From 9040aa06a55410f7b45c4f8f7cadc1620d2d3860 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 29 May 2024 18:50:18 +0200
Subject: [PATCH] fix usage of some reference files

---
 main.nf              | 12 +++---------
 nextflow.config      |  9 +++++++++
 nextflow_schema.json |  4 ++++
 3 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/main.nf b/main.nf
index 6e638a85..78c33003 100644
--- a/main.nf
+++ b/main.nf
@@ -16,19 +16,13 @@ nextflow.enable.dsl = 2
     GENOME PARAMETER VALUES
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
+
 params.fasta             = getGenomeAttribute('fasta')
-params.fasta_fai         = getGenomeAttribute('fasta_fai')
-params.dict              = getGenomeAttribute('dict')
+params.gene_bed          = getGenomeAttribute('bed12')
 params.gtf               = getGenomeAttribute('gtf')
-params.gff               = getGenomeAttribute('gff')
-params.exon_bed          = getGenomeAttribute('exon_bed')
-params.star_index        = getGenomeAttribute('star')
-params.dbsnp             = getGenomeAttribute('dbsnp')
-params.dbsnp_tbi         = getGenomeAttribute('dbsnp_tbi')
-params.known_indels      = getGenomeAttribute('known_indels')
-params.known_indels_tbi  = getGenomeAttribute('known_indels_tbi')
 params.snpeff_db         = getGenomeAttribute('snpeff_db')
 params.snpeff_genome     = getGenomeAttribute('snpeff_genome')
+params.star_index        = getGenomeAttribute('star')
 params.vep_cache_version = getGenomeAttribute('vep_cache_version')
 params.vep_genome        = getGenomeAttribute('vep_genome')
 params.vep_species       = getGenomeAttribute('vep_species')
diff --git a/nextflow.config b/nextflow.config
index eff8a185..6365f097 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -19,6 +19,15 @@ params {
     save_merged_fastq               = false
     feature_type                    = 'exon'
 
+    dbsnp                           = null
+    dbsnp_tbi                       = null
+    dict                            = null
+    exon_bed                        = null
+    fasta_fai                       = null
+    gff                             = null
+    known_indels                    = null
+    known_indels_tbi                = null
+
     // Sequence read information
     read_length                     = 150 // Required for STAR to build index and align reads
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index b3de2e1a..8c9ac00f 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -91,6 +91,10 @@
                     "description": "Path to GFF3 annotation file.",
                     "help_text": "This parameter must be specified if `--genome` or `--gtf` are not specified."
                 },
+                "gene_bed": {
+                    "type": "string",
+                    "description": "Path to BED file containing gene intervals. This will be created from the GTF file if not specified."
+                },
                 "exon_bed": {
                     "type": "string",
                     "description": "Path to BED file containing exon intervals. This will be created from the GTF file if not specified."