v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch

• [#328] - Fix casting issue in mirtrace module
• [#334] - Fix input channel cardinality in MIRDEEP2_RUN module
• [#334] - Fix bowtie conda version in BOWTIE_MAP_SEQ module
• [#335] - Final fix for casting issue in mirtrace module
• [#337] - Fix three_prime_adapter issue, allow auto-detect as value
• [#342] - Fix phred offset issue, allow specifying phred offset for FASTQ files
• [#343] - Fix mirdeep2 output missing, fix mirdeep2 outputs missing in outdir

v2.3.0 - 2024-02-23 - Gray Zinc Dalmatian

• [#307] - Clean up config file and improve output folder structure
• [#299] - Bugfix for missing inputs in BAM stats (genome_quant.r)
• [#164] - UMI Handling Feature implemented in the pipeline
• [#302] - Merged in nf-core template v2.11.1
• [#294] - Fixed contamination screening issues
• [#309] - Merged in nf-core template v2.12.0
• [#310] - Removed unnecessarily separate mirtrace subworkflow, now using module instead
• [#311] - Fix use of FASTP, set three_prime_adapter per default
• [#314] - Add parameters to control publishing of intermediate results
• [#317] - Fixed issue with bowtie indices directly supplied
• [#318] - Merged in nf-core template v2.13.0 and pinned nf-validator

Parameters

Software dependencies

v2.2.4 - 2023-11-03

• Update template to 2.10
• [#289] - Bugfix for issue with mirdeep2 channels ()
• [#288] - Bugfix for issue with handling malformed GFF3 from mirbase
• Updated dependencies, including FASTQC, MultiQC 1.17, fastP and samtools to latest versions

v2.2.3 - 2023-09-06

• [#271] - Bugfix for parsing hairpin and mature fasta files

v2.2.2 - 2023-09-05 Carmine Mercury Borzoi

• [#253] - Remove globs from process alias when using ECR containers
• [#237] - Fix illumina protocol clip parameters to default
• Remove public_aws_ecr profile
• [#269] - Updated miRBase URLs with new location (old ones were broken)

Software dependencies

Enhancements & fixes

• [#238] - Restored the missing mirtop outputs
• [#242] - Fixed mirtrace using wrong input fastq files (untrimmed)

Enhancements & fixes

• #220 - Fixed an issue where miRTrace reports fastq basename instead of sample ID
• #208 - Fixed usability of —skip_qc parameter
• #205 - Fix mirTrace Report to be a single report again instead of per sample reports
• #206 - Use % as separator in sed commands to enable conda working properly on OSX and Linux
• #224 - Fix Samplesheet print error
• Updated FASTP module to allow direct addition of adapter_fasta file to it
• Group samples by adapter sequence before running mirtrace
• Remove —skip_qc parameter

v2.1.0 - 2022-10-25 Maroon Tin Dalmatian

Enhancements & fixes

• [#12] - Enabled the use of MirGeneDB as an alternative database insted of miRBase
• [#113] - Added a optional contamination filtering step, including MultiQC plot
• [#137] - Fixed issue with mirTop and MultiQC by upgrading to MultiQC V1.13dev
• [#159] - Index files were not collected when bowtie_index was used and thus mapping was failing
• [#161] - Trimmed output was not as documented and not correctly published
• [#168] - Removed mirtrace_protocol as the parameter was redundant and params.protocol is entirely sufficient
• Updated pipeline template to nf-core/tools 2.6.0
• [#188] - Dropped TrimGalore in favor of fastp QC and adapter trimming, improved handling of adapters and trimming parameters
• [#194] - Added default adapters file for FastP improved miRNA adapter trimming

Parameters

v2.0.0 - 2022-05-31 Aqua Zinc Chihuahua

Major enhancements

• Updated pipeline template to nf-core/tools 2.4.1
• [#137] - Update mirtop container to version 0.4.25 to fix multiqc error
• Port pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
• Bump minimum Nextflow version from 20.04.0 -> 21.10.3
• Point to the proper test data branch
• Software version(s) will now be reported for every module imported during a given pipeline execution
• Updated nextflow_schema.json should now display correctly on Nextflow Tower
• Added mirtop logs to multiqc
• Allow a gene to be associated to a non null number of reads in all samples (in edgeR_miRBase.r script)

Other enhancements & fixes

• #134 - Fixed colSum of zero issues for edgeR_miRBase.R script
• #55 - update seqcluster to fix UMI-detecting bug

Parameters

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.

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.

What’s Changed in terms of PRs

• bump version to 1.2.0dev by @KevinMenden in #92
• fix errors in miRDeep2 analysis when reads map to unplaced contigs in $refgenome by @Daniel-VM in #100
• Allow a gene to have reads in all samples in the edgeR analysis by @sdjebali in #93
• DSL2 update, mostly schema and config, a few linting items by @klkeys in #111
• DSL2: updated modules by @klkeys in #112
• migration to DSL2 by @lpantano in #104
• Important! Template update for nf-core/tools v2.1 by @nf-core-bot in #101
• Add new version syntax based on yml files to the pipeline by @JoseEspinosa in #119
• fix testdata file by @lpantano in #120
• Samplesheet versioning by @JoseEspinosa in #121
• Merge template 2.2 and update to latest DSL2 syntax by @JoseEspinosa in #125
• Important! Template update for nf-core/tools v2.2 by @nf-core-bot in #123
• Update modules, bump multiqc version and other minor fixes by @JoseEspinosa in #129
• Fix #134 by @apeltzer in #136
• Merging template updates 2.3 by @JoseEspinosa in #141
• Important! Template update for nf-core/tools v2.3.2 by @nf-core-bot in #138
• Update publishDir mode by @JoseEspinosa in #142
• Bump mirtop version 0.4.25 by @JoseEspinosa in #143
• Fix seqcluster umi bug by @abartlett004 in #144
• Merging template 2.4.0 by @JoseEspinosa in #148
• Important! Template update for nf-core/tools v2.4 by @nf-core-bot in #147
• Fix zenodo link and update changelog by @JoseEspinosa in #150
• Fix linting by @JoseEspinosa in #157
• Update mirdeep2_run.nf by @wbau in #154
• PR for 2.0.0 by @apeltzer in #151

New Contributors

• @Daniel-VM made their first contribution in #100
• @klkeys made their first contribution in #111
• @JoseEspinosa made their first contribution in #119
• @abartlett004 made their first contribution in #144
• @wbau made their first contribution in #154

Full Changelog: 1.1.0…2.0.0

v1.1.0 - 2021-05-11

Major changes

⚠️ Breaking changes!

This release contains several major (potentially breaking) changes:

• The main input parameter has been changed from --reads to --input to standardize the pipeline with other nf-core pipelines
• All parameter documentation has moved into a new nextflow_schema.json file
• A lib folder with groovy helper classes has been added to the pipeline. This includes validation of input parameters using the schema defined in the nextflow_schema.json file

General improvements

• remove spaces in genome headers and replace special nt by N in hairpin file for mirdeep2 to work. [#69]
• Accept custom genome and remove non-canonical letters in the genome. Thanks to @sdjebali. Follow up from [#63]
• Fix error when only one sample is in the input [#31]
• Made CamelCase pipeline parameters snake_case and lower case
  • clip_R1 -> clip_r1
  • three_prime_clip_R1 -> three_prime_clip_r1
  • saveReference -> save_reference
  • skipQC -> skip_qc
  • skipFastqc -> skip_fastqc
  • skipMultiqc -> skip_multiqc
• Update with the latest TEMPLATE version for nf-core 1.12.1
• Update conda environment with new packages and updates
• Added --protocol custom to allow custom adapter trimming modes [#41]]
• Fix error when UMI is on the reads header: [#35]
• Updated params.mirtrace_species to be properly initialised when using --genome, for all iGenomes species
• Made params.mature and params.hairpin default to miRBase FTP URL so that the file is automatically downloaded if not provided
• Allow .fa or .fa.gz files for mature and hairpin FASTA files.
• Add full-size benchmark / test dataset to run on AWS for each release (see test_full.config)
• Add -f flag to gunzip commands to deal with soft-links
• Add --mirtrace_protocol parameter to allow for more flexible selection of this parameter
• Added --trim_galore_max_length option [#77]
• Solved memory usage issue for mirtrace in the main process and in the get_software_versions process [#68]
• Removed logging of single_end parameter and added missing parameters to schema and config files
• Added “custom” as option for --protocol in the nextflow_schema.json

Packaged software updates

• fastqc=0.11.8 -> 0.11.9
• trim-galore=0.6.3 -> 0.6.5
• bowtie=1.2.2 -> 1.2.3
• multiqc=1.7 -> 1.9
• mirtop=0.4.22 -> 0.4.23
• seqcluster=1.2.5 -> 1.2.7
• htseq=0.11.2 -> 0.11.3
• fastx_toolkit=0.0.14 -> 0.0.14
• seqkit=0.10.1 -> 0.12.0
• mirtrace=1.0.0 -> 1.0.1
• Added conda-forge::python=3.7.3
• Added conda-forge::markdown=3.1.1
• Added conda-forge::pymdown-extensions=6.0
• Added conda-forge::pygments=2.5.2
• Removed conda-forge::r-markdown=1.0

v1.0.0 - 2019-09-21

• Add figures to output documentation
• Add samtools stats for genome alignments
• Add seqkit and remove razers
• Add mirtop and razers tools
• Adapt code and docs to nf-core template
• Update tools and Dockerfile/Singularity to match current template

Other

• Add “protocol” with pre-defined settings
• Add miRTrace in the pipeline.
• Switch from SciLifeLab/NGI-smRNAseq to nf-core/smrnaseq.
• Use Bowtie 1 instead of Bowtie 2 for the alignment to host reference genome.
• Add option for sequencing center in BAM file.

Dependency Updates

• openjdk 8.0.144 -> 11.0.1
• fastqc 0.11.7 -> 0.11.8
• trim-galore 0.5.0 -> 0.6.2
• bioconductor-edger 3.20.7 -> 3.26.0
• bioconductor-limma 3.34.9 -> 3.40.0
• conda-forge::r-data.table 1.11.4 -> 1.12.2
• conda-forge::r-gplots 3.0.1 -> 3.0.1.1
• conda-forge::r-r.methodss3 1.7.1 -> 1.7.1
• htseq 0.9.1 -> 0.11.2
• r-markdown 0.9
• Added mirtop 0.4.18a
• Removed razers3 3.5.3
• Added seqkit 0.10.1-1
• Added seqcluster 1.2.5
• conda-forge::r-base=3.5.1 -> 3.6.1
• conda-forge::r-statmod=1.4.30 -> 1.4.32
• conda-forge::r-markdown=0.9 -> 1.0
• trim-galore=0.6.2 -> 0.6.3
• mirtop=0.4.18a -> 0.4.22
• bioconductor-edger=3.26.0 -> 3.26.5
• bioconductor-limma=3.40.0 -> 3.40.2