Releases: nf-core/rnaseq
nf-core/rnaseq v3.9 - Niobium Nightingale
[3.9] - 2022-09-30
Enhancements & fixes
- [#746] - Add
tin.py
output to MultiQC report - [#841] - Turn
--deseq2_vst
on by default - [#853] - Pipeline fails at email step: Failed to invoke
workflow.onComplete
event handler - [#857] - Missing parameter required by StringTie if using STAR as aligner
- [#862] - Filter samples that have no reads after trimming
- [#864] - Pre-process transcripts fasta when using
--gencode
- Expose additional arguments to UMI-tools as pipeline params:
--umitools_bc_pattern2
is required if the UMI is located on read 2.--umitools_umi_separator
will often be needed in conjunction with--skip_umi_extract
as most other tools such as Illumina'sBCL Convert
use a colon instead of an underscore to separate the UMIs. The--umitools_grouping_method
allows to fine-tune handling of similar but non-identical UMIs. - Updated pipeline template to nf-core/tools 2.5.1
Parameters
Old parameter | New parameter |
---|---|
--umitools_bc_pattern2 |
|
--umitools_umi_separator |
|
--umitools_grouping_method |
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 |
---|---|---|
hisat2 |
2.2.0 | 2.2.1 |
multiqc |
1.11 | 1.13 |
picard |
2.26.10 | 2.27.4 |
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 version information isn't present.
nf-core/rnaseq v3.8.1 - Plastered Magnesium Mongoose
nf-core/rnaseq v3.8 - Magnesium Mongoose
[3.8] - 2022-05-25
⚠️ Major enhancements
Fixed a well hidden bug in the UMI processing mode of the pipeline when using --with_umi --aligner star_salmon
as reported by Lars Roed Ingerslev. Paired-end BAM files were not appropriately name sorted after umi_tools dedup
which ultimately resulted in incorrect reading and quantification with Salmon. If you have used previous versions of the pipeline to analyse paired-end UMI data it will need to be reprocessed using this version of the pipeline. See #828 for more context.
Enhancements & fixes
- [#824] - Add explicit docs for usage of featureCounts in the pipeline
- [#825] - Pipeline fails due to trimming related removal of all reads from a sample
- [#827] - Control generation of --output-stats when running umi-tools dedup
- [#828] - Filter BAM output of UMI-tools dedup before passing to Salmon quant
- Updated pipeline template to nf-core/tools 2.4.1
Parameters
Old parameter | New parameter |
---|---|
--min_trimmed_reads |
|
--umitools_dedup_stats |
nf-core/rnaseq v3.7 - Iron Iguana
[3.7] - 2022-05-03
⚠️ Major enhancements
- Updated default STAR version to latest available (
2.7.10a
; see #808) - Vanilla Linux Docker container changed from
biocontainers/biocontainers:v1.2.0_cv1
toubuntu:20.04
to fix issues observed on GCP (see #764)
Enhancements & fixes
- [#762] - Explicitly set
--skip_bbsplit false
with--bbsplit_fasta_list
to use BBSplit - [#764] - Test fails when using GCP due to missing tools in the basic biocontainer
- [#765] - Add docs for the usage of nf-core/rnaseq with prokaryotic data
- [#775] - Incorrect columns in Salmon transcript files
- [#791] - Add outputs for umitools dedup summary stats
- [#797] - Add
--skip_umi_extract
to account for pre-existing UMIs header embeddings. - [#798] - Decompress transcript fasta error
- [#799] - Issue with using
--retain_unpaired
with theFASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE
module - [#802] -
--bam_csi_index
error generated if--skip_alignment
specified - [#808] - Auto-detect usage of Illumina iGenomes reference
- [#809] - Add metro map for pipeline
- [#814] - Use decimal values for
--min_mapped_reads
- Updated pipeline template to nf-core/tools 2.3.2
Parameters
Old parameter | New parameter |
---|---|
--skip_umi_extract |
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 |
---|---|---|
samtools |
1.14 | 1.15.1 |
star |
2.6.1d | 2.7.10a |
stringtie |
2.1.7 | 2.2.1 |
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.
nf-core/rnaseq v3.6 - Platinum Platypus
[3.6] - 2022-03-04
Enhancements & fixes
- nf-core/tools#1415 - Make
--outdir
a mandatory parameter - [#734] - Is a vulnerable picard still used ? log4j vulnerability
- [#744] - Auto-detect and raise error if CSI is required for BAM indexing
- [#750] - Optionally ignore R1 / R2 after UMI extraction process
- [#752] - How to set publishing mode for all processes?
- [#753] - Add warning when user provides
--transcript_fasta
- [#754] - DESeq2 QC issue linked to
--count_col
parameter - [#755] - Rename RSEM_PREPAREREFERENCE_TRANSCRIPTS process
- [#759] - Empty lines in samplesheet.csv cause a crash
- [#769] - Do not run RSeQC tin.py by default
Parameters
Old parameter | New parameter |
---|---|
--publish_dir_mode |
|
--umi_discard_read |
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.
nf-core/rnaseq v3.5 - Copper Chameleon
[3.5] - 2021-12-17
Enhancements & fixes
- Port pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
- Removed
--publish_dir_mode
as it is no longer required for the new syntax
- Removed
- Bump minimum Nextflow version from
21.04.0
->21.10.3
- Updated pipeline template to nf-core/tools 2.2
- [#664] - Conflict of library names for technical replicates
- [#720] - KeyError 'gene_id' in salmon_tx2gene.py
- [#724] - Deal with warnings generated when native NF processes are used
- [#725] - Untar needs
--no-same-owner
on DNAnexus - [#727] - Fix transcriptome staging issues on DNAnexus for rsem/prepareference
- [#728] - Add RSeQC TIN.py as a quality metric for the pipeline
nf-core/rnaseq v3.4 - Aluminium Aardvark
[3.4] - 2021-10-05
Enhancements & fixes
- Software version(s) will now be reported for every module imported during a given pipeline execution
- Added
python3
shebang to appropriate scripts inbin/
directory - [#407] - Filter mouse reads from PDX samples
- [#570] - Update SortMeRNA to use SilvaDB 138 (for commercial use)
- [#690] - Error with post-trimmed read 2 sample names from FastQC in MultiQC
- [#693] - Cutadapt version missing from MultiQC report
- [#697] - pipeline_report.{txt,html} missing from pipeline_info directory
- [#705] - Sample sheet error check false positive
Parameters
Old parameter | New parameter |
---|---|
--bbsplit_fasta_list |
|
--bbsplit_index |
|
--save_bbsplit_reads |
|
--skip_bbsplit |
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 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 |
---|---|---|
bbmap |
38.93 | |
hisat2 |
2.2.0 | 2.2.1 |
picard |
2.23.9 | 2.25.7 |
salmon |
1.4.0 | 1.5.2 |
samtools |
1.12 | 1.13 |
sortmerna |
4.2.0 | 4.3.4 |
trim-galore |
0.6.6 | 0.6.7 |
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.
nf-core/rnaseq v3.3 - Bronze Bear
[3.3] - 2021-07-29
Enhancements & fixes
- Updated pipeline template to nf-core/tools 2.1
- [#556] - Genome index isn't recreated with --additional_fasta unless --star_index false
- [#668] - Salmon quant with UMI-tools does not work
- [#674] - Launch pipeline regex fails
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 |
---|---|---|
samtools |
1.10 | 1.12 |
stringtie |
2.1.4 | 2.1.7 |
umi_tools |
1.1.1 | 1.1.2 |
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.
nf-core/rnaseq v3.2 - Copper Flamingo
[3.2] - 2021-06-18
Enhancements & fixes
- Removed workflow to download data from public databases in favour of using nf-core/fetchngs
- Added a stand-alone Python script
bin/fastq_dir_to_samplesheet.py
to auto-create samplesheet from a directory of FastQ files - Added docs about overwriting default container definitions to use latest versions e.g. Pangolin
- [#637] - Add
--salmon_quant_libtype
parameter to provide the--libType
option to salmon quantification - [#645] - Remove trailing slash from
params.igenomes_base
- [#649] - DESeq2 fails with only one sample
- [#652] - Results files have incorrect file names
- [nf-core/viralrecon#201] - Conditional include are not expected to work
Parameters
Old parameter | New parameter |
---|---|
--public_data_ids |
|
--skip_sra_fastq_download |
|
--salmon_quant_libtype |
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 parameter information isn't present.
nf-core/rnaseq v3.1 - Lead Alligator
[3.1] - 2021-05-13
⚠️ Major enhancements
- Samplesheet format has changed from
group,replicate,fastq_1,fastq_2,strandedness
tosample,fastq_1,fastq_2,strandedness
- This gives users the flexibility to name their samples however they wish (see #550)
- PCA generated by DESeq2 will now be monochrome and will not be grouped by using the replicate id
- Updated Nextflow version to
v21.04.0
(see nextflow#572) - Restructure pipeline scripts into
modules/
,subworkflows/
andworkflows/
directories
Enhancements & fixes
- Updated pipeline template to nf-core/tools
1.14
- Initial implementation of a standardised samplesheet JSON schema to use with user interfaces and for validation
- Only FastQ files that require to be concatenated will be passed to
CAT_FASTQ
process - [#449] -
--genomeSAindexNbases
will now be auto-calculated before building STAR indices - [#460] - Auto-detect and bypass featureCounts execution if biotype doesn't exist in GTF
- [#544] - Update test-dataset for pipeline
- [#553] - Make tximport output files using all the samples; identified by @j-andrews7
- [#561] - Add gene symbols to merged output; identified by @grst
- [#563] - samplesheet.csv merge error
- [#567] - Update docs to mention trimgalore core usage nuances
- [#568] -
--star_index
argument is ignored with--aligner star_rsem
option - [#569] - nextflow edge release documentation for running 3.0
- [#575] - Remove duplicated salmon output files
- [#576] - umi_tools dedup : Run before salmon to dedup counts
- [#582] - Generate a separate bigwig tracks for each strand
- [#583] - Samtools error during run requires use of BAM CSI index
- [#585] - Clarify salmon uncertainty for some transcripts
- [#604] - Additional fasta with GENCODE annotation results in biotype error
- [#610] - save R objects as RDS
- [#619] - implicit declaration of the workflow in main
- [#629] - Add and fix EditorConfig linting in entire pipeline
- [nf-core/modules#423] - Replace
publish_by_id
module option topublish_by_meta
- [nextflow#2060] - Pipeline execution hang when native task fail to be submitted
Parameters
Old parameter | New parameter |
---|---|
--hisat_build_memory |
--hisat2_build_memory |
--gtf_count_type |
--featurecounts_feature_type |
--gtf_group_features_type |
--featurecounts_group_type |
--bam_csi_index |
|
--schema_ignore_params |
|
--show_hidden_params |
|
--validate_params |
|
--clusterOptions |
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 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 |
---|---|---|
bedtools |
2.29.2 | 2.30.0 |
multiqc |
1.9 | 1.10.1 |
preseq |
2.0.3 | 3.1.2 |
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.