nf-core/rnaseq v3.11.0 - Radium Rhino
[3.11.0] - 2023-03-30
Credits
Special thanks to the following for their code contributions to the release:
Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
Enhancements & fixes
- Add infrastructure and CI for multi-cloud full-sized tests run via Nextflow Tower (see #981)
- Added fastp support.
- Users can now select between
--trimmer trimgalore
(default) and--trimmer fastp
. - Trim Galore! specific pipeline parameters have been deprecated:
--clip_r1
,--clip_r2
,--three_prime_clip_r1
,--three_prime_clip_r2
and--trim_nextseq
- Any additional options can now be specified via the
--extra_trimgalore_args
and--extra_fastp_args
parameters, respectively.
- Users can now select between
- [#663] - Alternative trimming step for polyA/T removal
- [#781] - Add Warning for poly(A) libraries
- [#878] - Allow tabs in fasta header when creating decoys for salmon index
- [#931] - Save transcriptome BAM files when using
--save_umi_intermeds
/--save_align_intermeds
- [#934] - Union of
ext.args
andparams.extra_star_align_args
prevents parameter clashes in the STAR module - [#940] - Bugfix in
salmon_summarizedexperiment.r
to ensurerbind
doesn't fail whenrowdata
has notx
column. - [#944] - Read clipping using clip_r1, clip_r2, three_prime_clip_r1, three_prime_clip_r2 disabled in 3.10
- [#956] - Implement 'auto' as default strandedness argument in
fastq_dir_to_samplesheet.py
script - [#960] - Failure with awsbatch when running processes that are using
executor: local
- [#961] - Add warnings to STDOUT for all skipped and failed strandedness check samples
- [#975] -
SALMON_INDEX
runs when using--aligner star_rsem
even if samples have explicit strandedness - Remove HISAT2 from automated AWS full-sized tests
Parameters
Old parameter | New parameter |
---|---|
--trimmer |
|
--extra_trimgalore_args |
|
--clip_r1 |
|
--clip_r2 |
|
--three_prime_clip_r1 |
|
--three_prime_clip_r2 |
|
--tracedir |
|
--trim_nextseq |
NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.
Software dependencies
Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
Dependency | Old version | New version |
---|---|---|
fastp |
0.23.2 | |
multiqc |
1.13 | 1.14 |
picard |
2.27.4 | 3.0.0 |
salmon |
1.9.0 | 1.10.1 |
umi_tools |
1.1.2 | 1.1.4 |
NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if new version information isn't present.