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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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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,6 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
|
|
||
| dependencies: | ||
| - bioconda::gunc=1.0.5 | ||
| - bioconda::gunc=1.0.6 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,6 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
|
|
||
| dependencies: | ||
| - bioconda::gunc=1.0.5 | ||
| - bioconda::gunc=1.0.6 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,175 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process GUNC_MERGECHECKM" | ||
| script "../main.nf" | ||
| process "GUNC_MERGECHECKM" | ||
| config "./nextflow.config" | ||
|
|
||
| tag "modules_nfcore" | ||
| tag "modules" | ||
| tag "gunc" | ||
| tag "gunc/mergecheckm" | ||
| tag "gunc/run" | ||
| tag "gunc/downloaddb" | ||
| tag "checkm/lineagewf" | ||
| tag "checkm/qa" | ||
|
|
||
| // 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 | ||
| // """ | ||
| // } | ||
| // } | ||
|
|
||
| // 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] = [] | ||
| // """ | ||
| // } | ||
| // } | ||
|
|
||
| // run("GUNC_DOWNLOADDB") { | ||
| // script "../../downloaddb/main.nf" | ||
| // process { | ||
| // """ | ||
| // input[0] = 'progenomes' | ||
| // """ | ||
| // } | ||
| // } | ||
|
|
||
| // 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 | ||
| // """ | ||
| // } | ||
| // } | ||
| // } | ||
|
|
||
| // when { | ||
| // params { | ||
| // outdir = "${launchDir}/tests/results" | ||
| // } | ||
| // process { | ||
| // """ | ||
| // input[0] = GUNC_RUN.out.maxcss_level_tsv.join(CHECKM_QA.out.output) | ||
| // """ | ||
| // } | ||
| // } | ||
|
|
||
| // then { | ||
| // assertAll( | ||
| // { assert process.success }, | ||
| // { assert snapshot(process.out).match() } | ||
| // ) | ||
| // } | ||
|
|
||
| // } | ||
|
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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' | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| 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 | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
| 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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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| { | ||
| "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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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| process { | ||
| withName: CHECKM_QA { | ||
| ext.args = '--tab_table' | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| 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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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,6 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
|
|
||
| dependencies: | ||
| - bioconda::gunc=1.0.5 | ||
| - bioconda::gunc=1.0.6 |
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