Merge pull request #574 from alanmmobbs93/update_arriba-arriba_module

Update arriba_arriba module
nf-core · Dec 5, 2024 · a7e1b53 · a7e1b53
2 parents 8e1aa7e + 275889e
commit a7e1b53
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Showing 8 changed files with 187 additions and 46 deletions.
diff --git a/modules.json b/modules.json
@@ -12,7 +12,7 @@
                     },
                     "arriba/arriba": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "7741dfc830e77a8ead2fcb50b01461ee09d0cdfe",
                         "installed_by": ["modules"]
                     },
                     "arriba/download": {

diff --git a/modules/nf-core/arriba/arriba/environment.yml b/modules/nf-core/arriba/arriba/environment.yml
diff --git a/modules/nf-core/arriba/arriba/main.nf b/modules/nf-core/arriba/arriba/main.nf
diff --git a/modules/nf-core/arriba/arriba/meta.yml b/modules/nf-core/arriba/arriba/meta.yml
diff --git a/modules/nf-core/arriba/arriba/tests/main.nf.test b/modules/nf-core/arriba/arriba/tests/main.nf.test
diff --git a/modules/nf-core/arriba/arriba/tests/main.nf.test.snap b/modules/nf-core/arriba/arriba/tests/main.nf.test.snap
diff --git a/modules/nf-core/arriba/arriba/tests/nextflow.config b/modules/nf-core/arriba/arriba/tests/nextflow.config
diff --git a/subworkflows/local/arriba_workflow.nf b/subworkflows/local/arriba_workflow.nf
@@ -28,7 +28,7 @@ workflow ARRIBA_WORKFLOW {
                     .map { meta, reads, fusions -> [ meta, fusions ] }
                 ch_arriba_fusion_fail = ch_dummy_file
             } else {
-                ARRIBA_ARRIBA ( STAR_FOR_ARRIBA.out.bam, ch_fasta, ch_gtf, ch_arriba_ref_blacklist, ch_arriba_ref_known_fusions, [[],[]], [[],[]], ch_arriba_ref_protein_domains )
+                ARRIBA_ARRIBA ( STAR_FOR_ARRIBA.out.bam, ch_fasta, ch_gtf, ch_arriba_ref_blacklist, ch_arriba_ref_known_fusions, [[],[]], ch_arriba_ref_protein_domains )
                 ch_versions = ch_versions.mix(ARRIBA_ARRIBA.out.versions)
 
                 ch_arriba_fusions     = ARRIBA_ARRIBA.out.fusions