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's BCL 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

[3.8.1] - 2022-05-27

• [#834] - nf-core download fails with version 3.8 of the pipeline

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 to ubuntu: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 the FASTQC_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
• 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 in bin/ 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 to sample,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/ and workflows/ 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 to publish_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.