Add nf-test for FUSIONCATCHER subworkflow
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| include { FUSIONCATCHER_DETECT } from '../../../modules/local/fusioncatcher/detect/main' | ||
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| // TODO: Remove fusioncatcher_fusions as parameter. | ||
| // TODO: remove dummy file. Work with Channel.empty() | ||
| // TODO: if the files were already produced and the user want to skip the module because of this, they should be taken them from the sample sheet | ||
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| // TODO: harmonize `run_fusioncatcher` and `fusioncatcher_only` parameters at main workflow level to activate/skip this one. | ||
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| workflow FUSIONCATCHER_WORKFLOW { | ||
| take: | ||
| reads // channel [ meta, [ fastqs ] ] | ||
| fusioncatcher_ref // channel [ meta, path ] | ||
| run_fusioncatcher // boolean | ||
| all // boolean | ||
| fusioninspector_only // boolean | ||
| fusioncatcher_fusions // path, string | ||
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| main: | ||
| ch_versions = Channel.empty() | ||
| ch_dummy_file = file("$baseDir/assets/dummy_file_fusioncatcher.txt", checkIfExists: true) | ||
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| if (( run_fusioncatcher || all) && !fusioninspector_only ) { | ||
| if (fusioncatcher_fusions){ | ||
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| ch_fusioncatcher_fusions = reads.combine(Channel.value(file(fusioncatcher_fusions, checkIfExists:true))) | ||
| .map { meta, reads, fusions -> [ meta, fusions ] } | ||
| } else { | ||
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| FUSIONCATCHER_DETECT ( | ||
| reads, | ||
| fusioncatcher_ref | ||
| ) | ||
| ch_fusioncatcher_fusions = FUSIONCATCHER_DETECT.out.fusions | ||
| ch_versions = ch_versions.mix(FUSIONCATCHER_DETECT.out.versions) | ||
| } | ||
| } | ||
| else { | ||
| ch_fusioncatcher_fusions = reads.combine(Channel.value(file(ch_dummy_file, checkIfExists:true))) | ||
| .map { meta, reads, fusions -> [ meta, fusions ] } | ||
| } | ||
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| emit: | ||
| fusions = ch_fusioncatcher_fusions // channel [ meta, fusions ] | ||
| versions = ch_versions // channel [ versions ] | ||
| } | ||
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| nextflow_workflow { | ||
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| name "Test Subworkflow FUSIONCATCHER_WORKFLOW" | ||
| script "../main.nf" | ||
| workflow "FUSIONCATCHER_WORKFLOW" | ||
| tag "subworkflow" | ||
| tag "fusioncatcher" | ||
| tag "fusioncatcher/download" | ||
| tag "fusioncatcher/detect" | ||
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| // Test | ||
| test("FUSIONCATCHER_WORKFLOW - Homo sapiens - FASTQs chr4") { | ||
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| setup { | ||
| // Download reference files for fusioncatch | ||
| run("FUSIONCATCHER_DOWNLOAD") { | ||
| script "../../../../modules/local/fusioncatcher/download/main.nf" | ||
| process { | ||
| """ | ||
| // No arguments required. Human version v102 | ||
| """ | ||
| } | ||
| } | ||
| } | ||
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| when { | ||
| workflow { | ||
| """ | ||
| // ch_reads | ||
| input[0] = Channel.of( | ||
| [ | ||
| [ id: "test_fastqs", single_end: false ], | ||
| [ | ||
| file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/rnafusion/testdata/human/reads_1.fq.gz", checkIfExists: true), | ||
| file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/rnafusion/testdata/human/reads_2.fq.gz", checkIfExists: true) | ||
| ] | ||
| ] ) | ||
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| // ch_references | ||
| input[1] = FUSIONCATCHER_DOWNLOAD.out.reference | ||
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| // fusioncatcher (boolean) | ||
| input[2] = true | ||
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| // all (boolean) | ||
| input[3] = true | ||
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| // fusioninspector_only (boolean) | ||
| input[4] = false | ||
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| // fusioncatcher_fusions (string path) | ||
| input[5] = null | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert snapshot(workflow.out).match() } | ||
| ) | ||
| } | ||
| } | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,37 @@ | ||
| { | ||
| "FUSIONCATCHER_WORKFLOW - Homo sapiens - FASTQs chr4": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test_fastqs", | ||
| "single_end": false | ||
| }, | ||
| "test_fastqs.fusioncatcher.fusion-genes.txt:md5,c826a24c49abfcec8164c478e1e74892" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,6462518e02774293fa221cead8373305" | ||
| ], | ||
| "fusions": [ | ||
| [ | ||
| { | ||
| "id": "test_fastqs", | ||
| "single_end": false | ||
| }, | ||
| "test_fastqs.fusioncatcher.fusion-genes.txt:md5,c826a24c49abfcec8164c478e1e74892" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,6462518e02774293fa221cead8373305" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.0" | ||
| }, | ||
| "timestamp": "2024-12-18T21:26:47.477736" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,94 @@ | ||
| { | ||
| "test cosmic no fastp trim": { | ||
| "content": [ | ||
| 1, | ||
| { | ||
| "FASTQC": { | ||
| "fastqc": "0.12.1" | ||
| }, | ||
| "Workflow": { | ||
| "nf-core/rnafusion": "v4.0.0dev" | ||
| } | ||
| }, | ||
| [ | ||
| "fastqc", | ||
| "fastqc/test_1_fastqc.html", | ||
| "fastqc/test_1_fastqc.zip", | ||
| "fastqc/test_2_fastqc.html", | ||
| "fastqc/test_2_fastqc.zip", | ||
| "pipeline_info", | ||
| "pipeline_info/nf_core_pipeline_software_mqc_versions.yml" | ||
| ], | ||
| [ | ||
| "test_1_fastqc.html:md5,fce82f01594d12b109776ced37ec0739", | ||
| "test_1_fastqc.zip:md5,166d13bbf5ebfcb24eb30c78b129a172", | ||
| "test_2_fastqc.html:md5,40f5f42c62a0e36def4fc3d3c48089cd", | ||
| "test_2_fastqc.zip:md5,4747768318b29ce4effe6c572ccbc36c" | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.0" | ||
| }, | ||
| "timestamp": "2024-12-18T21:06:31.911972" | ||
| }, | ||
| "test cosmic with fastp trim": { | ||
| "content": [ | ||
| 3, | ||
| { | ||
| "FASTP": { | ||
| "fastp": "0.23.4" | ||
| }, | ||
| "FASTQC": { | ||
| "fastqc": "0.12.1" | ||
| }, | ||
| "FASTQC_FOR_FASTP": { | ||
| "fastqc": "0.12.1" | ||
| }, | ||
| "Workflow": { | ||
| "nf-core/rnafusion": "v4.0.0dev" | ||
| } | ||
| }, | ||
| [ | ||
| "fastp", | ||
| "fastp/test.fastp.html", | ||
| "fastp/test.fastp.json", | ||
| "fastp/test.fastp.log", | ||
| "fastp/test_1.fastp.fastq.gz", | ||
| "fastp/test_2.fastp.fastq.gz", | ||
| "fastqc", | ||
| "fastqc/test_1_fastqc.html", | ||
| "fastqc/test_1_fastqc.zip", | ||
| "fastqc/test_2_fastqc.html", | ||
| "fastqc/test_2_fastqc.zip", | ||
| "fastqc_for_fastp", | ||
| "fastqc_for_fastp/test_trimmed_1_fastqc.html", | ||
| "fastqc_for_fastp/test_trimmed_1_fastqc.zip", | ||
| "fastqc_for_fastp/test_trimmed_2_fastqc.html", | ||
| "fastqc_for_fastp/test_trimmed_2_fastqc.zip", | ||
| "pipeline_info", | ||
| "pipeline_info/nf_core_pipeline_software_mqc_versions.yml" | ||
| ], | ||
| [ | ||
| "test.fastp.html:md5,d26a7f988fd5ed667832d391ab06e202", | ||
| "test.fastp.json:md5,ebf549d5793aa40efcd9e1ca41504f26", | ||
| "test.fastp.log:md5,1c04b14e212aac5ace51f9bd25859f23", | ||
| "test_1.fastp.fastq.gz:md5,2a5519a03fb226ae2379b1150b02ff0b", | ||
| "test_2.fastp.fastq.gz:md5,4b8d3865b857e6bfae0035a45b2cdc27", | ||
| "test_1_fastqc.html:md5,fce82f01594d12b109776ced37ec0739", | ||
| "test_1_fastqc.zip:md5,f9e7e4dbf71703d98214cfd5cb79ee07", | ||
| "test_2_fastqc.html:md5,40f5f42c62a0e36def4fc3d3c48089cd", | ||
| "test_2_fastqc.zip:md5,7428e5d3c26f0934c75b15de29d6af5c", | ||
| "test_trimmed_1_fastqc.html:md5,2c2256226962e9be8c20e5720b8a51ab", | ||
| "test_trimmed_1_fastqc.zip:md5,3b8731204e07bfe7a6ecce66ba8617db", | ||
| "test_trimmed_2_fastqc.html:md5,343c493ba215089723e9d4df7180a0fc", | ||
| "test_trimmed_2_fastqc.zip:md5,fcec86b3067854ffdadd00db615f0cdd" | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.0" | ||
| }, | ||
| "timestamp": "2024-12-18T21:06:00.758494" | ||
| } | ||
| } |
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Nice!