fix: Update CHM13

nf-core · Jul 8, 2024 · 63f5074 · 63f5074
1 parent 2aeb303
commit 63f5074
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Showing 2 changed files with 3 additions and 6 deletions.
diff --git a/conf/igenomes.config b/conf/igenomes.config
@@ -37,11 +37,8 @@ params {
             blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
         }
         'CHM13' {
-            fasta       = "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.fna.gz"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/"
-            bwamem2     = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/"
-            gtf         = "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gtf.gz"
-            gff         = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz"
+            fasta       = "https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0.fa.gz"
+            gff         = "https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13v2.0_RefSeq_Liftoff_v5.1.gff3.gz"
             mito_name   = "chrM"
         }
         'GRCm38' {

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -190,7 +190,7 @@
                     "type": "string",
                     "format": "file-path",
                     "mimetype": "text/plain",
-                    "pattern": "^\\S+\\.gff(\\.gz)?$",
+                    "pattern": "^\\S+\\.gff(3)?(\\.gz)?$",
                     "fa_icon": "fas fa-code-branch",
                     "description": "Path to GFF3 annotation file.",
                     "help_text": "This parameter must be specified if `--genome` or `--gtf` are not specified."