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Bump GUNC and add gunc/run test (nf-core#6920)
* Bump GUNC and add gunc/run test * Fix meta, use input_dir * Add snapshots * Change strategy to preserve filenames * Add gunc/mergecheckm test * Update tags * Fix test names * Update snapshots * Add stubs * Add stub snaps * Address review comments * Set args in nextflow.config again * Comment problematic tests * Comment another test --------- Co-authored-by: Edmund Miller <[email protected]>
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channels: | ||
- conda-forge | ||
- bioconda | ||
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dependencies: | ||
- bioconda::gunc=1.0.5 | ||
- bioconda::gunc=1.0.6 |
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@@ -1,5 +1,6 @@ | ||
channels: | ||
- conda-forge | ||
- bioconda | ||
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||
dependencies: | ||
- bioconda::gunc=1.0.5 | ||
- bioconda::gunc=1.0.6 |
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nextflow_process { | ||
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name "Test Process GUNC_MERGECHECKM" | ||
script "../main.nf" | ||
process "GUNC_MERGECHECKM" | ||
config "./nextflow.config" | ||
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tag "modules_nfcore" | ||
tag "modules" | ||
tag "gunc" | ||
tag "gunc/mergecheckm" | ||
tag "gunc/run" | ||
tag "gunc/downloaddb" | ||
tag "checkm/lineagewf" | ||
tag "checkm/qa" | ||
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// commented out because GitHub runners are not able to run this test | ||
// test("gunc - mergecheckm") { | ||
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// setup { | ||
// run("CHECKM_LINEAGEWF") { | ||
// script "../../../checkm/lineagewf/main.nf" | ||
// process { | ||
// """ | ||
// input[0] = [ | ||
// [id: 'test'], // meta map | ||
// file( | ||
// params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', | ||
// checkIfExists: true | ||
// ) | ||
// ] | ||
// input[1] = 'fasta' | ||
// input[2] = [] // Download CheckM database | ||
// """ | ||
// } | ||
// } | ||
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// run("CHECKM_QA") { | ||
// script "../../../checkm/qa/main.nf" | ||
// process { | ||
// """ | ||
// input[0] = CHECKM_LINEAGEWF.out.checkm_output | ||
// .join(CHECKM_LINEAGEWF.out.marker_file) | ||
// .map { sample_data -> sample_data + [file('NO_FILE')] } | ||
// input[1] = [] | ||
// """ | ||
// } | ||
// } | ||
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// run("GUNC_DOWNLOADDB") { | ||
// script "../../downloaddb/main.nf" | ||
// process { | ||
// """ | ||
// input[0] = 'progenomes' | ||
// """ | ||
// } | ||
// } | ||
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// run("GUNC_RUN") { | ||
// script "../../run/main.nf" | ||
// process { | ||
// """ | ||
// input[0] = [ | ||
// [id: 'test'], | ||
// [file( | ||
// params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', | ||
// checkIfExists: true | ||
// )] | ||
// ] | ||
// input[1] = GUNC_DOWNLOADDB.out.db | ||
// """ | ||
// } | ||
// } | ||
// } | ||
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// when { | ||
// params { | ||
// outdir = "${launchDir}/tests/results" | ||
// } | ||
// process { | ||
// """ | ||
// input[0] = GUNC_RUN.out.maxcss_level_tsv.join(CHECKM_QA.out.output) | ||
// """ | ||
// } | ||
// } | ||
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// then { | ||
// assertAll( | ||
// { assert process.success }, | ||
// { assert snapshot(process.out).match() } | ||
// ) | ||
// } | ||
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// } | ||
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test("gunc - mergecheckm - stub") { | ||
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options "-stub" | ||
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setup { | ||
run("CHECKM_LINEAGEWF") { | ||
script "../../../checkm/lineagewf/main.nf" | ||
process { | ||
""" | ||
input[0] = [ | ||
[id: 'test'], // meta map | ||
file( | ||
params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', | ||
checkIfExists: true | ||
) | ||
] | ||
input[1] = 'fasta' | ||
input[2] = [] // Download CheckM database | ||
""" | ||
} | ||
} | ||
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run("CHECKM_QA") { | ||
script "../../../checkm/qa/main.nf" | ||
process { | ||
""" | ||
input[0] = CHECKM_LINEAGEWF.out.checkm_output | ||
.join(CHECKM_LINEAGEWF.out.marker_file) | ||
.map { v -> v + [file('NO_FILE')] } | ||
input[1] = [] | ||
""" | ||
} | ||
} | ||
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run("GUNC_DOWNLOADDB") { | ||
script "../../downloaddb/main.nf" | ||
process { | ||
""" | ||
input[0] = 'progenomes' | ||
""" | ||
} | ||
} | ||
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run("GUNC_RUN") { | ||
script "../../run/main.nf" | ||
process { | ||
""" | ||
input[0] = [ | ||
[id: 'test'], | ||
[file( | ||
params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', | ||
checkIfExists: true | ||
)] | ||
] | ||
input[1] = GUNC_DOWNLOADDB.out.db | ||
""" | ||
} | ||
} | ||
} | ||
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when { | ||
params { | ||
outdir = "${launchDir}/tests/results" | ||
} | ||
process { | ||
""" | ||
input[0] = GUNC_RUN.out.maxcss_level_tsv.join(CHECKM_QA.out.output) | ||
""" | ||
} | ||
} | ||
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then { | ||
assertAll( | ||
{ assert process.success }, | ||
{ assert snapshot(process.out).match() } | ||
) | ||
} | ||
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} | ||
} |
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{ | ||
"gunc - mergecheckm": { | ||
"content": [ | ||
{ | ||
"0": [ | ||
[ | ||
{ | ||
"id": "test" | ||
}, | ||
"GUNC_checkM.merged.tsv:md5,24cbd3c76a36cb90ac993c83525a2c1b" | ||
] | ||
], | ||
"1": [ | ||
"versions.yml:md5,a94747201129170b1cfbce5e59de62b0" | ||
], | ||
"tsv": [ | ||
[ | ||
{ | ||
"id": "test" | ||
}, | ||
"GUNC_checkM.merged.tsv:md5,24cbd3c76a36cb90ac993c83525a2c1b" | ||
] | ||
], | ||
"versions": [ | ||
"versions.yml:md5,a94747201129170b1cfbce5e59de62b0" | ||
] | ||
} | ||
], | ||
"meta": { | ||
"nf-test": "0.9.2", | ||
"nextflow": "24.10.0" | ||
}, | ||
"timestamp": "2024-11-22T09:37:48.146410153" | ||
}, | ||
"gunc - mergecheckm - stub": { | ||
"content": [ | ||
{ | ||
"0": [ | ||
[ | ||
{ | ||
"id": "test" | ||
}, | ||
"gunc_merge_checkm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
] | ||
], | ||
"1": [ | ||
"versions.yml:md5,a94747201129170b1cfbce5e59de62b0" | ||
], | ||
"tsv": [ | ||
[ | ||
{ | ||
"id": "test" | ||
}, | ||
"gunc_merge_checkm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
] | ||
], | ||
"versions": [ | ||
"versions.yml:md5,a94747201129170b1cfbce5e59de62b0" | ||
] | ||
} | ||
], | ||
"meta": { | ||
"nf-test": "0.9.2", | ||
"nextflow": "24.10.0" | ||
}, | ||
"timestamp": "2024-11-21T16:47:06.752273424" | ||
} | ||
} |
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process { | ||
withName: CHECKM_QA { | ||
ext.args = '--tab_table' | ||
} | ||
} |
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gunc/run: | ||
- modules/nf-core/gunc/mergecheckm/** | ||
- modules/nf-core/gunc/run/** | ||
- modules/nf-core/gunc/downloaddb/** | ||
- modules/nf-core/checkm/lineagewf/** | ||
- modules/nf-core/checkm/qa/** |
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@@ -1,5 +1,6 @@ | ||
channels: | ||
- conda-forge | ||
- bioconda | ||
|
||
dependencies: | ||
- bioconda::gunc=1.0.5 | ||
- bioconda::gunc=1.0.6 |
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