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