add human_gencode_filter to starfusion build

nf-core · Dec 11, 2024 · 117884c · 117884c
1 parent ef5ab96
commit 117884c
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Showing 5 changed files with 244 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -27,7 +27,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Updated to nf-core/tools 3.0.2 [#504](https://github.com/nf-core/rnafusion/pull/504)
 - Remove local module `RRNA_TRANSCRIPTS` (replaced by nf-core module) [#541](https://github.com/nf-core/rnafusion/pull/541)
 - Allow fastq files without a dot before .fn(.gz)/.fastq(.gz) files [#548](https://github.com/nf-core/rnafusion/pull/548)
-        ext.args = "-genePredExt -geneNameAsName2 -ignoreGroupsWithoutExons" GTF_TO_REFFLAT
+  ext.args = "-genePredExt -geneNameAsName2 -ignoreGroupsWithoutExons" GTF_TO_REFFLAT
+
 ### Fixed
 
 - Fixed some Nextflow run-commands in the docs [#491](https://github.com/nf-core/rnafusion/pull/491)

diff --git a/modules/local/fusioncatcher/download/main.nf b/modules/local/fusioncatcher/download/main.nf
@@ -19,7 +19,6 @@ process FUSIONCATCHER_DOWNLOAD {
     script:
 
     def args = task.ext.args ?: ''
-    def args2 = task.ext.args2 ?: ''
         // TODO: move to S3
 
     // def url =

diff --git a/modules/local/starfusion/build/main.nf b/modules/local/starfusion/build/main.nf
@@ -33,6 +33,7 @@ process STARFUSION_BUILD {
         --pfam_db Pfam-A.hmm \\
         --dfam_db homo_sapiens_dfam.hmm \\
         --max_readlength $params.read_length \\
+        --human_gencode_filter \\
         --CPU $task.cpus
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/subworkflows/local/arriba_workflow.nf b/subworkflows/local/arriba_workflow.nf
@@ -52,7 +52,7 @@ workflow ARRIBA_WORKFLOW {
         }
         else {
             ch_arriba_fusions       = reads.combine(Channel.value( file(ch_dummy_file, checkIfExists:true ) ) )
-                                        .map { meta, reads, fusions -> [ meta, fusions ] }
+                                        .map { it -> [ it[0], it[2] ] }
 
             ch_arriba_fusion_fail   = ch_dummy_file
         }