2.1.0 - 2022/07/12
IMPORTANT
Since STAR has been updated, a new STAR index needs to be built as reference.
nextflow run nf-core/rnafusion --genomes_base /PATH/TO/REFERENCES --starindex --build_references --outdir OUTDIR -profile singularity or docker
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 inMultiQC
report
Changed
seq_platform
andseq_center
changed from boolean to stringseq_platform
set to an empty string andseq_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