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Update FastK + MerquryFK versions + allow conda, add merquryfk/hapmaker module, port to nf-test #7847
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Update FastK + MerquryFK versions + allow conda, add merquryfk/hapmaker module, port to nf-test #7847
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0570f28
Start updating FastK modules to allow conda
prototaxites 8201768
Migrate all Merquryfk modules to nf-test
prototaxites a3682e5
Update to container with explicit R
prototaxites 40efb3f
Merge branch 'nf-core:master' into merquryfk
prototaxites 7fafd8c
Fix container for FastK
prototaxites 3375956
Start fixing fastk modules
prototaxites e5fd9dc
Fix FastK tests, add merquryfk/hapmaker module
prototaxites 81ebf7d
Fix linting for some merquryFK modules
prototaxites 14fe121
Fix merquryfk/merquryfk linting
prototaxites a7357aa
Fix linting for everything except hapmaker
prototaxites e40d01c
Merge branch 'master' into merquryfk
prototaxites d0d668f
Fix snapshots?
prototaxites 4e9d130
Update tests
prototaxites 9c5cb46
Fix tests pt 1000
prototaxites 8ad6b4b
Sort fastk/merge test inputs to try and ensure repeatability
prototaxites ad573f4
Rename output channels to avoid linting error
prototaxites 7a3af97
Fix hapmaker snapshot
prototaxites 771847e
Harshill alignment
prototaxites 49eb228
Stub output format determined by args; add details to meta.yml files …
prototaxites c78bbc5
Merge branch 'master' into merquryfk
prototaxites fa59e18
Remove def again from variables - causes error otherwise
prototaxites 0b9db11
Fix Fastk/merge stub
prototaxites 5433a3e
Update snapshot
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -4,4 +4,4 @@ channels: | |
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bioconda::false_flag | ||
| - bioconda::fastk=1.1.0 | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bioconda::fastk=1.1.0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process FASTK_HISTEX" | ||
| script "../main.nf" | ||
| process "FASTK_HISTEX" | ||
|
|
||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "fastk" | ||
| tag "fastk/fastk" | ||
| tag "fastk/histex" | ||
|
|
||
| setup { | ||
| run("FASTK_FASTK") { | ||
| script "../../fastk/" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
| test("homo_sapiens - Illumina") { | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = FASTK_FASTK.out.hist | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| test("homo_sapiens - Illumina - stub") { | ||
|
|
||
| options '-stub' | ||
|
|
||
| when { | ||
|
|
||
| process { | ||
| """ | ||
| input[0] = FASTK_FASTK.out.hist | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| 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 @@ | ||
| { | ||
| "homo_sapiens - Illumina - stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test.hist:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,c341f76b03e55e3eaaadc0bad07674e0" | ||
| ], | ||
| "hist": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test.hist:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,c341f76b03e55e3eaaadc0bad07674e0" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.5" | ||
| }, | ||
| "timestamp": "2025-03-18T17:03:13.01032408" | ||
| }, | ||
| "homo_sapiens - Illumina": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test.hist:md5,afd7d60759c76f23d80b3b75b1ceed7f" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,c341f76b03e55e3eaaadc0bad07674e0" | ||
| ], | ||
| "hist": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test.hist:md5,afd7d60759c76f23d80b3b75b1ceed7f" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,c341f76b03e55e3eaaadc0bad07674e0" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.5" | ||
| }, | ||
| "timestamp": "2025-03-19T08:55:19.961441005" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bioconda::fastk=1.1.0 |
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