# nf-core/rnafusion: Changelog

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).

## v2.4.0 - [2023/09/22]

### Added

### Changed

- Use institutional configs by default [#381](https://github.com/nf-core/rnafusion/pull/381)
- Remove redundant indexing in starfusion and qc workflows [#387](https://github.com/nf-core/rnafusion/pull/387)
- Output bai files in same directory as bam files [#387](https://github.com/nf-core/rnafusion/pull/387)
- Update and review documentation [#396](https://github.com/nf-core/rnafusion/pull/396)
- Update picard container for `PICARD_COLLECTRNASEQMETRICS` to 3.0.0 [#395](https://github.com/nf-core/rnafusion/pull/395)
- Renamed output files [#395](https://github.com/nf-core/rnafusion/pull/395)
  - `Arriba` visualisation pdf from meta.id to meta.id_combined_fusions_arriba_visualisation
  - cram file from output bam of `STAR_FOR_ARRIBA`: meta.id to meta.id_star_for_arriba
  - cram file from output bam of `STAR_FOR_STARFUSION`: meta.id to meta.id.star_for_starfusion.Aligned.sortedByCoord.out
  - `fusion-report` index.html file to meta.id_fusionreport_index.html
  - meta.id.vcf output from `MEGAFUSION` to meta.id_fusion_data.vcf

### Fixed

- Tail trimming for reverse reads [#379](https://github.com/nf-core/rnafusion/pull/379)
- Set html files as optional in fusionreport [#380](https://github.com/nf-core/rnafusion/pull/380)
- Provide gene count file by default when running STAR_FOR_STARFUSION [#385](https://github.com/nf-core/rnafusion/pull/385)
- Fix fusion-report issue with MACOXS directories [#386](https://github.com/nf-core/rnafusion/pull/386)
- The fusion lists is updated to contain two branches, one in case no fusions are detected and one for if fusions are detected, that will be used to feed to fusioninspector, megafusion, arriba visualisation [#388](https://github.com/nf-core/rnafusion/pull/388)
- Update fusionreport to 2.1.5p4 to fix 403 error in downloading databases [#403](https://github.com/nf-core/rnafusion/pull/403)

### Removed

- `samtools sort` and `samtools index` for `arriba` workflow were dispensable and were removed [#395](https://github.com/nf-core/rnafusion/pull/395)
- Removed trimmed fastqc report from multiqc [#394](https://github.com/nf-core/rnafusion/pull/394)

## v2.3.0 - [2023/04/24]

### Added

- Shell specification to bash
- COSMIC password put into quotes
- Trimmed reads QC in MultiQC
- Add `ARRIBA_VISUALISATION` to processed affected by `--skip_vis`
- Option `fusionreport_filter` to in/activate fusionreport displaying of fusions detected by 2 or more tools

### Changed

- `Arriba` visualisation now runs for FusionInspector (combined tools) results, not only `Arriba` results
- Updated metro map with trimming options and placed `Arriba` visualisation after `FusionInspector`
- Exit with error when using squid in combination with any ensembl version different from 102

### Fixed

- Channel issue with indexing of files with using `--cram squid`
- `Arriba` references published in the correct folder

### Removed

## v2.2.0 - [2023/03/13]

### Added

- exitStatus 140 now part of the retry strategy
- stubs to all local modules
- `--stringtie` option added with StringTie v2.2.1 to detect splicing events. Not included in `fusion-report` or `fusionInspector` summaries. Included in the `--all` workflow
- Generation of ribosomal RNA interval list with build_references and use it in picard CollectRnaMetrics
- Add csv output to fusionreport
- Trimming workflow using `fastp`: use trimmed reads for all tools
- `whitelist` parameter to add custom fusions to the detected ones and consider the whole for the `fusionInspector` analysis
- Compression to CRAM files for arriba, squid and starfusion workflows (fusioncatcher and pizzly do not produce SAM/BAM files, fusioninspector BAM files are too small to benefit from compression)
- `--qiagen` option to download from QIAGEN instead of COSMIC (use QIAGEN user and password for `cosmic_username` and `cosmic_passwd`)
- Bumped `STAR genomegenerate` time request for building as it was always crashing for most users
- Fixed issue with arriba visualisation parameters [#326](https://github.com/nf-core/rnafusion/issues/326)

### Changed

- Test profiles unified under 'test' but if the references do not all need to be downloaded, run with `-stub`
- Update CUSTOM_DUMPSOFTWAREVERSIONS to use multiqc version 1.13
- Updated to nf-core template 2.7.2, with all module updates
- `MultiQC` updated to 1.13a in process dumpsoftwareversion
- Patch fusion-report version with fixed mittelman DB and DB extraction date written into software_version.yaml
- `Arriba` references back to downloading with `build_references` instead of taking from container
- `Arriba` visualisation now running with `Arriba` v2.3.0
- Updated `STAR-Fusion` to 1.12.0

### Fixed

- AWS megatest to display on nf-core website
- `arriba` visualisation references updated to 2.3.0
- Removed issue with multiple outputs in samtools view for squid

### Removed

- FUSIONINSPECTOR_DEV process as the option fusioninspector_limitSjdbInsertNsj is part of the main starfusion release

## v2.1.0 - [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

## v2.0.0 - [2022/05/19]

Update to DSL2 and newer software/reference versions

### Added

- Added `qualimap/rnaseq v2.2.2d` from nf-core modules
- Added UCSC `gtfToGenePred v377`
- Added `picard CollectRnaSeqMetrics v2.26.10`
- Added `picard MarkDuplicates v2.26.10` from nf-core modules
- Added `cat/fastqc` from nf-core modules
- Added possibility for manually feeding the results of fusions from different tools to speed-up reruns
- STAR-Fusion references can be downloaded or built but downloaded references are NOT RECOMMENDED as not thoroughly tested (--starfusion_build parameter is true by default, use --starfusion_build false to use downloaded STAR-Fusion references).

### Changed

- Upgrade default ensembl version to `102`
- Upgrade to `nf-core/tools v2.3.2`
- Upgrade `Arriba v1.2.0` to `Arriba v2.2.1`
- Upgrade `FusionCatcher v1.20` to `FusionCatcher v1.33`
- Upgrade `STAR-fusion v1.8.1` to `STAR-fusion v1.10.1`
- Upgrade `STAR v2.7.1` to `STAR v2.7.9`
- Upgrade `fusion-report v2.1.3` to `fusion-report v2.1.5`
- Upgrade `kallisto v0.44.0` to `kallisto v0.46.2`
- Upgrade `fastqc v0.11.8` to `fastqc v0.11.9`
- Upgrade `samtools v1.9` to `samtools v1.15.1`
- Upgrade `arriba` references from `v1.2.0` to `v2.1.0`
- Upgrade `fusioncatcher` references from `v98` to `v102`
- Use `arriba` (detect only), `kallisto` and `STAR` from nf-core modules
- Instead of separate script to build the references, added `--build_references` argument in the main
- `--fasta` argument is not required with `--build_references` and set by default to the ensembl references built in the detection workflow
- CI test done on stubs of reference building for subprocesses ensembl and arriba

Parameters for `STAR` for `arriba` changed from:

```bash
--readFilesCommand zcat \\
        --outSAMtype BAM Unsorted \\
--outStd BAM_Unsorted \\
--outSAMunmapped Within \\
--outBAMcompression 0 \\
--outFilterMultimapNmax 1 \\
--outFilterMismatchNmax 3 \\
--chimSegmentMin 10 \\
--chimOutType WithinBAM SoftClip \\
--chimJunctionOverhangMin 10 \\
--chimScoreMin 1 \\
--chimScoreDropMax 30 \\
--chimScoreJunctionNonGTAG 0 \\
--chimScoreSeparation 1 \\
--alignSJstitchMismatchNmax 5 -1 5 5 \\
--chimSegmentReadGapMax 3 \\
--sjdbOverhang ${params.read_length - 1}
```

to

```bash
--readFilesCommand zcat \
--outSAMtype BAM Unsorted \
--outSAMunmapped Within \
--outBAMcompression 0 \
--outFilterMultimapNmax 50 \
--peOverlapNbasesMin 10 \
--alignSplicedMateMapLminOverLmate 0.5 \
--alignSJstitchMismatchNmax 5 -1 5 5 \
--chimSegmentMin 10 \
--chimOutType WithinBAM HardClip \
--chimJunctionOverhangMin 10 \
--chimScoreDropMax 30 \
--chimScoreJunctionNonGTAG 0 \
--chimScoreSeparation 1 \
--chimSegmentReadGapMax 3 \
--chimMultimapNmax 50
```

As recommended [here](https://arriba.readthedocs.io/en/latest/workflow/).

Parameters for `STAR` for `STAR-fusion` changed from:

```bash
--twopassMode Basic \\
--outReadsUnmapped None \\
--chimSegmentMin 12 \\
--chimJunctionOverhangMin 12 \\
--alignSJDBoverhangMin 10 \\
--alignMatesGapMax 100000 \\
--alignIntronMax 100000 \\
--chimSegmentReadGapMax 3 \\
--alignSJstitchMismatchNmax 5 -1 5 5 \\
--runThreadN ${task.cpus} \\
--outSAMstrandField intronMotif ${avail_mem} \\
--outSAMunmapped Within \\
--outSAMtype BAM Unsorted \\
--outSAMattrRGline ID:GRPundef \\
--chimMultimapScoreRange 10 \\
--chimMultimapNmax 10 \\
--chimNonchimScoreDropMin 10 \\
--peOverlapNbasesMin 12 \\
--peOverlapMMp 0.1 \\
--readFilesCommand zcat \\
--sjdbOverhang ${params.read_length - 1} \\
--chimOutJunctionFormat 1
```

to

```bash
--outReadsUnmapped None \
--readFilesCommand zcat \
--outSAMtype BAM SortedByCoordinate \
--outSAMstrandField intronMotif \
--outSAMunmapped Within \
--chimSegmentMin 12 \
--chimJunctionOverhangMin 8 \
--chimOutJunctionFormat 1 \
--alignSJDBoverhangMin 10 \
--alignMatesGapMax 100000 \
--alignIntronMax 100000 \
--alignSJstitchMismatchNmax 5 -1 5 5 \
--chimMultimapScoreRange 3 \
--chimScoreJunctionNonGTAG -4 \
--chimMultimapNmax 20 \
--chimNonchimScoreDropMin 10 \
--peOverlapNbasesMin 12 \
--peOverlapMMp 0.1 \
--alignInsertionFlush Right \
--alignSplicedMateMapLminOverLmate 0 \
--alignSplicedMateMapLmin 30 \
--chimOutType Junctions
```

`Homo_sapiens.${params.genome}.${ensembl_version}.gtf.gz` used for squid and arriba, `Homo_sapiens.${params.genome}.${ensembl_version}.chr.gtf.gz` used for STAR-fusion and the quality control as the quality control is based on the STAR-fusion alignment.

### Fixed

### Removed

- Ericscript tool
- GRCh37 support. Subdirectory with params.genome are removed
- Running with conda

## v1.3.0 - [2020/07/15]

- Using official STAR-Fusion container [#160](https://github.com/nf-core/rnafusion/issues/160)

### Added

- Added social preview image [#107](https://github.com/nf-core/rnafusion/issues/107)
- Added support for GRCh37 genome assembly [#77](https://github.com/nf-core/rnafusion/issues/77)

### Changed

- Upgrade `fusion-report v2.1.2` to `fusion-report v2.1.3`
- Upgrade `fusion-report v2.1.1` to `fusion-report v2.1.2`
- Upgrade `fusion-report v2.1.0` to `fusion-report v2.1.1`
- Upgrade `Arriba v1.1.0` to `Arriba v1.2.0`
- Upgrade `fusion-report v2.0.2` to `fusion-report v2.1.0`

### Fixed

- Missing `strip-components` in `download-references.nf/star-fusion` [#148](https://github.com/nf-core/rnafusion/issues/148)
- Missing version prefix for cdna [#143](https://github.com/nf-core/rnafusion/issues/143)
- `samtools` missing header in empty file for FusionInspector [ref](https://github.com/STAR-Fusion/STAR-Fusion/issues/191)
- Removed `profile` from helper scripts [#139](https://github.com/nf-core/rnafusion/issues/139)
- Wrong url path for `Pfam-A.hmm.gz` [#140](https://github.com/nf-core/rnafusion/issues/140)

### Removed

- Removed `scripts/download-singularity-img.sh` and `download-singularity-img.nf` as they are not necessary any more

---

## v1.1.0 - [2020/02/10]

- Fusion gene detection tools:
  - `Arriba v1.1.0`
  - `Ericscript v0.5.5`
  - `Fusioncatcher v1.20`
  - `Pizzly v0.37.3`
  - `Squid v1.5`
  - `STAR-Fusion v1.6.0`
- Visualization tools:
  - `Arriba v1.1.0`
  - `FusionInspector v1.3.1`
- Other tools:
  - `fusion-report v2.0.1`
  - `FastQ v0.11.8`
  - `MultiQC v1.7`
  - `STAR aligner v2.7.0f`

### Added

- Added `Arriba 1.1.0` [#63](https://github.com/nf-core/rnafusion/issues/63)
- Added Batch mode [#54](https://github.com/nf-core/rnafusion/issues/54)

### Changed

- Updated examples and configurations
- Upgraded `fusion-report v1.0.0` to `fusion-report v2.0.1`
- Divided `running_tools` into fusion and visualization tools
- Updated `STAR` in `Squid`, `Fusion-Inspector` version to `2.7.0f`
- Upgraded `STAR-Fusion v1.5.0` to `STAR-Fusion v1.6.0` [#83](https://github.com/nf-core/rnafusion/issues/83)
- Parameter `igenomesIgnore` renamed to `igenome` [#81](https://github.com/nf-core/rnafusion/issues/81)
- Finished STAR-Fusion file renaming [#18](https://github.com/nf-core/rnafusion/issues/18)
- Updated logos
- Updated to nf-core `1.8` TEMPLATE

### Fixed

- iGenomes optional, but not really [#91](https://github.com/nf-core/rnafusion/issues/91)
- Updated `fusioncatcher` to latest `1.20` version also solving [#95](https://github.com/nf-core/rnafusion/issues/95)

### Removed

- Variables `pizzly_fasta` and `pizzly_gtf` have been removed and replaced with `transcript` and `gtf`
- `Jenkisfile`, test configuration, pylintrc configuration
- Removed `igenomes.config` because the pipeline only supports `Ensembl` version

---

## v1.0.2 - [2019/05/13]

### Changed

- Bumped nf-core template to 1.6 [#69](https://github.com/nf-core/rnafusion/pull/69)

### Fixed

- Fixed COSMIC parameters not wrapped in quotes [#75](https://github.com/nf-core/rnafusion/issues/75)
- Implemented output output for fusion tools [#72](https://github.com/nf-core/rnafusion/issues/72)
- Fixed reference download link for STAR-Fusion [#71](https://github.com/nf-core/rnafusion/issues/71)

---

## v1.0.1 - [2019/04/06]

### Added

- Added support for extra parameters for tools STAR-Fusion, FusionCatcher and fusion-report
- Added example configuration for `singularity` and `docker`
- Added [fusion-report](https://github.com/matq007/fusion-report) into the stack [#62](https://github.com/nf-core/rnafusion/issues/62), [#55](https://github.com/nf-core/rnafusion/issues/55), [#53](https://github.com/nf-core/rnafusion/issues/53), [#51](https://github.com/nf-core/rnafusion/issues/51)
- Added nextflow helper script `download-singularity-img.nf`
- Added nextflow helper script `download-references.nf`
- Added `Jenkinsfile` for in-house testing

### Changed

- Updated installation of `FusionCatcher` (available now on bioconda)

### Fixed

- Fixed empty symlinks (`input.X`) in fusion-report [#68](https://github.com/nf-core/rnafusion/issues/68)
- Fixed FASTA issues [#60](https://github.com/nf-core/rnafusion/issues/60)
- Fixed centralized nf-core/config [#64](https://github.com/nf-core/rnafusion/issues/64)
- Fixed `scrape_software_versions.py` to parse tools versions correctly [#65](https://github.com/nf-core/rnafusion/issues/65)

### Removed

- Removed `Singularity`

---

## v1.0 - [2018/02/14]

Version 1.0 marks the first production release of this pipeline under the nf-core flag.
The pipeline includes additional help scripts to download references for fusion tools and Singularity images.

Initial release of nf-core/rnafusion, created with the [nf-core](https://nf-co.re/) template.

### `Added`

### `Fixed`

### `Dependencies`

### `Deprecated`
