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SHAPEIT5_SWITCH Migrate to nf-test
#7066
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40ab615
Migrate to nf-test
7ede135
Remove md5sum
04471e3
Merge branch 'master' into shapeit5_switch
LouisLeNezet 8030855
Merge branch 'master' into shapeit5_switch
LouisLeNezet 886fc0e
Merge branch 'master' into shapeit5_switch
LouisLeNezet d5f2c20
Merge branch 'master' into shapeit5_switch
LouisLeNezet 4932c5b
Merge branch 'master' into shapeit5_switch
LouisLeNezet 218b8e8
Update nf-test datasets
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -2,4 +2,4 @@ channels: | |
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bioconda::shapeit5=1.0.0 | ||
| - bioconda::shapeit5=5.1.1 | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,104 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process SHAPEIT5_SWITCH" | ||
| script "../main.nf" | ||
| process "SHAPEIT5_SWITCH" | ||
|
|
||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "shapeit5" | ||
| tag "shapeit5/switch" | ||
| tag "shapeit5/phasecommon" | ||
| tag "bcftools/index" | ||
|
|
||
| test("homo sapiens - vcf, scaffold, []") { | ||
| config "./nextflow.config" | ||
| setup { | ||
| run("SHAPEIT5_PHASECOMMON") { | ||
| script "../../../shapeit5/phasecommon" | ||
| params { | ||
| shapeit5_phasecommon_args = "--filter-maf 0.001" | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'scaffold', single_end:false ], // meta map | ||
| file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true), | ||
| file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true), | ||
| [], | ||
| "chr21", | ||
| ]) | ||
| input[1] = Channel.of([[],[],[]]) | ||
| input[2] = Channel.of([[],[],[]]) | ||
| input[3] = Channel.of([[],[]]) | ||
| """ | ||
| } | ||
| } | ||
| run("BCFTOOLS_INDEX") { | ||
| script "../../../bcftools/index" | ||
| process { | ||
| """ | ||
| input[0] = SHAPEIT5_PHASECOMMON.out.phased_variant | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = SHAPEIT5_PHASECOMMON.out.phased_variant | ||
| .join(BCFTOOLS_INDEX.out.csi) | ||
| .combine(Channel.of("chr21")) | ||
| .combine(Channel.of([[]])) | ||
| input[1] = Channel.of([[ id:'truth_panel'], | ||
| file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf",checkIfExists:true), | ||
| file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi",checkIfExists:true) | ||
| ]) | ||
| input[2] = Channel.of([[ id:'freq_file'], | ||
| file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz",checkIfExists:true), | ||
| file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz.csi",checkIfExists:true) | ||
| ]) | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.errors.collect { meta, txt -> [ meta, txt.collect{ file(it).name } ] }, | ||
| process.out.versions | ||
| ).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| test("homo sapiens - vcf, scaffold, [] - stub") { | ||
| options "-stub" | ||
| when { | ||
| process { | ||
| """ | ||
| input[0] = Channel.of([[ id:'truth_panel'], | ||
| file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf",checkIfExists:true), | ||
| file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi",checkIfExists:true), | ||
| "chr21", | ||
| [] | ||
| ]) | ||
| input[1] = [[], [], []] | ||
| input[2] = [[], [], []] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| 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 +1,86 @@ | ||
| { | ||
| "homo sapiens - vcf, scaffold, [] - stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "truth_panel" | ||
| }, | ||
| [ | ||
| "truth_panel.block.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940", | ||
| "truth_panel.calibration.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940", | ||
| "truth_panel.flipsAndSwitches.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940", | ||
| "truth_panel.frequency.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940", | ||
| "truth_panel.sample.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940", | ||
| "truth_panel.sample.typing.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940", | ||
| "truth_panel.type.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940", | ||
| "truth_panel.variant.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940", | ||
| "truth_panel.variant.typing.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" | ||
| ] | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,95238962a141557f464b8e22c8057211" | ||
| ], | ||
| "errors": [ | ||
| [ | ||
| { | ||
| "id": "truth_panel" | ||
| }, | ||
| [ | ||
| "truth_panel.block.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940", | ||
| "truth_panel.calibration.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940", | ||
| "truth_panel.flipsAndSwitches.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940", | ||
| "truth_panel.frequency.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940", | ||
| "truth_panel.sample.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940", | ||
| "truth_panel.sample.typing.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940", | ||
| "truth_panel.type.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940", | ||
| "truth_panel.variant.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940", | ||
| "truth_panel.variant.typing.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" | ||
| ] | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,95238962a141557f464b8e22c8057211" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.1" | ||
| }, | ||
| "timestamp": "2024-11-22T19:04:42.303883153" | ||
| }, | ||
| "homo sapiens - vcf, scaffold, []": { | ||
| "content": [ | ||
| [ | ||
| [ | ||
| { | ||
| "id": "scaffold", | ||
| "single_end": false | ||
| }, | ||
| [ | ||
| "scaffold.block.switch.txt.gz", | ||
| "scaffold.calibration.switch.txt.gz", | ||
| "scaffold.flipsAndSwitches.txt.gz", | ||
| "scaffold.frequency.switch.txt.gz", | ||
| "scaffold.sample.switch.txt.gz", | ||
| "scaffold.sample.typing.txt.gz", | ||
| "scaffold.type.switch.txt.gz", | ||
| "scaffold.variant.switch.txt.gz", | ||
| "scaffold.variant.typing.txt.gz" | ||
| ] | ||
| ] | ||
| ], | ||
| [ | ||
| "versions.yml:md5,95238962a141557f464b8e22c8057211" | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.1" | ||
| }, | ||
| "timestamp": "2024-11-22T19:13:32.038870261" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| process { | ||
| withName: SHAPEIT5_PHASECOMMON { | ||
| ext.args = params.shapeit5_phasecommon_args | ||
| } | ||
| } |
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Can we please do something with this dataset on the test-data repository, rather than leave it in the delete_me folder? You've got multiple modules here using it.
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You're totally right.
I'll discuss it in the dedicated slack channel and update this pull request when done !
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Those files are also present on the
phaseimputebranch of the test-datasets repository.Should I use these files ?
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sure that also works