Merge pull request #1236 from maxulysse/fix_annotation_unused

FIX: remove check annotation folders existence when no annotation
nf-core · Sep 15, 2023 · c6ec5dc · c6ec5dc
2 parents a0c0cbd + e745db6
commit c6ec5dc
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 
 - [#1232](https://github.com/nf-core/sarek/pull/1232) - Fix Zenodo IDs in manifest
+- [#1236](https://github.com/nf-core/sarek/pull/1236) - Fix annotation cache folder verification when no annotation
 
 ### Dependencies
 

diff --git a/workflows/sarek.nf b/workflows/sarek.nf
@@ -50,14 +50,16 @@ def checkPathParamList = [
     params.multiqc_config,
     params.pon,
     params.pon_tbi,
-    params.snpeff_cache,
     params.spliceai_indel,
     params.spliceai_indel_tbi,
     params.spliceai_snv,
-    params.spliceai_snv_tbi,
-    params.vep_cache
+    params.spliceai_snv_tbi
 ]
 
+// only check if we are using the tools
+if (params.tools && params.tools.contains("snpeff")) checkPathParamList.add(params.snpeff_cache)
+if (params.tools && params.tools.contains("vep"))    checkPathParamList.add(params.vep_cache)
+
 // Validate input parameters
 WorkflowSarek.initialise(params, log)
 
@@ -288,19 +290,6 @@ if ((params.download_cache) && (params.snpeff_cache || params.vep_cache)) {
     error("Please specify either `--download_cache` or `--snpeff_cache`, `--vep_cache`.\nhttps://nf-co.re/sarek/dev/usage#how-to-customise-snpeff-and-vep-annotation")
 }
 
-if ( params.vep_cache ) {
-    def vep_cache_dir = file("$params.vep_cache", type: 'dir') / "${params.vep_cache_version}_${params.vep_genome}"
-    if ( !vep_cache_dir.exists() || !vep_cache_dir.isDirectory() ) {
-        error("Files within --vep_cache invalid. Make sure there is a directory named ${params.vep_cache_version}_${params.vep_genome} in ${params.vep_cache}.\nhttps://nf-co.re/sarek/dev/usage#how-to-customise-snpeff-and-vep-annotation")
-    }
-}
-
-if ( params.snpeff_cache ) {
-    def snpeff_cache_dir = file("$params.snpeff_cache", type: 'dir') / "${params.snpeff_genome}.${params.snpeff_db}"
-    if ( !snpeff_cache_dir.exists() || !snpeff_cache_dir.isDirectory() ) {
-        error("Files within --snpeff_cache invalid. Make sure there is a directory named ${params.snpeff_genome}.${params.snpeff_db} in ${params.snpeff_cache}.\nhttps://nf-co.re/sarek/dev/usage#how-to-customise-snpeff-and-vep-annotation")
-    }
-}
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT LOCAL MODULES/SUBWORKFLOWS
@@ -334,8 +323,26 @@ vep_genome         = params.vep_genome         ?: Channel.empty()
 vep_species        = params.vep_species        ?: Channel.empty()
 
 // Initialize files channels based on params, not defined within the params.genomes[params.genome] scope
-snpeff_cache       = params.snpeff_cache ? params.use_annotation_cache_keys ? Channel.fromPath("${params.snpeff_cache}/${params.snpeff_genome}.${params.snpeff_db}", checkIfExists: true).collect()   : Channel.fromPath(params.snpeff_cache).collect() : []
-vep_cache          = params.vep_cache    ? params.use_annotation_cache_keys ? Channel.fromPath("${params.vep_cache}/${params.vep_cache_version}_${params.vep_genome}", checkIfExists: true).collect() : Channel.fromPath(params.vep_cache).collect()    : []
+if (params.snpeff_cache && params.tools && params.tools.contains("snpeff")) {
+    def snpeff_annotation_cache_key = params.use_annotation_cache_keys ? "${params.snpeff_genome}.${params.snpeff_db}/" : ""
+    def snpeff_cache_dir =  "${snpeff_annotation_cache_key}${params.snpeff_genome}.${params.snpeff_db}"
+    def snpeff_cache_path_full = file("$params.snpeff_cache/$snpeff_cache_dir", type: 'dir')
+    if ( !snpeff_cache_path_full.exists() || !snpeff_cache_path_full.isDirectory() ) {
+        error("Files within --snpeff_cache invalid. Make sure there is a directory named ${snpeff_cache_dir} in ${params.snpeff_cache}.\nhttps://nf-co.re/sarek/dev/usage#how-to-customise-snpeff-and-vep-annotation")
+    }
+    snpeff_cache = Channel.fromPath(file("${params.snpeff_cache}/${snpeff_annotation_cache_key}"), checkIfExists: true).collect()
+        .map{ cache -> [ [ id:"${params.snpeff_genome}.${params.snpeff_db}" ], cache ] }
+} else snpeff_cache = []
+
+if (params.vep_cache && params.tools && params.tools.contains("vep")) {
+    def vep_annotation_cache_key = params.use_annotation_cache_keys ? "${params.vep_cache_version}_${params.vep_genome}/" : ""
+    def vep_cache_dir = "${vep_annotation_cache_key}${params.vep_species}/${params.vep_cache_version}_${params.vep_genome}"
+    def vep_cache_path_full = file("$params.vep_cache/$vep_cache_dir", type: 'dir')
+    if ( !vep_cache_path_full.exists() || !vep_cache_path_full.isDirectory() ) {
+        error("Files within --vep_cache invalid. Make sure there is a directory named ${vep_cache_dir} in ${params.vep_cache}.\nhttps://nf-co.re/sarek/dev/usage#how-to-customise-snpeff-and-vep-annotation")
+    }
+    vep_cache = Channel.fromPath(file("${params.vep_cache}/${vep_annotation_cache_key}"), checkIfExists: true).collect()
+} else vep_cache = []
 
 vep_extra_files = []