.. _home-page-changelog:

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CHANGELOG
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.. autosummary::
   :toctree: generated

Version 3.0
================
* mop_preprocess
   * We added a custom model for m6A basecalling. It is automatically installed when running INSTALL.sh. For using it you need to indicated ``--pars_tools "drna_tool_splice_m6A_opt.tsv" ``
   * We add support to cuda11 for guppy version > 4.4.1.
   * Added readucks for improving demultiplexing with guppy (optional).
   * New parameter "barcodes" where you can specify a file with barcodes to be kept. Example in **keep_barcodes.txt**
   * Adding a `new model for direct RNA basecalling <https://www.biorxiv.org/content/10.1101/2023.11.28.568965v1>`__.
   * Added seqTagger (add reference)
   * Added support to dorado basecalling. Not yet supported the demultiplexing
   * Also guppy version >= 6.5.x are supported. No need for indicating different command lines for different guppy versions inside tool_opts. The pipeline will get the version and act accordingly
   * pod5 are supported for dorado and guppy >= 6.5.x. No fast5 and stats files will be output. This will limit other pipelines.

* mop_tail
   * we upgraded tailfindR to version 1.3
   * Tailfinder can be used either in standard mode or nano3p mode (chemistry R10 and R9) by specifying the *tailfindr_mode* to: standard, n3ps_r9 or n3ps_r10.


Version 2.0
================

* Completely rewritten using the powerful `DSL2 <https://www.nextflow.io/docs/latest/dsl2.html>`__.
* Subworkflows are stored in the independent repository `BioNextflow <https://github.com/biocorecrg/BioNextflow>`__.
* Global nextflow config is broken down to different profiles (cluster, cloud, local...)
* Added the new module **mop_consensus**

* mop_preprocess (formerly known as nanoPreprocess + nanoPreprocessSimple)
     * now can read multiple runs per time using the syntax **"PATH/\*\*/*.fast5"**
     * can demultiplex fast5 using guppy too
     * deeplexicon can be run on GPU too
     * Parameters of each tool are stored in a tsv file. We have different ones already pre-set for cDNA, DNA and dRNA (option **--pars_tools**)
     * Added new process **discovery** with bambu / isoquant for discovering and quantifying new transcripts.
     * demultiplexing, filtering, mapping, counting and discovery can be switched off by setting "NO" as a parameter
     * saveSpace can be set to "YES" to reduce the amount of disk space required. **WARNING This will prevent the possibility to resume!**
     * Merged old NanoPreprocess and NanoPreprocessSimple in **mop_preprocess**. Using fastq or fast5 will switch among the two executions.
     * Htseq-count now accepts alignments generated by minimap2. https://github.com/htseq/htseq/issues/33
     * We can specify a **final_summary_**.txt** for extracting kit and flowcell info in the params.config file. If not present we should specify those info or a custom model via extra parameters in one of the **\*_opt.tsv** files or guppy will trigger an error.
     * This module can be run in AWS BATCH using the profile **awsbatch**
     * demultiplexing of fast5 with deeplexicon is now faster thanks to multithreading and parallelization

* mop_tail (formerly known as nanoTail)
     * now you can launch each analysis independently
     * Fine tuning of parameter for each step in tools_opt.tsv

* mop_mod (formerly known as nanoMod)
   * coming SOON!

Version 1.1
=================

* Added a new module called NanoPreprocessSimple that starts from fastq files instead of fast5 files. It allows the analysis of multiple files at a time.
* Added support to vbz compressed fast5 https://github.com/nanoporetech/vbz_compression in NanoPreprocess, NanoMod and NanoTail
* NanoPreprocess now outputs also CRAM files and can do downsampling with the parameter --downsampling
* NanoPreprocess allows performing variant calling using medaka (BETA)
* NanoPreprocess allows performing demultiplexing with GUPPY
* Added plots for Epinano output in NanoMod
* Added a conversion of Tombo results in bed format in NanoMod
* Added a INSTALL.sh file for automatically retrieve guppy 3.4.5 from https://mirror.oxfordnanoportal.com/, place it in NanoPreprocess/bin and making the required links
* Added profiles for being used locally and on the CRG SGE cluster


Version 1.0
================

This is the original version published in the paper `MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets <https://www.frontiersin.org/articles/10.3389/fgene.2020.00211/full>`__