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* Added nf-tests * Add missing tags * Fix conda tests * Update versions.yml file * Update version generation * Update versions command * Removed quotes from versions * add modules to pytest-workflow excludes * Addressing PR comments * Addressing PR comments * Addressing PR comments * Update container for matrix * Update snaps * Fix linting * Updated datasets paths * Replace base path in datasets * Adjust indentation of test inputs --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,100 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process CUSTOM_MATRIXFILTER" | ||
| script "../main.nf" | ||
| process "CUSTOM_MATRIXFILTER" | ||
| config "./nextflow.config" | ||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "custom_matrixfilter" | ||
| tag "custom" | ||
| tag "custom/matrixfilter" | ||
|
|
||
| test("test_custom_matrixfilter") { | ||
|
|
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| when { | ||
| params { | ||
| observations_id_col = 'sample' | ||
| filtering_min_samples = 1.0 | ||
| filtering_min_abundance = 10 | ||
| filtering_min_proportion = null | ||
| filtering_grouping_var = null | ||
| filtering_min_proportion_not_na = 0.5 | ||
| filtering_min_samples_not_na = null | ||
|
|
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| module_args = [ | ||
| "--sample_id_col \"${params.observations_id_col}\"", | ||
| "--minimum_samples ${params.filtering_min_samples}", | ||
| "--minimum_abundance ${params.filtering_min_abundance}", | ||
| (params.filtering_min_proportion ? "--minimum_proportion ${params.filtering_min_proportion}" : ''), | ||
| (params.filtering_grouping_var ? "--grouping_variable \"${params.filtering_grouping_var}\"" : ''), | ||
| (params.filtering_min_proportion_not_na ? "--minimum_proportion_not_na \"${params.filtering_min_proportion_not_na}\"" : ''), | ||
| (params.filtering_min_samples_not_na ? "--minimum_samples_not_na \"${params.filtering_min_samples_not_na}\"" : '') | ||
| ].join(' ').trim() | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = [ [id:"test"], | ||
| file(params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.assay.tsv",checkIfExists: true) | ||
| ] | ||
| input[1] = [ [id:"test"], | ||
| file(params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.sample_metadata.tsv",checkIfExists: true) | ||
| ] | ||
| """ | ||
|
|
||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll ( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out.filtered, | ||
| process.out.tests, | ||
| process.out.versions).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("test_custom_matrixfilter - stub") { | ||
|
|
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| options "-stub" | ||
|
|
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| when { | ||
| params { | ||
| observations_id_col = 'sample' | ||
| filtering_min_samples = 1.0 | ||
| filtering_min_abundance = 10 | ||
| filtering_min_proportion = null | ||
| filtering_grouping_var = null | ||
| filtering_min_proportion_not_na = 0.5 | ||
| filtering_min_samples_not_na = null | ||
| module_args = [ | ||
| "--sample_id_col \"${params.observations_id_col}\"", | ||
| "--minimum_samples ${params.filtering_min_samples}", | ||
| "--minimum_abundance ${params.filtering_min_abundance}", | ||
| (params.filtering_min_proportion ? "--minimum_proportion ${params.filtering_min_proportion}" : ''), | ||
| (params.filtering_grouping_var ? "--grouping_variable \"${params.filtering_grouping_var}\"" : ''), | ||
| (params.filtering_min_proportion_not_na ? "--minimum_proportion_not_na \"${params.filtering_min_proportion_not_na}\"" : ''), | ||
| (params.filtering_min_samples_not_na ? "--minimum_samples_not_na \"${params.filtering_min_samples_not_na}\"" : '') | ||
| ].join(' ').trim() | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = [ [id:"test"], | ||
| file(params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.assay.tsv",checkIfExists: true) | ||
| ] | ||
| input[1] = [ [id:"test"], | ||
| file(params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.sample_metadata.tsv",checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll ( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
| } | ||
| } |
95 changes: 95 additions & 0 deletions
95
modules/nf-core/custom/matrixfilter/tests/main.nf.test.snap
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,95 @@ | ||
| { | ||
| "test_custom_matrixfilter": { | ||
| "content": [ | ||
| [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.filtered.tsv:md5,ecc3ca4c6538f9248dce844108474a66" | ||
| ] | ||
| ], | ||
| [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.tests.tsv:md5,9a0f14988df8c1b8975039eed91b85e2" | ||
| ] | ||
| ], | ||
| [ | ||
| "versions.yml:md5,275e382be9ca5bdd30ff5d6fc4340616" | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.2" | ||
| }, | ||
| "timestamp": "2024-12-13T21:21:11.862199262" | ||
| }, | ||
| "test_custom_matrixfilter - stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.tests.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "2": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "3": [ | ||
| "versions.yml:md5,275e382be9ca5bdd30ff5d6fc4340616" | ||
| ], | ||
| "filtered": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "session_info": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "tests": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.tests.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,275e382be9ca5bdd30ff5d6fc4340616" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.2" | ||
| }, | ||
| "timestamp": "2024-12-13T21:22:31.144793503" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| process { | ||
| ext.args = params.module_args | ||
| } |
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63 changes: 63 additions & 0 deletions
63
modules/nf-core/custom/tabulartogseacls/tests/main.nf.test
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process CUSTOM_TABULARTOGSEACLS" | ||
| script "../main.nf" | ||
| process "CUSTOM_TABULARTOGSEACLS" | ||
| config "./nextflow.config" | ||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "custom_tabulartogseacls" | ||
| tag "custom" | ||
| tag "custom/tabulartogseacls" | ||
|
|
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| test("test_custom_tabulartogseacls") { | ||
|
|
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| when { | ||
| params { | ||
| module_args = [ "separator": "\t", "variable": "treatment" ] | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [id:'treatment_mCherry_hND6_sample_number', variable:'treatment', reference:'mCherry', target:'hND6', blocking:'sample_number'], | ||
| file(params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.sample_metadata.tsv", checkIfExists: true) | ||
| ] | ||
| """ | ||
|
|
||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll ( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
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| test("test_custom_tabulartogseacls - stub") { | ||
|
|
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| options "-stub" | ||
|
|
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| when { | ||
| params { | ||
| module_args = { [ "separator": "\t", "variable": "treatment" ] } | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [id:'treatment_mCherry_hND6_sample_number', variable:'treatment', reference:'mCherry', target:'hND6', blocking:'sample_number'], | ||
| file(params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.sample_metadata.tsv", checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
|
|
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| then { | ||
| assertAll ( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
| } | ||
| } |
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