fix starfusion local module from rnafusion to migrate it to nf-core/m…

modules/nf-core/starfusion/build/environment.yml

@@ -5,4 +5,4 @@ dependencies:
   - bioconda::dfam=3.7
   - bioconda::hmmer=3.4
   - bioconda::minimap2=2.28
-  - bioconda::star-fusion=1.14.0
+  - bioconda::star-fusion=1.15.0

modules/nf-core/starfusion/build/main.nf

@@ -4,14 +4,16 @@ process STARFUSION_BUILD {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/be/bed86145102fdf7e381e1a506a4723676f98b4bbe1db5085d02213cef18525c9/data' :
-        'community.wave.seqera.io/library/dfam_hmmer_minimap2_star-fusion:aa3a8e3951498552'}"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b0a58b9d30f9c72b22135f85746e10596d568c40a7d9634b13e0a0749cacd21b/data' :
+        'community.wave.seqera.io/library/dfam_hmmer_minimap2_star-fusion:c2bc5374f142ac93'}"
 
     input:
     tuple val(meta), path(fasta)
     tuple val(meta2), path(gtf)
     path fusion_annot_lib
     val dfam_species
+    val dfam_version
+    val pfam_version
 
     output:
     tuple val(meta), path("${prefix}_genome_lib_build_dir"), emit: reference
@@ -24,18 +26,30 @@ process STARFUSION_BUILD {
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     """
+    wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam${pfam_version}/Pfam-A.hmm.gz --no-check-certificate
+    wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm --no-check-certificate
+    wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm.h3f --no-check-certificate
+    wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm.h3i --no-check-certificate
+    wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm.h3m --no-check-certificate
+    wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm.h3p --no-check-certificate
+    gunzip Pfam-A.hmm.gz && hmmpress Pfam-A.hmm
+    wget https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/AnnotFilterRule.pm -O AnnotFilterRule.pm --no-check-certificate
+
+
     prep_genome_lib.pl \\
         --genome_fa $fasta \\
         --gtf $gtf \\
-        --dfam_db ${dfam_species} \\
-        --pfam_db current \\
+        --dfam_db ${dfam_species}_dfam.hmm \\
+        --pfam_db Pfam-A.hmm \\
         --fusion_annot_lib $fusion_annot_lib \\
+        --annot_filter_rule AnnotFilterRule.pm \\
         --CPU $task.cpus \\
         --output_dir ${prefix}_genome_lib_build_dir \\
         ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        wget: \$(wget --version | head -1 | cut -d ' ' -f 3)
         STAR-Fusion: \$(STAR-Fusion --version 2>&1 | grep -i 'version' | sed 's/STAR-Fusion version: //')
     END_VERSIONS
     """
@@ -128,6 +142,7 @@ process STARFUSION_BUILD {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        wget: \$(wget --version | head -1 | cut -d ' ' -f 3)
         STAR-Fusion: \$(STAR-Fusion --version 2>&1 | grep -i 'version' | sed 's/STAR-Fusion version: //')
     END_VERSIONS
     """

modules/nf-core/starfusion/build/meta.yml

@@ -47,6 +47,15 @@ input:
   - - dfam_species:
         type: string
         description: Dfam species name
+  - - dfam_version:
+        type: string
+        description: DNA transposable element database version, required for repeat
+          masking. Values such as '3.4' are accepted (will automatically pull the resources
+          from dfam).
+  - - pfam_version:
+        type: string
+        description: Protein families database version, to get domain information. Values
+          such as '37.4' are accepted (will automatically pull the resources from Pfam).
 output:
   - reference:
       - meta:

modules/nf-core/starfusion/build/tests/main.nf.test

@@ -22,7 +22,10 @@ nextflow_process {
                 ]
 
                 input [2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/CTAT_HumanFusionLib.mini.dat.gz')
-                input [3] = "human"
+                input [3] = "homo_sapiens"
+                input [4] = "3.8"
+                input [5] = "37.4"
+
                 """
             }
         }
@@ -124,7 +127,10 @@ nextflow_process {
                 ]
 
                 input [2] = file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/CTAT_HumanFusionLib.mini.dat.gz")
-                input [3] = "human"
+                input [3] = "homo_sapiens"
+                input [4] = "3.8"
+                input [5] = "37.4"
+
                 """
             }
         }

modules/nf-core/starfusion/build/tests/main.nf.test.snap

@@ -1,7 +1,7 @@
 {
     "STARFUSION_BUILD - human - minigenome": {
         "content": [
-            "AnnotFilterRule.pm:md5,5391fcc58d9c71cd1f0e45668c5ec597",
+            "AnnotFilterRule.pm:md5,f94966013cd0df9624a6dda0b75fefa0",
             "blast_pairs.dat.gz",
             "blast_pairs.idx",
             "annotfiltrule_cp.ok",
@@ -75,14 +75,14 @@
             "trans.blast.align_coords.align_coords.dbm",
             "trans.blast.dat.gz:md5,85ba5ea96c566f751ad83a3e4b8ab128",
             [
-                "versions.yml:md5,4a6ed47cb345f2a5af4d9f12b7918cdb"
+                "versions.yml:md5,99533491facb961016dafc1d45a8101e"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-03-31T19:58:54.583793842"
+        "timestamp": "2025-05-20T17:11:52.797058494"
     },
     "STARFUSION_BUILD - human - minigenome - stub": {
         "content": [
@@ -173,7 +173,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,4a6ed47cb345f2a5af4d9f12b7918cdb"
+                    "versions.yml:md5,99533491facb961016dafc1d45a8101e"
                 ],
                 "reference": [
                     [
@@ -261,14 +261,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,4a6ed47cb345f2a5af4d9f12b7918cdb"
+                    "versions.yml:md5,99533491facb961016dafc1d45a8101e"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-03-28T23:09:01.034159236"
+        "timestamp": "2025-05-19T19:52:36.457569412"
     }
 }