.. _home-page-changelog: ************** CHANGELOG ************** .. autosummary:: :toctree: generated Version 2.0 ================ * Completely rewritten using the powerful `DSL2 `__. * Subworkflows are stored in the independent repository `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 * A new test dataset allows to perform CI on mop_preprocess, mop_mod (excluding nanocompore) and mop_tail * 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) * 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 `__