Update db handling in snpeff_snpeff

Author: Aberdur

modules.json

@@ -224,13 +224,6 @@
                             "modules"
                         ]
                     },
-                    "kraken2/build": {
-                        "branch": "master",
-                        "git_sha": "b30b51e5d2d08f1f36f314a20ce4b9deddf2a5c1",
-                        "installed_by": [
-                            "modules"
-                        ]
-                    },
                     "kraken2/kraken2": {
                         "branch": "master",
                         "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",

subworkflows/local/additional_annotation.nf

@@ -15,7 +15,7 @@ workflow ADDITIONAL_ANNOTATION {
     take:
     vcf      // channel: [ val(meta), [ vcf ] ]
     tbi      // channel: [ val(meta), [ tbi ] ]
-    fasta    // path   : genome.fasta
+    fasta_path    // path   : genome.fasta
     annot    // path   : additional_annotation
     pangolin // channel: [ val(meta), [ csv ] ]
 
@@ -45,18 +45,34 @@ workflow ADDITIONAL_ANNOTATION {
     ch_snpeff_config = Channel.empty()
 
     SNPEFF_BUILD (
-        fasta,
+        fasta_path,
         ch_annot
     )
     ch_snpeff_db     = SNPEFF_BUILD.out.db
     ch_snpeff_config = SNPEFF_BUILD.out.config
     ch_versions      = ch_versions.mix(SNPEFF_BUILD.out.versions)
-    ch_cache_empty = Channel.empty()
+    
+    fasta = fasta_path
+        .map { file ->
+            def filename = file.name
+            def basename = filename.take(filename.lastIndexOf('.'))
+            basename
+        }
+
+    fasta_basename = fasta_path.map { files ->
+        def file = files[0]
+        def filename = file.getBaseName()
+        return filename
+    }
+
+    snpeff_cache = ch_snpeff_db.collect()
+        .map{ cache -> [ [ id:fasta.value ], cache ] }
 
     SNPEFF_SNPEFF (
         vcf,
-        ch_snpeff_db,
-        ch_cache_empty
+        fasta_basename,
+        snpeff_cache,
+        ch_snpeff_config
     )
     ch_versions = ch_versions.mix(SNPEFF_SNPEFF.out.versions.first())
 

subworkflows/local/snpeff_snpsift.nf

@@ -17,19 +17,25 @@ workflow SNPEFF_SNPSIFT {
     main:
 
     ch_versions = Channel.empty()
-
     fasta = fasta_path
         .map { file ->
             def filename = file.name
             def basename = filename.take(filename.lastIndexOf('.'))
             basename
         }
+
+    fasta_basename = fasta_path.map { files ->
+        def file = files[0]
+        def filename = file.getBaseName()
+        return filename
+    }
+
     snpeff_cache = db.collect()
         .map{ cache -> [ [ id:fasta.value ], cache ] }
 
     SNPEFF_SNPEFF (
         vcf,
-        "GCA_009858895.3_ASM985889v3_genomic.200409",
+        fasta_basename,
         snpeff_cache,
         config
     )