rnafusion

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Fusioncatcher build fails

6

### Description of the bug  ### Command used and terminal output ```console nextflow run nf-core/rnafusion -r master -profile bi,XXX (this is a singularity profile), without home mounting. ``` ###...

apeltzer

fix starfusion download output for gtf to refflat

1

Make `output.chrgtf` from STARFUSION_DOWNLOAD a tuple for compatibility with GTF_TO_REFFLAT. This fixes reference generation when --starfusion_build is false. ## PR checklist - [x] This comment contains a description of changes...

dodslaser

### Description of feature How to use the new version of nf-validation? If you want to be prepared for the new version of nf-validation, this will use the latest version...

rannick

ARRIBA_VISUALISATION : Process exceeded running time limit (8h)

9

### Description of the bug Process exceeded running time limit of (8h) for visualisation. That's weird it's taking so long. It was a recurrent one. I don't know if it's...

ZheFrench

### Description of feature - [x] convert2bed - [x] fusioncatcher: keep local, test won't work - [x] fusioninspector: keep local, test won't work - [x] fusionreport: keep local, specific to...

rannick

// Check mandatory parameters // //TODO: move this to utils_nf_core_rnafusion_pipeline // if (file(params.input).exists() || params.build_references) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet does not exist or...

rannick

### Description of feature New version is out, we need to update

rannick

Use references from CTAT

2

### Description of feature Use references from CTAT. Allows to shorten reference building time and maybe call a few more fusions with STAR-fusion as it is optimised for this

rannick

### Description of feature Add JAFFA subworkflow in rnafusion. As far as I know, the fusion-report module has supported the output of JAFFA. So please add JAFFA subworkflow in rnafusion.

yiyinzhang

Optimise STAR parameters to require only one STAR alignment

1

### Description of feature Hi, I was exploring this tool, and I see that you are using STAR alignment 3 times (for arriba, squid, and starfusion). Could you please explain...

joshua-biocoder