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Corrected workflows and ran editor config

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This commit is contained in:
sruthipsuresh 2021-01-08 12:21:55 -06:00
parent 672f94f2af
commit 32564137fd
8 changed files with 11 additions and 14 deletions
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0
.github/workflows/bedtools_complement → .github/workflows/bedtools_complement.yml vendored
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0
.github/workflows/bedtools_genomecov → .github/workflows/bedtools_genomecov.yml vendored
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.github/workflows/bedtools_intersect → .github/workflows/bedtools_intersect.yml vendored
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.github/workflows/bedtools_merge → .github/workflows/bedtools_merge.yml vendored
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.github/workflows/bedtools_slop → .github/workflows/bedtools_slop.yml vendored
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.github/workflows/bedtools_sort → .github/workflows/bedtools_sort.yml vendored
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20
tests/software/bedtools/main.nf
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@ -13,7 +13,7 @@ include { BEDTOOLS_SORT } from '../../../software/bedtools/sort/main.nf' addPara
workflow test_bedtools_complement {
def input = []
input = [ [ id:'test'],
input = [ [ id:'test'],
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
@ -22,7 +22,7 @@ workflow test_bedtools_complement {
workflow test_bedtools_genomecov {
def input = []
input = [ [ id:'test'],
input = [ [ id:'test'],
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
@ -31,7 +31,7 @@ workflow test_bedtools_genomecov {
workflow test_bedtools_intersect {
def input = []
input = [ [ id:'test'],
input = [ [ id:'test'],
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
file("${launchDir}/tests/data/bed/B.bed", checkIfExists: true) ] //metamap
@ -43,21 +43,21 @@ workflow test_bedtools_intersect {
workflow test_bedtools_merge {
test_bedtools_sort()
def input = []
input = [
test_bedtools_sort.out.sort.collect { it[1] }.ifEmpty([])
input = [
test_bedtools_sort.out.sort.collect { it[1] }.ifEmpty([])
]
BEDTOOLS_MERGE(*input)
}
// TODO streamline slop module
// To run with header and pct enabled, type --pct true and --header true with nextflow run command.
// To run with header and pct enabled, type --pct true and --header true with nextflow run command.
/*
Test with l/r method
*/
workflow test_bedtools_slop_asymmetrical {
def input = []
input = [ [ id:'test', symmetry: false],
input = [ [ id:'test', symmetry: false],
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
BEDTOOLS_SLOP_AS( input )
@ -67,7 +67,7 @@ Test with b method
*/
workflow test_bedtools_slop_symmetrical {
def input = []
input = [ [ id:'test', symmetry: true],
input = [ [ id:'test', symmetry: true],
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
BEDTOOLS_SLOP_S( input )
@ -75,11 +75,11 @@ workflow test_bedtools_slop_symmetrical {
workflow test_bedtools_sort {
def input = []
input = [ [ id:'test'],
input = [ [ id:'test'],
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
BEDTOOLS_SORT( input )
emit:
sort = BEDTOOLS_SORT.out.sort

5
tests/software/bedtools/test.yml
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@ -25,7 +25,7 @@
- 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:
@ -62,6 +62,3 @@
files:
- path: output/bedtools/test.slop.bed
md5sum: 4279202e33fcce3d19f420f1b27fddee