Changelogs » Staphb-toolkit

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This one took awhile!
  - Cecret
  - Bug Fixes
  - Updates for Pangolin V3
  - Configuration file changes
  - Monroe
  - Updates for Pangolin V3
  - Monroe ONT
  - Removed barcode prefix to allow broader naming schemes
  - Dryad
  - Bug Fixes
  - Added mlst formatting process
  - Added mapping and coverage processes
  - Updated amrfinder_summary


Cecret Updates:
  * process ivar_variants and ivar_consensus have memory designations so that it doesn't fail as often
  * process samtools_plot_ampliconstats has been added
  * process vadr has been added
  * process bedtools has been renamed to bedtools_multicov and now requires the user to supply the amplicon file (instead of me trying to imagine what it would be from the primer bedfile)
  * ivar variants now creates a pseudo vcf file for bamsnap.
  * `--annotation` has been added an option, just in case the end user wants to run pangolin, nextclade, vadr, mafft/snpdists/iqtree on a collection of fastas
  * process filter has been added
  * most processes now have a free text `*_options` parameter to make it easier for the end user to modify options
  * `container` and `stageInMode` have been added to processes in the main file
  * renaming files now has an external as opposed to internal script
  * I've adjusted the config file template into something that makes more sense to me and added more variables
  Monroe ONT Updates
  * Removed Nanopolish option
  * Updated ARTIC workflow and added Medaka models
  * Option to use reads that are already basecalled and de-multiplexed


This update fixes an issue where only one read pair was carried forward after iVar step.


This release applies a fix for Monroe where iVar was not trimming primers correctly in the pe and se assembly workflows. This release is considered a critical bug fix because the issue has the potential to affect downstream analyses and had gone undiscovered for a period of time.


This update includes the [Cecret]( workflow for analyzing SARS-CoV-2 sequences from the Illumina platform.
  This update introduces the clear labs workflow for the Monroe pipeline!
  This update introduces the single end workflow for the Monroe pipeline!
  This update also includes the following bug fixes:
  * Fixed task associated memory and CPU parameters
  * Fixed install packaging from script
  * Adjusted minimum read depth to call a variant in the pe_assembly and se_assembly Monroe pipeline to 10


Fixed an issue with Monroe Cluster Report failing when encountering a "/" in the fasta header


v1.2.2 had an issue with monroe's profile configuration that would prevent it from running. v1.2.4 fixes this issue.
  Also updated how versioning is tracked simplifying toolkit releases.


No significant code changes.


This release adds the following:
  * Updates to Monroe ONT pipeline to accommodate new ONT barcode kits.
  * Update to allow local singularity images or other container repositories to be used in the toolkit.
  * Dryad report tool path fix.
  * Memory checking issues in various workflows.
  * Fixes for default file name splitting.


  * added cutshaw workflow
  * added mafft
  * dryad index fix
  * update to NCBI AMRFinder plus
  * various bug fixes


  * Bash pipe bug fix
  * Collision issue in trimmomatic workflows
  * Report builder bug fix


  * Version information is now displayed from help menu
  * More output from update function


  * Tredegar cpu/mem set based on resource availability
  * Tredegar log files restructured
  * Hickory workflow for SNP-reference selection incorporated
  * Removed default "_" separator for sample names from workflows, will now default to using whole file names


Fixed issues surrounding the report builder for dryad.


Fixed the following:
  * application updating
  * dryad fromPath error
  * ont basecalling queue
  * added Nextflow tower to configs
  * param.name_split_on standardized


Altered trace and report files to prepend a date time stamp to prevent cloud issues.