Merge branch 'dev' into starfusion_detect

nf-core · Dec 19, 2024 · d08b0b2 · d08b0b2
2 parents 612723f + 34121d1
commit d08b0b2
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Showing 3 changed files with 10 additions and 10 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -320,7 +320,7 @@ process {
         ]
     }
 
-    withName: 'STARFUSION_BUILD' {
+    withName: 'NFCORE_RNAFUSION:BUILD_REFERENCES:STARFUSION_BUILD' {
         cpus   = { 24    * task.attempt }
         memory = { 100.GB * task.attempt }
         time   = { 2.d  * task.attempt }
@@ -329,7 +329,7 @@ process {
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
-        ext.args = "--max_readlength ${params.read_length}"
+        ext.args = "--max_readlength ${params.read_length} --human_gencode_filter"
     }
 
     withName: 'STARFUSION_DOWNLOAD' {

diff --git a/modules/local/starfusion/build/tests/main.nf.test.snap b/modules/local/starfusion/build/tests/main.nf.test.snap
@@ -62,12 +62,12 @@
             "exonGeTrInfo.tab:md5,3c35618d07a8e35a0f9108699fcdda42",
             "exonInfo.tab:md5,bcbb3f32fa31fe504cc737f337ad341c",
             "geneInfo.tab:md5,db5db4b6e003904e9908fce7c05f0125",
-            "Genome:md5,21aac51c5062f73d6305ae77691f5d4e",
+            "Genome:md5,9e3efdd0901cabb5a2d589664a63b372",
             true,
             true,
-            "SA:md5,4d6ee7c82328aa304300e51ab5677ff9",
-            "SAindex:md5,2d3498f7d84a69bbc65fe9de1887820c",
-            "sjdbInfo.txt:md5,0ad0c108e6d02ec541d6adeffbdea6fd",
+            "SA:md5,7dd9083264be9c6a2194d990bc10d237",
+            "SAindex:md5,ac4711df685109e04356db9e9cb9fb7f",
+            "sjdbInfo.txt:md5,e4cc1bbf8bd687cfc3d7c2c702e6def7",
             "sjdbList.fromGTF.out.tab:md5,8f3e8604b00d4067e4eb80aa476a8113",
             "sjdbList.out.tab:md5,5d78dd49d5db24ca2c056b7ebe5c2059",
             "transcriptInfo.tab:md5,b758c0ccaddcf0453bab5905b3cec4a2",
@@ -77,10 +77,10 @@
             null
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-12T14:57:13.528134845"
+        "timestamp": "2024-12-19T17:03:12.812884291"
     },
     "STARFUSION_BUILD - human - minigenome - stub": {
         "content": [

diff --git a/nextflow.config b/nextflow.config
@@ -30,7 +30,7 @@ params {
     read_length                = 100
     starfusion_build           = true
     genomes                    = [:]
-    fusion_annot_lib           = null       // path to  dat.gz CTAT genome lib (e.g. https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play.tar.gz)
+    fusion_annot_lib           = "https://github.com/FusionAnnotator/CTAT_HumanFusionLib/releases/download/v0.3.0/fusion_lib.Mar2021.dat.gz" // path to  dat.gz CTAT genome lib // TODO: Update to latest with s3 link when available
 
     // Genomes options
     fasta          = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.all.fa"