Remove containers with cache with snpEff too (nf-core#3670)

* update tests for snpeff * remove containers in config * fix cache version in tests * update meta.yml * fix meta.yml * fix meta data * fix md5sum * re-enable conda tests
JPejovicApis · Oct 10, 2023 · a127913 · a127913
1 parent 3a96faf
commit a127913
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Showing 12 changed files with 55 additions and 30 deletions.
diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
@@ -146,8 +146,6 @@ jobs:
             tags: gatk4/determinegermlinecontigploidy
           - profile: "conda"
             tags: subworkflows/bcl_demultiplex
-          - profile: "conda"
-            tags: subworkflows/vcf_annotate_ensemblvep_snpeff
           - profile: "conda"
             tags: subworkflows/fasta_clean_fcs
           - profile: "conda"

diff --git a/modules/nf-core/snpeff/download/meta.yml b/modules/nf-core/snpeff/download/meta.yml
@@ -2,6 +2,10 @@ name: SNPEFF_DOWNLOAD
 description: Genetic variant annotation and functional effect prediction toolbox
 keywords:
   - annotation
+  - effect prediction
+  - snpeff
+  - variant
+  - vcf
 tools:
   - snpeff:
       description: |
@@ -21,7 +25,7 @@ input:
       description: |
         vcf to annotate
   - db:
-      type: value
+      type: string
       description: |
         which db to annotate with
 output:

diff --git a/modules/nf-core/snpeff/snpeff/main.nf b/modules/nf-core/snpeff/snpeff/main.nf
@@ -10,7 +10,7 @@ process SNPEFF_SNPEFF {
     input:
     tuple val(meta), path(vcf)
     val   db
-    path  cache
+    tuple val(meta2), path(cache)
 
     output:
     tuple val(meta), path("*.ann.vcf"), emit: vcf

diff --git a/modules/nf-core/snpeff/snpeff/meta.yml b/modules/nf-core/snpeff/snpeff/meta.yml
@@ -2,8 +2,10 @@ name: SNPEFF_SNPEFF
 description: Genetic variant annotation and functional effect prediction toolbox
 keywords:
   - annotation
-  - variant
   - effect prediction
+  - snpeff
+  - variant
+  - vcf
 tools:
   - snpeff:
       description: |

diff --git a/tests/modules/nf-core/snpeff/download/main.nf b/tests/modules/nf-core/snpeff/download/main.nf
@@ -4,8 +4,10 @@ nextflow.enable.dsl = 2
 
 include { SNPEFF_DOWNLOAD } from '../../../../../modules/nf-core/snpeff/download/main.nf'
 
-workflow test_snpeff_download {
-    input = [ [ id:'test' ], "WBcel235", "105"]
+snpeff_cache_version = "105"
+snpeff_genome = "WBcel235"
+snpeff_cache_input = Channel.of([[id:"${snpeff_genome}.${snpeff_cache_version}"], snpeff_genome, snpeff_cache_version])
 
-    SNPEFF_DOWNLOAD ( input )
+workflow test_snpeff_download {
+    SNPEFF_DOWNLOAD(snpeff_cache_input)
 }
diff --git a/tests/modules/nf-core/snpeff/snpeff/main.nf b/tests/modules/nf-core/snpeff/snpeff/main.nf
@@ -2,13 +2,22 @@
 
 nextflow.enable.dsl = 2
 
-include { SNPEFF_SNPEFF } from '../../../../../modules/nf-core/snpeff/snpeff/main.nf'
+include { SNPEFF_DOWNLOAD } from '../../../../../modules/nf-core/snpeff/download/main'
+include { SNPEFF_SNPEFF   } from '../../../../../modules/nf-core/snpeff/snpeff/main'
+
+snpeff_cache_version = "105"
+snpeff_genome = "WBcel235"
+snpeff_cache_input = Channel.of([[id:"${snpeff_genome}.${snpeff_cache_version}"], snpeff_genome, snpeff_cache_version])
 
 workflow test_snpeff_snpeff {
-    input = [
+    input = Channel.of([
         [ id:'test' ], // meta map
         file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
-    ]
+    ])
+
+    SNPEFF_DOWNLOAD(snpeff_cache_input)
+
+    snpeff_cache = SNPEFF_DOWNLOAD.out.cache.first()
 
-    SNPEFF_SNPEFF ( input, "WBcel235.105", [] )
+    SNPEFF_SNPEFF(input, "${snpeff_genome}.${snpeff_cache_version}", snpeff_cache)
 }
diff --git a/tests/modules/nf-core/snpeff/snpeff/nextflow.config b/tests/modules/nf-core/snpeff/snpeff/nextflow.config
@@ -2,8 +2,4 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
-    withName: SNPEFF_SNPEFF {
-        container = 'docker.io/nfcore/snpeff:5.1.WBcel235'
-    }
-
 }
diff --git a/tests/modules/nf-core/snpeff/snpeff/test.yml b/tests/modules/nf-core/snpeff/snpeff/test.yml
@@ -5,7 +5,7 @@
     - snpeff/snpeff
   files:
     - path: output/snpeff/test.ann.vcf
-      md5sum: e933384e572fc5ed0cce0faf1c0b2cc9
+      md5sum: 9dc12cf54c78516abf3558672d3746d0
     - path: output/snpeff/test.csv
     - path: output/snpeff/test.genes.txt
       md5sum: 130536bf0237d7f3f746d32aaa32840a

diff --git a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf b/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
@@ -3,8 +3,12 @@
 nextflow.enable.dsl = 2
 
 include { ENSEMBLVEP_DOWNLOAD            } from '../../../../modules/nf-core/ensemblvep/download/main'
+include { SNPEFF_DOWNLOAD                } from '../../../../modules/nf-core/snpeff/download/main'
 include { VCF_ANNOTATE_ENSEMBLVEP_SNPEFF } from '../../../../subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main'
 
+snpeff_cache_version = "105"
+snpeff_genome = "WBcel235"
+snpeff_cache_input = Channel.of([[id:"${snpeff_genome}.${snpeff_cache_version}"], snpeff_genome, snpeff_cache_version])
 vep_cache_version = "110"
 vep_genome = "WBcel235"
 vep_species = "caenorhabditis_elegans"
@@ -61,6 +65,10 @@ workflow vcf_annotate_ensemblvep_snpeff_snpeff {
         ]
     ])
 
+    SNPEFF_DOWNLOAD(snpeff_cache_input)
+
+    snpeff_cache = SNPEFF_DOWNLOAD.out.cache.first()
+
     VCF_ANNOTATE_ENSEMBLVEP_SNPEFF (
         input,
         [[],[]],
@@ -69,8 +77,8 @@ workflow vcf_annotate_ensemblvep_snpeff_snpeff {
         [],
         [],
         [],
-        "WBcel235.99",
-        [],
+        "${snpeff_genome}.${snpeff_cache_version}",
+        snpeff_cache,
         ["snpeff"],
         5
     )
@@ -93,7 +101,9 @@ workflow vcf_annotate_ensemblvep_snpeff_both {
     ])
 
     ENSEMBLVEP_DOWNLOAD(vep_cache_input)
+    SNPEFF_DOWNLOAD(snpeff_cache_input)
 
+    snpeff_cache = SNPEFF_DOWNLOAD.out.cache.first()
     vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }.first()
 
     VCF_ANNOTATE_ENSEMBLVEP_SNPEFF (
@@ -104,8 +114,8 @@ workflow vcf_annotate_ensemblvep_snpeff_both {
         vep_cache_version,
         vep_cache,
         [],
-        "WBcel235.99",
-        [],
+        "${snpeff_genome}.${snpeff_cache_version}",
+        snpeff_cache,
         ["ensemblvep", "snpeff"],
         5
     )

diff --git a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/nextflow.config b/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/nextflow.config
@@ -17,8 +17,4 @@ process {
         ].join(" ")}
     }
 
-    withName: SNPEFF_SNPEFF {
-        container = 'docker.io/nfcore/snpeff:5.0.WBcel235'
-    }
-
 }
diff --git a/tests/subworkflows/nf-core/vcf_annotate_snpeff/main.nf b/tests/subworkflows/nf-core/vcf_annotate_snpeff/main.nf
@@ -2,13 +2,22 @@
 
 nextflow.enable.dsl = 2
 
-include { VCF_ANNOTATE_SNPEFF } from '../../../../subworkflows/nf-core/vcf_annotate_snpeff/main.nf'
+include { SNPEFF_DOWNLOAD     } from '../../../../modules/nf-core/snpeff/download/main'
+include { VCF_ANNOTATE_SNPEFF } from '../../../../subworkflows/nf-core/vcf_annotate_snpeff/main'
+
+snpeff_cache_version = "105"
+snpeff_genome = "WBcel235"
+snpeff_cache_input = Channel.of([[id:"${snpeff_genome}.${snpeff_cache_version}"], snpeff_genome, snpeff_cache_version])
 
 workflow vcf_annotate_snpeff {
-    input = [
+    input = Channel.of([
         [ id:'test' ], // meta map
         file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
-    ]
+    ])
+
+    SNPEFF_DOWNLOAD(snpeff_cache_input)
+
+    snpeff_cache = SNPEFF_DOWNLOAD.out.cache.first()
 
-    VCF_ANNOTATE_SNPEFF ( input, "WBcel235.99", [] )
+    VCF_ANNOTATE_SNPEFF ( input, "${snpeff_genome}.${snpeff_cache_version}", snpeff_cache )
 }
diff --git a/tests/subworkflows/nf-core/vcf_annotate_snpeff/nextflow.config b/tests/subworkflows/nf-core/vcf_annotate_snpeff/nextflow.config
@@ -3,7 +3,6 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
     withName: SNPEFF_SNPEFF {
-        container = 'docker.io/nfcore/snpeff:5.0.WBcel235'
         publishDir       = [
                 path: { "output/snpeff/test/" },
                 pattern: "*{csv,html,genes.txt}"