bed
md5sum: 55a43973abb1a08ac57290ff44f6c502
- name: Run bedtools genomecov test workflow
command: nextflow run ./tests/software/bedtools/ -profile docker -entry test_bedtools_genomecov -c tests/config/nextflow.config
tags:
- bedtools
- bedtools_genomecov
files:
- path: output/bedtools/test.bed
md5sum: 8c8238ca3cdac7a0e650ade95ee941f4
- name: Run bedtools intersect test workflow
command: nextflow run ./tests/software/bedtools/ -profile docker -entry test_bedtools_intersect -c tests/config/nextflow.config
tags:
- bedtools
- bedtools_intersect
files:
- path: output/bedtools/test.intersect.bed
md5sum: cc1bb317886e7df0a942b56f8a320d9c
- name: Run bedtools sort test workflow
command: nextflow run ./tests/software/bedtools/ -profile docker -entry test_bedtools_sort -c tests/config/nextflow.config
tags:
- bedtools
- bedtools_sort
files:
- path: output/bedtools/test.sort.bed
md5sum: 4279202e33fcce3d19f420f1b27fddee
# TODO link to sort module
- name: Run bedtools merge test workflow
command: nextflow run ./tests/software/bedtools/ -profile docker -entry test_bedtools_merge -c tests/config/nextflow.config
tags:
- bedtools
- bedtools_merge
files:
- path: output/bedtools/test.merged.bed
md5sum: 13e5a3b254fac35fe0da0c92cbaf1761
- name: Run bedtools slop test workflow (symmetrical)
command: nextflow run ./tests/software/bedtools/ -profile docker -entry test_bedtools_slop -c tests/config/nextflow.config
tags:
- bedtools
- bedtools_slop
files:
- path: output/bedtools/test.slop.bed
md5sum: 4279202e33fcce3d19f420f1b27fddee