update changelog, retrofit trim_workflowo

CHANGELOG.md

@@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add nf-test to local subworkflow: `TRIM_WORKFLOW` [#572](https://github.com/nf-core/rnafusion/pull/572)
 - Add nf-test to local module: `FUSIONREPORT_DETECT`. Improve `FUSIONREPORT_DOWNLOAD` module [#577](https://github.com/nf-core/rnafusion/pull/577)
 - Add nf-test to local subworkflow: `ARRIBA_WORKFLOW` [#578](https://github.com/nf-core/rnafusion/pull/578)
+- Add parameter `--references_only` when no data should be analysed, but only the references should be built [#505](https://github.com/nf-core/rnafusion/pull/505)
 
 ### Changed
 
@@ -31,7 +32,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Remove double nested folder introduced in [#577](https://github.com/nf-core/rnafusion/pull/577), [#581](https://github.com/nf-core/rnafusion/pull/581)
 - Use docker.io and galaxy containers for fusioncatcher and starfusion (incl. fusioninspector) instead of wave as they are not functional on wave [#588](https://github.com/nf-core/rnafusion/pull/588)
 - Update STAR-Fusion to 1.14 [#588](https://github.com/nf-core/rnafusion/pull/588)
-- Use -genePredExt -geneNameAsName2 -ignoreGroupsWithoutExons for GTF_TO_REFFLAT[#505](https://github.com/nf-core/rnafusion/pull/505)
+- Use "-genePredExt -geneNameAsName2 -ignoreGroupsWithoutExons" (to mimic gms/tomte) for GTF_TO_REFFLAT [#505](https://github.com/nf-core/rnafusion/pull/505)
+- Integrate reference building in the main workflow [#505](https://github.com/nf-core/rnafusion/pull/505)
+- Move from ensembl to gencode base [#505](https://github.com/nf-core/rnafusion/pull/505)
+- Update from ensembl 102 to gencode 46 default references [#505](https://github.com/nf-core/rnafusion/pull/505)
 
 ### Fixed
 
@@ -46,12 +50,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Removed
 
 - Remove fusionGDB from documentation and fusion-report download stubs [#503](https://github.com/nf-core/rnafusion/pull/503)
+- Removed test-build as reference building gets integrated in the main workflow [#505](https://github.com/nf-core/rnafusion/pull/505)
+- Removed parameter `--build_references`
+
 
 ### Parameters
 
-| Old parameter | New parameter |
-| ------------- | ------------- |
-|               | `--no_cosmic` |
+| Old parameter       | New parameter |
+| ------------------- | ------------------- |
+|                     | `--no_cosmic`       |
+| `-build_references` | `--references_only` |
+
 
 ## v3.0.2 - [2024-04-10]
 

subworkflows/local/trim_workflow/main.nf

@@ -7,15 +7,17 @@ workflow TRIM_WORKFLOW {
 
     take:
         reads           // channel [ meta, [ fastq files ] ]
+        adapter_fasta   // channel [ path ]
+        fastp_trim      // boolean
 
     main:
         ch_versions       = Channel.empty()
         ch_fastp_html     = Channel.empty()
         ch_fastp_json     = Channel.empty()
         ch_fastqc_trimmed = Channel.empty()
 
-        if ( {params.fastp_trim} ) {
-            FASTP(reads, {params.adapter_fasta}, false, false, false)
+        if ( fastp_trim ) {
+            FASTP(reads, adapter_fasta.ifEmpty( [] ), false, false, false)
             ch_versions = ch_versions.mix(FASTP.out.versions)
 
             FASTQC_FOR_FASTP(FASTP.out.reads)

workflows/rnafusion.nf

@@ -64,7 +64,9 @@ workflow RNAFUSION {
     // Trimming
     //
     TRIM_WORKFLOW (
-        ch_samplesheet
+        ch_samplesheet,
+        params.adapter_fasta,
+        params.fastp_trim
     )
     ch_reads = TRIM_WORKFLOW.out.ch_reads_all
     ch_versions = ch_versions.mix(TRIM_WORKFLOW.out.versions)