v2.4.0 - 2024-10-14 - Navy Iron Boxer

v2.4.0 - 2024-10-14 - Navy Iron Boxer

• [#349] - Fix MIRTOP_QUANT conda issue - change conda-base to conda-forge channel.
• [#350] - Fix MIRTOP_QUANT conda issue - set python version to 3.7 to fix pysam issue.
• [#361] - Fix [#332] - Fix documentation to use only single-end.
• [#364] - Fix Protocol inheritance issue - fixing protocol inheritance from subworkflow with move to config profile(s) for different protocols.
• [#372] - Fix Plain test profile - Updated default protocol value to "custom".
• [#374] - Fix default tests so that they do not require additional profiles in CI. Change GitHub CI fail-fast strategy to false.
• [#375] - Test technical repeats - Test merging of technical repeats.
• [#377] - Fix Linting - Fixed linting warnings and updated modules & subworkflows.
• [#378] - Fix --mirtrace_species bug - Make MIRTRACE process conditional. Add mirgenedb test.
• [#380] - Fix edgeR_mirBase.R - Fix checking number of samples which causes error in plotMDS. Add nf-tests for local modules using custom R scripts.
• [#381] - Update Convert tests to nf-tests - CI tests to nf-tests.
• [#382] - Add collapse_mirtop.R - Add nf-tests for local modules using custom R scripts.
• [#383] - Fix parameter --skip_fastp throws an error - Fix parameter --skip_fastp.
• [#384] - Fix filter status bug fix - Fix filter stats module and add filter contaminants test profile.
• [#386] - Fix Nextflex trimming support - Fix Nextflex trimming support.
• [#387] - Add contaminant filter failure because the Docker image for BLAT cannot be pulled - Add nf-test to local module blat_mirna and fixes . Adds a small test profile to test contaminant filter results.
• [#388] - Fix igenomes fix - Fix workflow scripts so that they can use igenome parameters.
• [#391] - Fix error because of large chromosomes - Change .bai index for .csi index in samtools_index to fix .
• [#392] - Update Reduce tests - Combine and optimize tests, and reduce samplesheets sizes.
• [#397] - Fix contaminant filter failure because of the Docker image for BLAT - Improvements to contaminant filter subworkflow and replacement for nf-core modules.
• [#398] - Update Input channels - Updated channel and params handling through workflows.
• [#405] - Fix Umicollapse algo wrong set - Fix potential bug in Umicollapse (not effective as we do not allow PE data in smrnaseq - but for consistency)
• [#420] - Fix mirTrace produces an error in test nextflex - Allow config mode to be used in mirtrace/qc
• [#425] - Raise minimum required NXF version for pipeline - usage of arity in some modules now requires this
• [#426] - Add nf-core mirtop - replace local for nf-core mirtop
• [#427] - Add nf-core pigz uncompress - replace local mirdeep_pigz
• [#429] - Make saving of intermediate files optional - Allows user to choose whether to save intermediate files or not. Replaces several params that referred to the same such as params.save_aligned and params.save_aligned_mirna_quant.
• [#430] - Emit a warning if paired-end end data is used - pipeline handles SE data
• [#432] - Update MultiQC and all modules to latest version - Include UMIcollapse module in MultiQC.
• [#435] - Replace local instances of bowtie for nf-core bowtie2 and bowtie1 - Additionally adds a bioawk module that cleans fasta files.
• [#438] - Update Mirtop to latest version - Process samples separately and join results with CSVTK_JOIN.
• [#439] - Fix Fix paired end samples processing - Fix paired end sample handling and add test profile.
• [#441] - Migrate local contaminant bowtie to nf-core - Replace local processes with BOWTIE2_ALIGN.
• [#443] - Migrate mirna and genome_quant bowtie to nf-core - Replace local processes with BOWTIE_ALIGN.
• [#447] - Fix Minor fixes and general pipeline cleanup - Update variable and processes names, update channel comments, remove unused modules and params.
• [#448] - Migrate local mirdeep to nf-core mirdeep2 modules and subworkflow and generate test profile for mirdeep2.
• [#452] - Fix Fix ch_bowtie_index channel structure and replace untarfiles with untar replace untarfiles with untar.
• [#457] - QC all input fasta files and clean them.
• [#459] - Update modules and subworkflows and fix linting.
• [#462] - Remove automatic wrapping of fasta files by seqkit replace. Minor documentation updates.
• [#464] - Added proper licences and authorship information to scripts in bin folder

Software dependencies

Dependency	Old version	New version
bioawk	-	1.0
bowtie	1.3.1	1.3.0
bowtie2	2.4.5	2.5.2
csvtk	-	0.30
gawk	-	5.3.0
mirtop	0.4.25	0.4.28
multiqc	1.21	1.25.1
samtools	1.19.2	1.21
seqkit	2.6.1	2.8.1

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

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

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

Old parameter	New parameter
	--with_umi
	--umitools_extract_method
	--umitools_method
	--skip_umi_extract
	--umitools_bc_pattern
	--umi_discard_read
	--save_umi_intermeds
	--save_aligned
	--save_aligned_mirna_quant
	--save_merged

Software dependencies

Dependency	Old version	New version
multiqc	1.15	1.20
edgeR	3.36.0	4.0.2
limma	3.50.0	3.58.1
bioconvert	0.4.3	1.1.1
mirdeep	2.0.1	2.0.1.3
seqkit	2.3.1	2.6.1
fastqc	0.11.4	0.12.1
samtools	1.17	1.19.2
umitools		1.1.5
umicollapse		1.0.0

v2.2.4 - 2023-11-03 Carmine Mercury Borzoi

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 Carmine Mercury Borzoi

v2.2.3 - 2023-09-06

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

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

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

Dependency	Old version	New version
multiqc	1.13	1.15
fastp	0.23.2	0.23.4

v2.2.1 - 2023-05-12 Carmine Mercury Borzoi

Enhancements & fixes

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

v2.2.0 - 2023-04-26 Carmine Mercury Borzoi

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

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

Old parameter	New parameter
	--mirgenedb
	--mirgenedb_species
	--mirgenedb_gff
	--mirgenedb_mature
	--mirgenedb_hairpin
	--contamination_filter
	--rrna
	--trna
	--cdna
	--ncrna
	--pirna
	--other_contamination

v 2.0.0 - 2022-05-31 Aqua Zinc Chihuahua

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

Old parameter	New parameter
--conda	--enable_conda
--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
bioconductor-edger	3.26.5	3.36.0
bioconductor-limma	3.40.2	3.50.0
mirdeep2	2.0.1.2	2.0.1.3
mirtop	0.4.23	0.4.25
multiqc	1.10.1	1.12.0
python	3.7.3	3.8.3
r-base	3.6.3	4.0.3
r-data.table	1.12.4	1.14.2
r-gplots	3.0.1.1	3.1.1
r-statmod	1.4.32	1.4.36
samtools	1.12	1.13
seqcluster	1.2.7	1.2.9
seqkit	0.16.0	2.0.0
trim-galore	0.6.6	0.6.7
bioconvert	-	0.4.3
htseq	-	-
markdown	-	-
pymdown-extensions	-	-
pygments	-	-
r-r.methodss3	-	-

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