Merge pull request #265 from nf-core/dev

Release 2.1.0

CHANGELOG.md

@@ -3,7 +3,41 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [2.0.0] nfcore/rnafusion - 2022/04/14
+## [2.1.0] nfcore/rnafusion - 2022/07/12
+
+### Added
+
+- `FusionCatcher` single_end support for single reads ABOVE 130 bp
+- `--fusioninspector_only` parameter to run FusionInspector standalone feeding gene list manually with parameter `--fusioninspector_fusions PATH`
+- `--fusioncatcher_limitSjdbInsertNsj` parameter to feed --limitSjdbInsertNsj to FusionCatcher
+- `--fusioninspector_limitSjdbInsertNsj` parameter to feed --limitSjdbInsertNsj to FusionInspector !!Any other value than default will use the dev version of FusionInspector!!
+- OPTIONAL trimming option `--trim` for hard trimming to 75 bp in case of high read-through. Only fusioncatcher uses trimmed reads as STAR-based fusion detection tools are less sensitive to read-through
+- `picard` metrics, STAR final log, and QualiMap output included in `MultiQC` report
+
+### Changed
+
+- `seq_platform` and `seq_center` changed from boolean to string
+- `seq_platform` set to an empty string and `seq_center` set to an empty string if not existing
+- Arriba use ensembl references-built starindex independently of `starfusion_build` parameter
+- ftp to http protocol for STARFUSION_BUILD process `Pfam-A.hmm.gz` download as ftp causes issues on some servers
+- Updated README and usage documentation with more detailed information and metro map
+- Arriba use ensembl references-built starindex independently of starfusion_build parameter
+- Update of the single-end reads support table in README, added recommendation to use single-end reads only in last resort
+- STAR updated to 2.7.10a
+- Arriba updated to 2.3.0, references for blacklist and protein domains changed to 2.3.0 from singularity/docker container -> arriba download of references not necessary any more
+- multiQC updated to 1.13a
+- picard updated to 2.27.4
+- dumpsoftwareversions module updated to use multiqc=1.12 containers
+
+### Fixed
+
+- FusionInspector does not mix sample reads with fusion lists and meta information from other samples anymore
+- Arriba visualisation does not mix sample reads with fusion lists and meta information from other samples anymore
+- logging of STAR-fusion and fusionreport version
+
+### Removed
+
+## [2.0.0] nfcore/rnafusion - 2022/05/19
 
 Update to DSL2 and newer software/reference versions
 

README.md

@@ -27,19 +27,22 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 | Tool                                                      |  Single-end reads  | Version  |
 | --------------------------------------------------------- | :----------------: | :------: |
-| [Arriba](https://github.com/suhrig/arriba)                |        :x:         | `2.2.1`  |
+| [Arriba](https://github.com/suhrig/arriba)                |        :x:         | `2.3.0`  |
 | [FusionCatcher](https://github.com/ndaniel/fusioncatcher) | :white_check_mark: |  `1.33`  |
-| [Fusion-report](https://github.com/matq007/fusion-report) |         -          | `2.1.5`  |
 | [Pizzly](https://github.com/pmelsted/pizzly)              |        :x:         | `0.37.3` |
 | [Squid](https://github.com/Kingsford-Group/squid)         |        :x:         |  `1.5`   |
 | [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion) | :white_check_mark: | `1.10.1` |
 
+> Single-end reads are to be use as last-resort. Paired-end reads are recommended. FusionCatcher cannot be used with single-end reads shorter than 130 bp.
+
 On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/rnafusion/results).
 
 In rnafusion the full-sized test includes reference building and fusion detection. The test dataset is taken from [here](https://github.com/nf-core/test-datasets/tree/rnafusion/testdata/human).
 
 ## Pipeline summary
 
+![nf-core/rnafusion metro map](docs/images/nf-core-rnafusion_metro_map.png)
+
 #### Build references
 
 `--build_references` triggers a parallel workflow to build all references
@@ -70,11 +73,11 @@ In rnafusion the full-sized test includes reference building and fusion detectio
    - [STAR](https://github.com/alexdobin/STAR) alignment
    - [Samtools view](http://www.htslib.org/): convert sam output from STAR to bam
    - [Samtools sort](http://www.htslib.org/): bam output from STAR
-   - [Squid](https://github.com/Kingsford-Group/squid) fusion detection
-   - [Squid](https://github.com/Kingsford-Group/squid) annotate
+   - [SQUID](https://github.com/Kingsford-Group/squid) fusion detection
+   - [SQUID](https://github.com/Kingsford-Group/squid) annotate
 7. STAR-fusion subworkflow
    - [STAR](https://github.com/alexdobin/STAR) alignment
-   - [STAR-fusion](https://github.com/STAR-Fusion/STAR-Fusion) fusion detection
+   - [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion) fusion detection
 8. Fusioncatcher subworkflow
    - [FusionCatcher](https://github.com/ndaniel/fusioncatcher) fusion detection
 9. Fusion-report subworkflow