diff --git a/tests/software/bedtools/main.nf b/tests/software/bedtools/main.nf deleted file mode 100644 index a523f5b4..00000000 --- a/tests/software/bedtools/main.nf +++ /dev/null @@ -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 ) - -} - - diff --git a/tests/software/bedtools/test.yml b/tests/software/bedtools/test.yml deleted file mode 100644 index c20019a1..00000000 --- a/tests/software/bedtools/test.yml +++ /dev/null @@ -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 -