fix: specific genome versions

nf-core · Jul 3, 2023 · bb0feab · bb0feab
1 parent bb42e09
commit bb0feab
Show file tree

Hide file tree

Showing 3 changed files with 14 additions and 12 deletions.
diff --git a/README.md b/README.md
@@ -36,7 +36,7 @@ Next, you have to generate genome references to incorporate ERCC spike-ins. Refe
 ```bash
 nextflow run nf-core/marsseq \
   -profile <docker/singularity/.../institute> \
-  --genome <mm10,mm9,GRCh38> \
+  --genome <mm10,mm9,GRCh38_v43> \
   --build_references \
   --input samplsheet.csv \
   --outdir <OUTDIR>
@@ -47,7 +47,7 @@ Now, you can run the pipeline using:
 ```bash
 nextflow run nf-core/marsseq \
   -profile <docker/singularity/.../institute> \
-  --genome <mm10,mm9,GRCh38> \
+  --genome <mm10,mm9,GRCh38_v43> \
   --input samplesheet.csv \
   --outdir <OUTDIR>
 ```

diff --git a/conf/genomes.config b/conf/genomes.config
@@ -13,12 +13,12 @@ params {
     // GENCODE references (https://www.gencodegenes.org/)
     genomes {
         'mm10_v32' {
-            bowtie2     = "${params.genomes_base}/mm10/bowtie2/"
-            fasta       = "${params.genomes_base}/mm10/GRCm39.fa"
+            bowtie2     = "${params.genomes_base}/mm10_v32/bowtie2/"
+            fasta       = "${params.genomes_base}/mm10_v32/GRCm39.fa"
             fasta_url   = "http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M32/GRCm39.primary_assembly.genome.fa.gz"
-            gtf         = "${params.genomes_base}/mm10/GRCm39.gtf"
+            gtf         = "${params.genomes_base}/mm10_v32/GRCm39.gtf"
             gtf_url     = "http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M32/gencode.vM32.annotation.gtf.gz"
-            star        = "${params.genomes_base}/mm10/star/"
+            star        = "${params.genomes_base}/mm10_v32/star/"
         }
         'mm10' {
             bowtie2     = "${params.genomes_base}/mm10/bowtie2/"
@@ -36,11 +36,13 @@ params {
             gtf_url     = "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M1/gencode.vM1.annotation.gtf.gz"
             star        = "${params.genomes_base}/mm9/star/"
         }
-        'GRCh38' {
-            fasta       = "${params.genomes_base}/mm10/GRCh38.fa"
-            gtf         = "${params.genomes_base}/mm10/GRCh38.gtf"
-            bowtie2     = "${params.genomes_base}/mm10/Bowtie2Index/"
-            star        = "${params.genomes_base}/mm10/STARIndex/"
+        'GRCh38_v43' {
+            bowtie2     = "${params.genomes_base}/GRCh38_v43/bowtie2/"
+            fasta       = "${params.genomes_base}/GRCh38_v43/GRCh38.fa"
+            fasta_url   = "http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/GRCh38.primary_assembly.genome.fa.gz"
+            gtf         = "${params.genomes_base}/GRCh38_v43/GRCh38.gtf"
+            gtf_url     = "http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/gencode.v43.annotation.gtf.gz"
+            star        = "${params.genomes_base}/GRCh38_v43/star/"
         }
     }
 }
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -78,7 +78,7 @@
                     "description": "Name of Genomes reference.",
                     "default": "mm10",
                     "fa_icon": "fas fa-book",
-                    "help_text": "Currently supported mouse: `mm9`, `mm10` and human `GRCh38`. The references are downloaded from [GENCODE](https://www.gencodegenes.org) database."
+                    "help_text": "Currently supported mouse: `mm9`, `mm10` and human `GRCh38_v43`. The references are downloaded from [GENCODE](https://www.gencodegenes.org) database."
                 },
                 "fasta": {
                     "type": "string",