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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
|
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| nextflow_process { | ||
|
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| name "Test Process ARRIBA_DOWNLOAD" | ||
| script "../main.nf" | ||
| process "ARRIBA_DOWNLOAD" | ||
|
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| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "arriba" | ||
| tag "arriba/download" | ||
|
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| test("test-arriba-download") { | ||
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| when { | ||
| process { | ||
| """ | ||
| """ | ||
| } | ||
| } | ||
|
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||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.reference[0].collect { file(it).name }.toSorted(), | ||
| process.out.versions | ||
| ).match() | ||
| } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| { | ||
| "test-arriba-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" | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-08-22T17:00:38.086459" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| name: VERIFYBAMID_VERIFYBAMID | ||
| name: verifybamid_verifybamid | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
|
|
||
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44 changes: 44 additions & 0 deletions
44
modules/nf-core/verifybamid/verifybamid/tests/main.nf.test
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
|
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| nextflow_process { | ||
|
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| name "Test Process VERIFYBAMID_VERIFYBAMID" | ||
| script "../main.nf" | ||
| process "VERIFYBAMID_VERIFYBAMID" | ||
| config "./nextflow.config" | ||
|
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| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "verifybamid" | ||
| tag "verifybamid/verifybamid" | ||
|
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| test("test-verifybamid-verifybamid") { | ||
|
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| when { | ||
| process { | ||
| """ | ||
| input[0] = [ [ id:'test', single_end:false ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) | ||
| ] | ||
| input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz', checkIfExists: true) | ||
| """ | ||
| } | ||
| } | ||
|
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| file(process.out.log[0][1]).name, | ||
| process.out.depthrg, | ||
| process.out.depthsm, | ||
| process.out.selfrg, | ||
| process.out.selfsm, | ||
| process.out.versions, | ||
| ).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| } |
51 changes: 51 additions & 0 deletions
51
modules/nf-core/verifybamid/verifybamid/tests/main.nf.test.snap
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| { | ||
| "test-verifybamid-verifybamid": { | ||
| "content": [ | ||
| "test.log", | ||
| [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test.depthRG:md5,2374504c4138c04f3b29210dcb3da96f" | ||
| ] | ||
| ], | ||
| [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test.depthSM:md5,4f5367f2be8567b95b57278b2e7372c3" | ||
| ] | ||
| ], | ||
| [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test.selfRG:md5,3772283d3eaa88683f562a2157b92d55" | ||
| ] | ||
| ], | ||
| [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test.selfSM:md5,5d2808d70f76e2f753b670fc9b2a6d55" | ||
| ] | ||
| ], | ||
| [ | ||
| "versions.yml:md5,36b44d66ecfdbef7191f47a33f688b7f" | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-08-22T17:54:07.273193" | ||
| } | ||
| } |
3 changes: 3 additions & 0 deletions
3
modules/nf-core/verifybamid/verifybamid/tests/nextflow.config
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| process { | ||
| ext.args = '--ignoreRG' | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,60 @@ | ||
|
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||
| nextflow_process { | ||
|
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| name "Test Process VT_DECOMPOSE" | ||
| script "../main.nf" | ||
| process "VT_DECOMPOSE" | ||
| config "./nextflow.config" | ||
|
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| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "vt" | ||
| tag "vt/decompose" | ||
|
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| test("test-vt-decompose") { | ||
|
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| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), | ||
| [] | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
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| test("test-vt-decompose-intervals") { | ||
|
|
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| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
|
|
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| { | ||
| "test-vt-decompose-intervals": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "decompose.vcf.gz:md5,892b6b5c55c69afd3a96cd9bfd8ab743" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,f10f0ae7e4b74341393c2a9fc87afa87" | ||
| ], | ||
| "vcf": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "decompose.vcf.gz:md5,892b6b5c55c69afd3a96cd9bfd8ab743" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,f10f0ae7e4b74341393c2a9fc87afa87" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-08-22T17:30:33.250927" | ||
| }, | ||
| "test-vt-decompose": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "decompose.vcf.gz:md5,892b6b5c55c69afd3a96cd9bfd8ab743" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,f10f0ae7e4b74341393c2a9fc87afa87" | ||
| ], | ||
| "vcf": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "decompose.vcf.gz:md5,892b6b5c55c69afd3a96cd9bfd8ab743" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,f10f0ae7e4b74341393c2a9fc87afa87" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-08-22T17:30:27.223776" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| process { | ||
| withName: VT_DECOMPOSE { | ||
| ext.prefix = "decompose" | ||
| } | ||
| } |
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