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* Update environment.yml * Update main.nf Updated containers to 3.8.2 * Update meta.yml * Update main.nf * Create nf-test.config * Create main.nf.test nf-test module * Create main.nf.test.snap * Create nextflow.config * Update main.nf fixing biocontainer issue * Update meta.yml * nextclade version bump from 2.12 to 3.8.2 * Update meta.yml * Update test.yml regenerated test.yml * Update modules/nf-core/nextclade/datasetget/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/nextclade/run/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Delete tests/modules/nf-core/nextclade/run/test.yml deleted * Delete modules/nf-core/nextclade/run/tests/nextflow.config Deleting * Delete modules/nf-core/nextclade/run/nf-test.config * Delete modules/nf-core/nextclade/datasetget/tests/nextflow.config * Delete modules/nf-core/nextclade/datasetget/nf-test.config * Update main.nf.test * Update main.nf.test making tag adhere to guidelines * Update main.nf.test add params block [this mainly because I couldn't run the test locally without it) * Update main.nf.test.snap * Update main.nf.test * Update main.nf.test add stub * Update main.nf.test * Update tests/config/pytest_modules.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update pytest_modules.yml * Delete tests/modules/nf-core/nextclade/datasetget/main.nf * Delete tests/modules/nf-core/nextclade/datasetget/test.yml * Delete tests/modules/nf-core/nextclade/run/main.nf * Update main.nf.test add stub to nextclade/datasetget test * Delete tests/modules/nf-core/nextclade/datasetget/nextflow.config * Update snapshot * Update meta.yml * Update main.nf.test updated main.nf.test * Update main.nf.test.snap * Add stubs and swap to only snapshoting part of the json * Update modules/nf-core/nextclade/datasetget/main.nf --------- Co-authored-by: shahirnm <uoi4@cdc.gov> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -2,4 +2,4 @@ channels: | |
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bioconda::nextclade=2.12.0 | ||
| - bioconda::nextclade=3.8.2 | ||
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36 changes: 17 additions & 19 deletions
36
modules/nf-core/nextclade/datasetget/tests/main.nf.test.snap
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,43 +1,41 @@ | ||
| { | ||
| "test-nextclade-datasetget": { | ||
| "species-tag": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| "genemap.gff:md5,21ebebfd0f416eeb959e55ebffd808e8", | ||
| "primers.csv:md5,5990c3483bf66ce607aeb90a44e7ef2e", | ||
| "qc.json:md5,c512f51fda0212b21ffff05779180963", | ||
| "CHANGELOG.md:md5,ebbe8be5a3c378ed903c1afb4d8c441d", | ||
| "README.md:md5,c69387d632361334f0d7c9b66065f947", | ||
| "genome_annotation.gff3:md5,4dff84d2d6ada820e0e3a8bc6798d402", | ||
| "pathogen.json:md5,db5bbec52359c1e168ffc5e6dc0ea32a", | ||
| "reference.fasta:md5,c7ce05f28e4ec0322c96f24e064ef55c", | ||
| "sequences.fasta:md5,41129d255b99e0e92bdf20e866b99a1b", | ||
| "tag.json:md5,402ac2b87e2a6a64a3fbf5ad16497af3", | ||
| "tree.json:md5,b8f32f547ff9e2131d6fc66b68fc54b1", | ||
| "virus_properties.json:md5,5f2de3949e07cb633f3d9e4a7654dc81" | ||
| "sequences.fasta:md5,c2a4d6cbb837dce22d81f9c36dd0629e", | ||
| "tree.json:md5,e180607cd34a6cb6bab101d295f6cedf" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,12e8751f1d841b9aee87d31206c102a7" | ||
| "versions.yml:md5,8c64a653330d1c5cb58ee1b8363b22d3" | ||
| ], | ||
| "dataset": [ | ||
| [ | ||
| "genemap.gff:md5,21ebebfd0f416eeb959e55ebffd808e8", | ||
| "primers.csv:md5,5990c3483bf66ce607aeb90a44e7ef2e", | ||
| "qc.json:md5,c512f51fda0212b21ffff05779180963", | ||
| "CHANGELOG.md:md5,ebbe8be5a3c378ed903c1afb4d8c441d", | ||
| "README.md:md5,c69387d632361334f0d7c9b66065f947", | ||
| "genome_annotation.gff3:md5,4dff84d2d6ada820e0e3a8bc6798d402", | ||
| "pathogen.json:md5,db5bbec52359c1e168ffc5e6dc0ea32a", | ||
| "reference.fasta:md5,c7ce05f28e4ec0322c96f24e064ef55c", | ||
| "sequences.fasta:md5,41129d255b99e0e92bdf20e866b99a1b", | ||
| "tag.json:md5,402ac2b87e2a6a64a3fbf5ad16497af3", | ||
| "tree.json:md5,b8f32f547ff9e2131d6fc66b68fc54b1", | ||
| "virus_properties.json:md5,5f2de3949e07cb633f3d9e4a7654dc81" | ||
| "sequences.fasta:md5,c2a4d6cbb837dce22d81f9c36dd0629e", | ||
| "tree.json:md5,e180607cd34a6cb6bab101d295f6cedf" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,12e8751f1d841b9aee87d31206c102a7" | ||
| "versions.yml:md5,8c64a653330d1c5cb58ee1b8363b22d3" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-08-23T11:33:31.41372" | ||
| "timestamp": "2024-08-27T19:55:42.211731791" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -2,4 +2,4 @@ channels: | |
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bioconda::nextclade=2.12.0 | ||
| - bioconda::nextclade=3.8.2 | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,82 @@ | ||
|
|
||
| nextflow_process { | ||
|
|
||
| name "Test Process NEXTCLADE_RUN" | ||
| script "../main.nf" | ||
| process "NEXTCLADE_RUN" | ||
|
|
||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "nextclade" | ||
| tag "nextclade/datasetget" | ||
| tag "nextclade/run" | ||
|
|
||
| setup { | ||
| run("NEXTCLADE_DATASETGET") { | ||
| script "../../datasetget/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = 'nextstrain/sars-cov-2/wuhan-hu-1/orfs' | ||
| input[1] = '2024-01-16--20-31-02Z' | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
| test("sarscov2 default") { | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [[id: 'test'], | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
| ] | ||
| input[1] = NEXTCLADE_DATASETGET.out.dataset | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll ( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.csv, | ||
| process.out.csv_errors, | ||
| process.out.csv_insertions, | ||
| process.out.fasta_aligned, | ||
| process.out.fasta_translation, | ||
| file(process.out.json[0][1]).readLines()[4..10], | ||
| process.out.json_auspice, | ||
| process.out.ndjson, | ||
| process.out.nwk, | ||
| process.out.tsv, | ||
| process.out.versions | ||
| ).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("sarscov2 default-stub") { | ||
| options '-stub' | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [[id: 'test'], | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
| ] | ||
| input[1] = NEXTCLADE_DATASETGET.out.dataset | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll ( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| } |
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