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Update glimpse2 modules (nf-core#6825)
* Update glimpse2 modules * Update glimpse2 phase tuple * Update snapshot * Add versions --------- Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Sateesh_Peri <[email protected]>
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199 changes: 199 additions & 0 deletions
199
modules/nf-core/glimpse2/concordance/tests/main.nf.test
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,199 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process GLIMPSE2_CONCORDANCE" | ||
| script "../main.nf" | ||
| process "GLIMPSE2_CONCORDANCE" | ||
| tag "glimpse2" | ||
| tag "glimpse2/concordance" | ||
| tag "glimpse2/phase" | ||
| tag "bcftools/index" | ||
| tag "modules_nfcore" | ||
| tag "modules" | ||
|
|
||
| setup { | ||
| run("GLIMPSE2_PHASE") { | ||
| script "../../phase/main.nf" | ||
| process { | ||
| """ | ||
| input_vcf = Channel.of([ | ||
| [ id:'input'], // meta map | ||
| file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true), | ||
| file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true), | ||
| [] | ||
| ]) | ||
| samples_infos = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt') | ||
| region = Channel.of(["chr21:16600000-16800000","chr21:16650000-16750000"]) | ||
| ch_ref_panel = Channel.of([ | ||
| file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true), | ||
| file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true) | ||
| ]) | ||
| ch_map = Channel.of([ | ||
| file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true), | ||
| ]) | ||
| // [meta, vcf, index, sample_infos, regionin, regionout, regionindex, ref, ref_index, map] | ||
| input[0] = input_vcf | ||
| .combine(samples_infos) | ||
| .combine(region) | ||
| .combine( ch_ref_panel ) | ||
| .combine( ch_map ) | ||
| input[1]= Channel.of([[],[],[]]) | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| run("BCFTOOLS_INDEX") { | ||
| script "../../../bcftools/index/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = GLIMPSE2_PHASE.output.phased_variants | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
|
|
||
| test("test_glimpse2_concordance") { | ||
| config "./nextflow.config" | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| allele_freq = Channel.of([ | ||
| file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz",checkIfExists:true), | ||
| file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz.csi",checkIfExists:true) | ||
| ]) | ||
| truth = Channel.of([ | ||
| file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf",checkIfExists:true), | ||
| file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf.csi",checkIfExists:true) | ||
| ]) | ||
| list_inputs = GLIMPSE2_PHASE.output.phased_variants | ||
| .join( BCFTOOLS_INDEX.out.csi ) | ||
| .combine( truth ) | ||
| .combine( allele_freq ) | ||
| .combine( Channel.of([[]]) ) | ||
| .combine( Channel.of(["chr21"]) ) | ||
| input[0] = list_inputs | ||
| input[1] = Channel.of([[id:"params"],[],"0 0.01 0.05 0.1 0.2 0.5",[],[]]) | ||
| input[2] = 0.9999 | ||
| input[3] = 8 | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.errors_cal.collect{ file(it[1]).name }, | ||
| process.out.errors_grp.collect{ file(it[1]).name }, | ||
| process.out.errors_spl.collect{ file(it[1]).name }, | ||
| process.out.rsquare_grp.collect{ file(it[1]).name }, | ||
| process.out.rsquare_spl.collect{ file(it[1]).name }, | ||
| process.out.versions | ||
| ).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| test("test_list_region") { | ||
| config "./nextflow.config" | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| allele_freq = Channel.of([ | ||
| file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz",checkIfExists:true), | ||
| file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz.csi",checkIfExists:true) | ||
| ]) | ||
| truth = Channel.of([ | ||
| file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf",checkIfExists:true), | ||
| file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf.csi",checkIfExists:true) | ||
| ]) | ||
| list_inputs = GLIMPSE2_PHASE.output.phased_variants | ||
| .join( BCFTOOLS_INDEX.out.csi ) | ||
| .combine( truth ) | ||
| .combine( allele_freq ) | ||
| .combine( Channel.of([[]]) ) | ||
| .combine( Channel.of(["chr21", "chr21"]) ) | ||
| input[0] = list_inputs | ||
| input[1] = Channel.of([[id:"params"],[],"0 0.01 0.05 0.1 0.2 0.5",[],[]]) | ||
| input[2] = 0.9999 | ||
| input[3] = 8 | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.errors_cal.collect{ file(it[1]).name }, | ||
| process.out.errors_grp.collect{ file(it[1]).name }, | ||
| process.out.errors_spl.collect{ file(it[1]).name }, | ||
| process.out.rsquare_grp.collect{ file(it[1]).name }, | ||
| process.out.rsquare_spl.collect{ file(it[1]).name }, | ||
| process.out.versions | ||
| ).match() | ||
| } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| test("test_r2_per_site") { | ||
| config "./nextflow_R2.config" | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| allele_freq = Channel.of([ | ||
| file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz",checkIfExists:true), | ||
| file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz.csi",checkIfExists:true) | ||
| ]) | ||
| truth = Channel.of([ | ||
| file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf",checkIfExists:true), | ||
| file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf.csi",checkIfExists:true) | ||
| ]) | ||
| list_inputs = GLIMPSE2_PHASE.output.phased_variants | ||
| .join( BCFTOOLS_INDEX.out.csi ) | ||
| .combine( truth ) | ||
| .combine( allele_freq ) | ||
| .combine( Channel.of([[]]) ) | ||
| .combine( Channel.of(["chr21"]) ) | ||
| input[0] = list_inputs | ||
| input[1] = Channel.of([[id:"params"],[],"0 0.01 0.05 0.1 0.2 0.5",[],[]]) | ||
| input[2] = 0.9999 | ||
| input[3] = 8 | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.errors_cal.collect{ file(it[1]).name }, | ||
| process.out.errors_grp.collect{ file(it[1]).name }, | ||
| process.out.errors_spl.collect{ file(it[1]).name }, | ||
| process.out.rsquare_grp.collect{ file(it[1]).name }, | ||
| process.out.rsquare_spl.collect{ file(it[1]).name }, | ||
| process.out.rsquare_per_site.collect{ file(it[1]).name }, | ||
| process.out.versions | ||
| ).match() | ||
| } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| } |
86 changes: 86 additions & 0 deletions
86
modules/nf-core/glimpse2/concordance/tests/main.nf.test.snap
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,86 @@ | ||
| { | ||
| "test_r2_per_site": { | ||
| "content": [ | ||
| [ | ||
| "input.error.cal.txt.gz" | ||
| ], | ||
| [ | ||
| "input.error.grp.txt.gz" | ||
| ], | ||
| [ | ||
| "input.error.spl.txt.gz" | ||
| ], | ||
| [ | ||
| "input.rsquare.grp.txt.gz" | ||
| ], | ||
| [ | ||
| "input.rsquare.spl.txt.gz" | ||
| ], | ||
| [ | ||
| "input_r2_sites.txt.gz" | ||
| ], | ||
| [ | ||
| "versions.yml:md5,ba729289bab6b9fbb8c36a620c86bb82" | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.3" | ||
| }, | ||
| "timestamp": "2024-10-22T16:23:00.623182365" | ||
| }, | ||
| "test_glimpse2_concordance": { | ||
| "content": [ | ||
| [ | ||
| "input.error.cal.txt.gz" | ||
| ], | ||
| [ | ||
| "input.error.grp.txt.gz" | ||
| ], | ||
| [ | ||
| "input.error.spl.txt.gz" | ||
| ], | ||
| [ | ||
| "input.rsquare.grp.txt.gz" | ||
| ], | ||
| [ | ||
| "input.rsquare.spl.txt.gz" | ||
| ], | ||
| [ | ||
| "versions.yml:md5,ba729289bab6b9fbb8c36a620c86bb82" | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.3" | ||
| }, | ||
| "timestamp": "2024-10-22T16:22:26.823581573" | ||
| }, | ||
| "test_list_region": { | ||
| "content": [ | ||
| [ | ||
| "input.error.cal.txt.gz" | ||
| ], | ||
| [ | ||
| "input.error.grp.txt.gz" | ||
| ], | ||
| [ | ||
| "input.error.spl.txt.gz" | ||
| ], | ||
| [ | ||
| "input.rsquare.grp.txt.gz" | ||
| ], | ||
| [ | ||
| "input.rsquare.spl.txt.gz" | ||
| ], | ||
| [ | ||
| "versions.yml:md5,ba729289bab6b9fbb8c36a620c86bb82" | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.3" | ||
| }, | ||
| "timestamp": "2024-10-22T16:22:43.352729014" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| process { | ||
| withName: GLIMPSE2_CHUNK { | ||
| ext.prefix = { "${meta.id}" } | ||
| } | ||
| publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } | ||
| } |
14 changes: 7 additions & 7 deletions
14
...core/glimpse2/concordance/nextflow.config → ...pse2/concordance/tests/nextflow_R2.config
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| process { | ||
| publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } | ||
|
|
||
| withName:GLIMPSE2_CONCORDANCE_R2_PER_SITE { | ||
| ext.args = "--out-r2-per-site" | ||
| } | ||
| } | ||
| process { | ||
| publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } | ||
|
|
||
| withName:GLIMPSE2_CONCORDANCE { | ||
| ext.args = "--out-r2-per-site" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| glimpse2/concordance: | ||
| - modules/nf-core/glimpse2/concordance/** |
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