diff --git a/modules/nf-core/arriba/arriba/environment.yml b/modules/nf-core/arriba/arriba/environment.yml index d0883a0d205..c3a88ffbdf8 100644 --- a/modules/nf-core/arriba/arriba/environment.yml +++ b/modules/nf-core/arriba/arriba/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda + dependencies: - bioconda::arriba=2.4.0 diff --git a/modules/nf-core/arriba/arriba/main.nf b/modules/nf-core/arriba/arriba/main.nf index 761d0bf3587..75dbf93ad9f 100644 --- a/modules/nf-core/arriba/arriba/main.nf +++ b/modules/nf-core/arriba/arriba/main.nf @@ -8,14 +8,13 @@ process ARRIBA_ARRIBA { 'biocontainers/arriba:2.4.0--h0033a41_2' }" input: - tuple val(meta), path(bam) + tuple val(meta), path(bam) tuple val(meta2), path(fasta) tuple val(meta3), path(gtf) - tuple val(meta4), path(blacklist) - tuple val(meta5), path(known_fusions) - tuple val(meta6), path(structural_variants) - tuple val(meta7), path(tags) - tuple val(meta8), path(protein_domains) + path(blacklist) + path(known_fusions) + path(cytobands) + path(protein_domains) output: tuple val(meta), path("*.fusions.tsv") , emit: fusions @@ -30,8 +29,7 @@ process ARRIBA_ARRIBA { def prefix = task.ext.prefix ?: "${meta.id}" def blacklist = blacklist ? "-b $blacklist" : "-f blacklist" def known_fusions = known_fusions ? "-k $known_fusions" : "" - def structural_variants = structural_variants ? "-d $structual_variants" : "" - def tags = tags ? "-t $tags" : "" + def cytobands = cytobands ? "-d $cytobands" : "" def protein_domains = protein_domains ? "-p $protein_domains" : "" """ @@ -43,8 +41,7 @@ process ARRIBA_ARRIBA { -O ${prefix}.fusions.discarded.tsv \\ $blacklist \\ $known_fusions \\ - $structural_variants \\ - $tags \\ + $cytobands \\ $protein_domains \\ $args diff --git a/modules/nf-core/arriba/arriba/meta.yml b/modules/nf-core/arriba/arriba/meta.yml index f230dda1fbe..91ba2103961 100644 --- a/modules/nf-core/arriba/arriba/meta.yml +++ b/modules/nf-core/arriba/arriba/meta.yml @@ -43,48 +43,19 @@ input: type: file description: Annotation GTF file pattern: "*.{gtf}" - - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - blacklist: + - - blacklist: type: file description: Blacklist file pattern: "*.{tsv}" - - - meta5: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - known_fusions: + - - known_fusions: type: file description: Known fusions file pattern: "*.{tsv}" - - - meta6: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - structural_variants: - type: file - description: Structural variants file - pattern: "*.{tsv}" - - - meta7: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - tags: + - - cytobands: type: file - description: Tags file + description: Cytobands file pattern: "*.{tsv}" - - - meta8: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - protein_domains: + - - protein_domains: type: file description: Protein domains file pattern: "*.{gff3}" diff --git a/modules/nf-core/arriba/arriba/tests/main.nf.test b/modules/nf-core/arriba/arriba/tests/main.nf.test new file mode 100644 index 00000000000..13d855ecbe5 --- /dev/null +++ b/modules/nf-core/arriba/arriba/tests/main.nf.test @@ -0,0 +1,138 @@ + +nextflow_process { + + name "Test Process ARRIBA_ARRIBA" + script "../main.nf" + process "ARRIBA_ARRIBA" + + tag "modules" + tag "modules_nfcore" + tag "arriba" + tag "arriba/arriba" + tag "arriba/download" + tag "star/genomegenerate" + tag "star/align" + + setup { + config "./nextflow.config" + run("ARRIBA_DOWNLOAD") { + script "../../../arriba/download/main.nf" + process { + """ + input[0] = 'GRCh38' + """ + } + } + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + run("STAR_ALIGN") { + script "../../../star/align/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + } + + test("homo_sapiens - paired_end") { + + when { + process { + """ + input[0] = STAR_ALIGN.out.bam + input[1] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[2] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = [] + + input[4] = [] + + input[5] = [] + + input[6] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - paired_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[2] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = [] + + input[4] = [] + + input[5] = [] + + input[6] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/arriba/arriba/tests/main.nf.test.snap b/modules/nf-core/arriba/arriba/tests/main.nf.test.snap new file mode 100644 index 00000000000..3ef45674b38 --- /dev/null +++ b/modules/nf-core/arriba/arriba/tests/main.nf.test.snap @@ -0,0 +1,108 @@ +{ + "homo_sapiens - paired_end": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fusions.tsv:md5,7c3383f7eb6d79b84b0bd30a7ef02d70" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fusions.discarded.tsv:md5,445cb87a27f063e751f93498cf8d10b5" + ] + ], + "2": [ + "versions.yml:md5,d323796555db4a58fe4c6bc08d1dec30" + ], + "fusions": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fusions.tsv:md5,7c3383f7eb6d79b84b0bd30a7ef02d70" + ] + ], + "fusions_fail": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fusions.discarded.tsv:md5,445cb87a27f063e751f93498cf8d10b5" + ] + ], + "versions": [ + "versions.yml:md5,d323796555db4a58fe4c6bc08d1dec30" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-08T15:14:51.73747" + }, + "homo_sapiens - paired_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fusions.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fusions.discarded.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "2": [ + "versions.yml:md5,d323796555db4a58fe4c6bc08d1dec30" + ], + "fusions": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fusions.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "fusions_fail": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fusions.discarded.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "versions": [ + "versions.yml:md5,d323796555db4a58fe4c6bc08d1dec30" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-08T15:41:23.945072" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/arriba/arriba/nextflow.config b/modules/nf-core/arriba/arriba/tests/nextflow.config similarity index 84% rename from tests/modules/nf-core/arriba/arriba/nextflow.config rename to modules/nf-core/arriba/arriba/tests/nextflow.config index 1b66d8dfa7f..d3d5b00f665 100644 --- a/tests/modules/nf-core/arriba/arriba/nextflow.config +++ b/modules/nf-core/arriba/arriba/tests/nextflow.config @@ -1,13 +1,8 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: STAR_GENOMEGENERATE { ext.args = '--genomeSAindexNbases 11' } - withName: STAR_ALIGN { ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0 --outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 10 --chimOutType WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50' } - } diff --git a/modules/nf-core/arriba/download/main.nf b/modules/nf-core/arriba/download/main.nf index 96a4e33628f..2e63b2d0b17 100644 --- a/modules/nf-core/arriba/download/main.nf +++ b/modules/nf-core/arriba/download/main.nf @@ -8,10 +8,14 @@ process ARRIBA_DOWNLOAD { 'biocontainers/arriba:2.4.0--h0033a41_2' }" input: + val(genome) output: - path "*" , emit: reference - path "versions.yml" , emit: versions + path "blacklist*${genome}*.tsv.gz" , emit: blacklist + path "cytobands*${genome}*.tsv" , emit: cytobands + path "protein_domains*${genome}*.gff3" , emit: protein_domains + path "known_fusions*${genome}*.tsv.gz" , emit: known_fusions + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -36,7 +40,6 @@ process ARRIBA_DOWNLOAD { touch protein_domains_hg38_GRCh38_v2.4.0.gff3 touch cytobands_hg38_GRCh38_v2.4.0.tsv touch known_fusions_hg38_GRCh38_v2.4.0.tsv.gz - touch protein_domains_hg38_GRCh38_v2.4.0.gff3 cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/arriba/download/meta.yml b/modules/nf-core/arriba/download/meta.yml index 531c66c2f77..892b7ac9b78 100644 --- a/modules/nf-core/arriba/download/meta.yml +++ b/modules/nf-core/arriba/download/meta.yml @@ -15,12 +15,34 @@ tools: licence: ["MIT"] identifier: biotools:Arriba +input: + - - genome: + type: string + description: hg38, hg19, GRCh38, GRCh37 for humans are accepted output: - - reference: - - "*": - type: directory - description: Folder with arriba references - pattern: "*" + - blacklist: + - blacklist*${genome}*.tsv.gz: + type: str + description: The blacklist removes recurrent alignment artifacts and transcripts + which are present in healthy tissue + pattern: ".tsv.gz" + - cytobands: + - cytobands*${genome}*.tsv: + type: file + description: Coordinates of the Giemsa staining bands. This information is used + to draw ideograms + pattern: ".tsv" + - protein_domains: + - protein_domains*${genome}*.gff3: + type: file + description: Protein domain annotations + patter: "*.gff3" + - known_fusions: + - known_fusions*${genome}*.tsv.gz: + type: file + description: Arriba is more sensitive to those fusions to improve the detection + rate of expected or highly relevant events, such as recurrent fusions + patter: "*.tsv.gz" - versions: - versions.yml: type: file diff --git a/modules/nf-core/arriba/download/tests/main.nf.test b/modules/nf-core/arriba/download/tests/main.nf.test index cccc95db2c0..2c32c7a0f3a 100644 --- a/modules/nf-core/arriba/download/tests/main.nf.test +++ b/modules/nf-core/arriba/download/tests/main.nf.test @@ -11,11 +11,10 @@ nextflow_process { tag "arriba/download" test("test-arriba-download") { - when { process { """ - + input[0] = 'GRCh38' """ } } @@ -23,11 +22,27 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.reference[0].collect { file(it).name }.toSorted(), - process.out.versions - ).match() - } + { assert snapshot(process.out).match() } + ) + } + + } + + test("download - stub") { + + options "-stub" + + when { + process { + """ + input[0] = 'GRCh38' + """ + } + } + + then { + assertAll( + { assert process.success } ) } } diff --git a/modules/nf-core/arriba/download/tests/main.nf.test.snap b/modules/nf-core/arriba/download/tests/main.nf.test.snap index eda3f706640..fe9b18b9483 100644 --- a/modules/nf-core/arriba/download/tests/main.nf.test.snap +++ b/modules/nf-core/arriba/download/tests/main.nf.test.snap @@ -1,35 +1,43 @@ { - "test-arriba-download": { + "download": { "content": [ - [ - "CREDITS", - "RefSeq_viral_genomes_v2.4.0.fa.gz", - "blacklist_hg19_hs37d5_GRCh37_v2.4.0.tsv.gz", - "blacklist_hg38_GRCh38_v2.4.0.tsv.gz", - "blacklist_mm10_GRCm38_v2.4.0.tsv.gz", - "blacklist_mm39_GRCm39_v2.4.0.tsv.gz", - "cytobands_hg19_hs37d5_GRCh37_v2.4.0.tsv", - "cytobands_hg38_GRCh38_v2.4.0.tsv", - "cytobands_mm10_GRCm38_v2.4.0.tsv", - "cytobands_mm39_GRCm39_v2.4.0.tsv", - "known_fusions_hg19_hs37d5_GRCh37_v2.4.0.tsv.gz", - "known_fusions_hg38_GRCh38_v2.4.0.tsv.gz", - "known_fusions_mm10_GRCm38_v2.4.0.tsv.gz", - "known_fusions_mm39_GRCm39_v2.4.0.tsv.gz", - "protein_domains_hg19_hs37d5_GRCh37_v2.4.0.gff3", - "protein_domains_hg38_GRCh38_v2.4.0.gff3", - "protein_domains_mm10_GRCm38_v2.4.0.gff3", - "protein_domains_mm39_GRCm39_v2.4.0.gff3", - "versions.yml" - ], - [ - "versions.yml:md5,98c69df5eaea5caf0b4af7b8d7af4893" - ] + { + "0": [ + "blacklist_hg38_GRCh38_v2.4.0.tsv.gz:md5,e3098a4be51aece78aede64b55c39318" + ], + "1": [ + "cytobands_hg38_GRCh38_v2.4.0.tsv:md5,7bd504feefb33fcfc9be0517439a423c" + ], + "2": [ + "protein_domains_hg38_GRCh38_v2.4.0.gff3:md5,43c387a784ebeed71b4147076cebf978" + ], + "3": [ + "known_fusions_hg38_GRCh38_v2.4.0.tsv.gz:md5,4f00f81ccb5f4db283f1a22b8b0da67c" + ], + "4": [ + "versions.yml:md5,98c69df5eaea5caf0b4af7b8d7af4893" + ], + "blacklist": [ + "blacklist_hg38_GRCh38_v2.4.0.tsv.gz:md5,e3098a4be51aece78aede64b55c39318" + ], + "cytobands": [ + "cytobands_hg38_GRCh38_v2.4.0.tsv:md5,7bd504feefb33fcfc9be0517439a423c" + ], + "known_fusions": [ + "known_fusions_hg38_GRCh38_v2.4.0.tsv.gz:md5,4f00f81ccb5f4db283f1a22b8b0da67c" + ], + "protein_domains": [ + "protein_domains_hg38_GRCh38_v2.4.0.gff3:md5,43c387a784ebeed71b4147076cebf978" + ], + "versions": [ + "versions.yml:md5,98c69df5eaea5caf0b4af7b8d7af4893" + ] + } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T17:00:38.086459" + "timestamp": "2024-10-08T11:12:17.010496" } } \ No newline at end of file diff --git a/modules/nf-core/arriba/download/tests/tags.yml b/modules/nf-core/arriba/download/tests/tags.yml new file mode 100644 index 00000000000..f510bbf1a14 --- /dev/null +++ b/modules/nf-core/arriba/download/tests/tags.yml @@ -0,0 +1,2 @@ +arriba/download: + - "modules/nf-core/arriba/download/**" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 5d8a9be3c4f..584db480a14 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1,9 +1,18 @@ amps: - modules/nf-core/amps/** - tests/modules/nf-core/amps/** -arriba/arriba: - - modules/nf-core/arriba/arriba/** - - tests/modules/nf-core/arriba/arriba/** +angsd/contamination: + - modules/nf-core/angsd/contamination/** + - tests/modules/nf-core/angsd/contamination/** +angsd/docounts: + - modules/nf-core/angsd/docounts/** + - tests/modules/nf-core/angsd/docounts/** +arcashla/extract: + - modules/nf-core/arcashla/extract/** + - tests/modules/nf-core/arcashla/extract/** +ariba/getref: + - modules/nf-core/ariba/getref/** + - tests/modules/nf-core/ariba/getref/** artic/guppyplex: - modules/nf-core/artic/guppyplex/** - tests/modules/nf-core/artic/guppyplex/** diff --git a/tests/modules/nf-core/arriba/arriba/main.nf b/tests/modules/nf-core/arriba/arriba/main.nf deleted file mode 100644 index 2d5b9a3ce71..00000000000 --- a/tests/modules/nf-core/arriba/arriba/main.nf +++ /dev/null @@ -1,61 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { STAR_GENOMEGENERATE } from '../../../../../modules/nf-core/star/genomegenerate/main.nf' -include { STAR_ALIGN } from '../../../../../modules/nf-core/star/align/main.nf' -include { ARRIBA_ARRIBA } from '../../../../../modules/nf-core/arriba/arriba/main.nf' - -workflow test_arriba_single_end { - - input = [ [ id:'test', single_end:true ], // meta map - [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - ] - ] - fasta = [ - [ id:'test_fasta' ], // meta map - [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - ] - fai = [ - [ id:'test_fai' ], // meta map - [ file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] - ] - gtf = [ - [ id:'test_fasta_gtf' ], // meta map - [ file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) ] - ] - star_ignore_sjdbgtf = false - seq_platform = 'illumina' - seq_center = false - - STAR_GENOMEGENERATE ( fasta, gtf ) - STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center ) - ARRIBA_ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf , [[],[]], [[],[]], [[],[]], [[],[]], [[],[]]) -} - -workflow test_arriba_paired_end { - - input = [ [ id:'test', single_end:false ], // meta map - [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) ] - ] - fasta = [ - [ id:'test_fasta' ], // meta map - [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - ] - fai = [ - [ id:'test_gtf' ], // meta map - [ file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] - ] - gtf = [ - [ id:'test_fasta_fai' ], // meta map - [ file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) ] - ] - star_ignore_sjdbgtf = false - seq_platform = 'illumina' - seq_center = false - - STAR_GENOMEGENERATE ( fasta, gtf ) - STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center ) - ARRIBA_ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf, [[],[]], [[],[]], [[],[]], [[],[]], [[],[]]) -} diff --git a/tests/modules/nf-core/arriba/arriba/test.yml b/tests/modules/nf-core/arriba/arriba/test.yml deleted file mode 100644 index 19db9f0d6b6..00000000000 --- a/tests/modules/nf-core/arriba/arriba/test.yml +++ /dev/null @@ -1,87 +0,0 @@ -- name: arriba arriba test_arriba_single_end - command: nextflow run ./tests/modules/nf-core/arriba/arriba -entry test_arriba_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/arriba/arriba/nextflow.config - tags: - - arriba - - arriba/arriba - files: - - path: output/arriba/test.fusions.discarded.tsv - - path: output/arriba/test.fusions.tsv - md5sum: 7c3383f7eb6d79b84b0bd30a7ef02d70 - - path: output/star/star/Genome - md5sum: a654229fbca6071dcb6b01ce7df704da - - path: output/star/star/Log.out - - path: output/star/star/SA - md5sum: 8c3edc46697b72c9e92440d4cf43506c - - path: output/star/star/SAindex - md5sum: 9f085c626553b1c52f2827421972ac10 - - path: output/star/star/chrLength.txt - md5sum: c81f40f27e72606d7d07097c1d56a5b5 - - path: output/star/star/chrName.txt - md5sum: 5ae68a67b70976ee95342a7451cb5af1 - - path: output/star/star/chrNameLength.txt - md5sum: b190587cae0531f3cf25552d8aa674db - - path: output/star/star/chrStart.txt - md5sum: 8d3291e6bcdbe9902fbd7c887494173f - - path: output/star/star/exonInfo.tab - md5sum: 0d560290fab688b7268d88d5494bf9fe - - path: output/star/star/geneInfo.tab - md5sum: 8b608537307443ffaee4927d2b428805 - - path: output/star/star/genomeParameters.txt - md5sum: 9e42067b1ec70b773257529230dd7b3a - - path: output/star/star/sjdbInfo.txt - md5sum: 5690ea9d9f09f7ff85b7fd47bd234903 - - path: output/star/star/sjdbList.fromGTF.out.tab - md5sum: 8760c33e966dad0b39f440301ebbdee4 - - path: output/star/star/sjdbList.out.tab - md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1 - - path: output/star/star/transcriptInfo.tab - md5sum: 0c3a5adb49d15e5feff81db8e29f2e36 - - path: output/star/test.Aligned.out.bam - - path: output/star/test.Log.final.out - - path: output/star/test.Log.out - - path: output/star/test.Log.progress.out - - path: output/star/test.SJ.out.tab - -- name: arriba arriba test_arriba_paired_end - command: nextflow run ./tests/modules/nf-core/arriba/arriba -entry test_arriba_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/arriba/arriba/nextflow.config - tags: - - arriba - - arriba/arriba - files: - - path: output/arriba/test.fusions.discarded.tsv - - path: output/arriba/test.fusions.tsv - md5sum: 7c3383f7eb6d79b84b0bd30a7ef02d70 - - path: output/star/star/Genome - md5sum: a654229fbca6071dcb6b01ce7df704da - - path: output/star/star/Log.out - - path: output/star/star/SA - md5sum: 8c3edc46697b72c9e92440d4cf43506c - - path: output/star/star/SAindex - md5sum: 9f085c626553b1c52f2827421972ac10 - - path: output/star/star/chrLength.txt - md5sum: c81f40f27e72606d7d07097c1d56a5b5 - - path: output/star/star/chrName.txt - md5sum: 5ae68a67b70976ee95342a7451cb5af1 - - path: output/star/star/chrNameLength.txt - md5sum: b190587cae0531f3cf25552d8aa674db - - path: output/star/star/chrStart.txt - md5sum: 8d3291e6bcdbe9902fbd7c887494173f - - path: output/star/star/exonInfo.tab - md5sum: 0d560290fab688b7268d88d5494bf9fe - - path: output/star/star/geneInfo.tab - md5sum: 8b608537307443ffaee4927d2b428805 - - path: output/star/star/genomeParameters.txt - md5sum: 9e42067b1ec70b773257529230dd7b3a - - path: output/star/star/sjdbInfo.txt - md5sum: 5690ea9d9f09f7ff85b7fd47bd234903 - - path: output/star/star/sjdbList.fromGTF.out.tab - md5sum: 8760c33e966dad0b39f440301ebbdee4 - - path: output/star/star/sjdbList.out.tab - md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1 - - path: output/star/star/transcriptInfo.tab - md5sum: 0c3a5adb49d15e5feff81db8e29f2e36 - - path: output/star/test.Aligned.out.bam - - path: output/star/test.Log.final.out - - path: output/star/test.Log.out - - path: output/star/test.Log.progress.out - - path: output/star/test.SJ.out.tab