RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Full Changelog: https://github.com/nf-core/rnaseq/compare/3.13.2...3.14.0
Full Changelog: https://github.com/nf-core/rnaseq/compare/3.13.1...3.13.2
Full Changelog: https://github.com/nf-core/rnaseq/compare/3.13.0...3.13.1
Full Changelog: https://github.com/nf-core/rnaseq/compare/3.12.0...3.13.0
Special thanks to the following for their contributions to the release:
Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
public_aws_ecr.config
to source mulled containers when using public.ecr.aws
Docker Biocontainer registry--additional_fasta
Old parameter | New parameter |
---|---|
--skip_pseudo_alignment |
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.
Dependency | Old version | New version |
---|---|---|
fastp |
0.23.2 | 0.23.4 |
samtools |
1.16.1 | 1.17 |
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.
Special thanks to the following for their contributions to the release:
Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX
is launched multiple times and failsSpecial thanks to the following for their code contributions to the release:
DESEQ2_QC_STAR_SALMON
fails when sample names have many componentswait: false
option from Tower Actions which is the default[ci fast]
to commit message now skips all tests except for standard -profile test
pipeline runSpecial 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.
--trimmer trimgalore
(default) and --trimmer fastp
.--clip_r1
, --clip_r2
, --three_prime_clip_r1
, --three_prime_clip_r2
and --trim_nextseq
--extra_trimgalore_args
and --extra_fastp_args
parameters, respectively.--save_umi_intermeds
/ --save_align_intermeds
ext.args
and params.extra_star_align_args
prevents parameter clashes in the STAR modulesalmon_summarizedexperiment.r
to ensure rbind
doesn't fail when rowdata
has no tx
column.fastq_dir_to_samplesheet.py
scriptexecutor: local
SALMON_INDEX
runs when using --aligner star_rsem
even if samples have explicit strandednessOld 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.
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.
21.10.3
-> 22.10.1
--genome
parametercopyTo
call for iGenomes README--skip_preseq
by default--recursive
option to fastq_dir_to_samplesheet.py
scriptcheck_samplesheet.py
script doesn't output optional columns in samplesheet--extra_star_align_args
and --extra_salmon_quant_args
parameterOld parameter | New parameter |
---|---|
--enable_conda |
|
--extra_star_align_args |
|
--extra_salmon_quant_args |
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.
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 |
---|---|---|
bbmap |
38.93 | 39.01 |
bioconductor-dupradar |
1.18.0 | 1.28.0 |
bioconductor-summarizedexperiment |
1.20.0 | 1.24.0 |
bioconductor-tximeta |
1.8.0 | 1.12.0 |
fq |
0.9.1 | |
salmon |
1.5.2 | 1.9.0 |
samtools |
1.15.1 | 1.16.1 |
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 version information isn't present.