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Update stranger #5717
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caf1503
everything but snapshot
fellen31 2c47987
fix gz snap
fellen31 4f21062
update testdata paths
fellen31 d35747c
Merge branch 'master' into update-stranger
SPPearce 411c7cf
Update main.nf.test
fellen31 4305e65
Merge branch 'master' into update-stranger
fellen31 174bc6b
update test
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -4,4 +4,4 @@ channels: | |
| - bioconda | ||
| - defaults | ||
| dependencies: | ||
| - bioconda::stranger=0.8.1 | ||
| - bioconda::stranger=0.9.0 | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,82 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process STRANGER" | ||
| script "../main.nf" | ||
| process "STRANGER" | ||
| config "./nextflow.config" | ||
|
|
||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "stranger" | ||
| tag "expansionhunter" | ||
|
|
||
| setup { | ||
| run("EXPANSIONHUNTER") { | ||
| script "../../expansionhunter/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) | ||
| ] | ||
| input[1] = [ | ||
| [id:'fasta'], | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) | ||
| ] | ||
| input[2] = [ | ||
| [id:'fai'], | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) | ||
| ] | ||
| input[3] = [ | ||
| [id:'catalogue'], | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/loci/repeat_expansions.json', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
| test("homo_sapiens - vcf, repeat_catalogue") { | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = EXPANSIONHUNTER.out.vcf | ||
| input[1] = [ | ||
| [id:'catalogue'], | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/loci/repeat_expansions.json', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assert process.success | ||
| assert snapshot(process.out).match() | ||
| } | ||
|
|
||
| } | ||
|
|
||
| test("homo_sapiens - vcf, repeat_catalogue - stub") { | ||
|
|
||
| options "-stub" | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = EXPANSIONHUNTER.out.vcf | ||
| input[1] = [ | ||
| [id:'catalogue'], | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/loci/repeat_expansions.json', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| 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 @@ | ||
| { | ||
| "homo_sapiens - vcf, repeat_catalogue - stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "stranger.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,369e472eaaf24bf7d154b41bc731ac50" | ||
| ], | ||
| "vcf": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "stranger.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,369e472eaaf24bf7d154b41bc731ac50" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.2" | ||
| }, | ||
| "timestamp": "2024-06-24T06:58:08.232701026" | ||
| }, | ||
| "homo_sapiens - vcf, repeat_catalogue": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "stranger.vcf.gz:md5,bce108ecdcff045eebd6cf831be9b5a8" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,369e472eaaf24bf7d154b41bc731ac50" | ||
| ], | ||
| "vcf": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "stranger.vcf.gz:md5,bce108ecdcff045eebd6cf831be9b5a8" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,369e472eaaf24bf7d154b41bc731ac50" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.2" | ||
| }, | ||
| "timestamp": "2024-06-24T06:57:54.749238699" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| process { | ||
| withName: 'STRANGER' { | ||
| ext.prefix = "stranger" | ||
| } | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| stranger: | ||
| - "modules/nf-core/stranger/**" |
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Do you need this now?
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Otherwise the input vcf and output will be named the same.