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@jvhagey jvhagey released this 06 Mar 16:13
· 864 commits to main since this release
v1.1.0
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Learn about vigilant mode.

Implemented Enhancements:

  • Default branch set to main thanks @erinyoung #84.
  • Added emits to allow linking of workflows to close #42 #e32132d.
  • MLST output is now scanned for completeness of profiles by consolidating any allele tags to the ST column for easier scanning as well as known paralog alleles are marked for easier identification. In CDC_PHOENIX workflow ST types are consolidated, if applicable, to show concordance bewteen tools.
  • Addition of 🔥🐎🐦🔥 GRiPhin: General Report Pipeline from PHoeNIx output to -entry CDC_PHOENIX #6291e9c. This was implemented to replace common report generated internally, which is why it is only in the -entry CDC_PHOENIX.
  • Changes to allow relative paths for kraken2 and BUSCO database to be passed rather than it requiring it to be a full path #ecb3618 and #d938a64.
  • Phoenix_Output_Report.tsv now has antibiotic genes and plasmid markers filtered to ensure quality #d0fa32c.
    • Plasmid markers require >=60% length and >=98% identity to be reported
    • Antibiotic Genes require >=90% length and >=98% identity to be reported

Output File Changes:

  • Removed spaces in header of *_all_genes.tsv file from AMRFinder+ output and replace with underscore to allow for more friendly parsing #fd048d1.
  • Fixed error causing PROKKA output to not be in Annotation folder #d014aa0.
  • Added headers to 2 files: *.fastANI.txt and *.wtasmbld_summary.txt.
  • Also, added headers to phoenix_line_summary.tsv see wiki for details.
  • MLST final output that includes different headers and organization was renamed to *_combined.tsv which includes srst2 types, if appicable, paralog tags, and any extra allele/profile tags.

Fixed Bugs:

  • Edit to allow nf-tower to work #b21d61f
  • Fixed pipeline failure when prokka throws error for sample names being too long (Error: ID must <= 37 chars long) #e48e01f. Now sample name length doesn't matter.
  • Fixed bug where samples wouldn't end up in the Phoenix_Output_Report.tsv due to srst2 not finding any AR genes so the file wasn't created. Now blank file is created and remaining sample informatin is in the Phoenix_Output_Report.tsv #2f52edc. This change only occured in -entry CDC_PHOENIX.
  • Fixed issue where cp error was thrown when relative path was given for output directory #0c0ca55 and #d938a64.

Database Updates:

  • AMRFinder+ database is now static and included in the database folder #a5d2d03. We removed the automatic updating for more control of the pipeline and lockdown to prepare for possible CLIA requirements.
    • Version 2022-08-09.1 currently used to be the same as the one in the curated db.
  • Curated AR gene database was updated on 2022-09-15 (yyyy-mm-dd) which includes:
  • Fresh pull of plasmidfinder database on 2022-09-16 up to commit 9002e72
  • Updated Mash sketch from all complete refseq bacteria on 2022-09-15
  • Updated a NCBI Assembly stats file, which is calculated based on this file

Container Updates:

  • MLST updated from 2.22.1 to 2.23.0.
  • BBTools updated from 38.96 to 39.01.
  • AMRFinder+ was updated from 3.10.40 to 3.10.45.
  • Scripts the utilize the phoenix_base container were updated to quay.io/jvhagey/phoenix:base_v1.1.0 which had the python library xlsxwriter added to it for GRiPHin.py.

Contributors

erinyoung
Assets 2
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