CHANGELOG

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