Code

Extend annotations#1

Code

Closed

tgurbich wants to merge 106 commits intomainEBI-Metagenomics/mettannotator:mainfrom extend-annotationsEBI-Metagenomics/mettannotator:extend-annotationsCopy head branch name to clipboard

+2,902-389

Commits

Commits on Nov 16, 2023

• Added pre-processing script for UniRule

  tgurbich

  committed
  33341ac

Commits on Nov 17, 2023

• Added species names to UniRule prep script

  tgurbich

  committed
  123be4b

• Added GECCO

  tgurbich

  committed
  4ca71fb

Commits on Nov 20, 2023

• Added accounting for empty GECCO results

  tgurbich

  committed
  fc88a23

• Removed old code

  tgurbich

  committed
  83dbf96

• Fixed typo

  tgurbich

  committed
  4f153c6

• Edited syntax

  tgurbich

  committed
  05ab91d

• Edited syntax

  tgurbich

  committed
  43778d7

• Bug fixes

  tgurbich

  committed
  121d831

• Added Defense Finder

  tgurbich

  committed
  089762c

• Bug fixes

  tgurbich

  committed
  d72f870

• Added UniFire

  tgurbich

  committed
  37b2cba

• Bug fix

  tgurbich

  committed
  590a513

Commits on Nov 21, 2023

• A few fixes to the new tools

  Show description for 2371b8c
  mberacochea

  committed
  2371b8c

• Fix GECCO invocation and some typos

  mberacochea

  committed
  6a92fb6

Commits on Nov 22, 2023

• Fixed GECCO, UniRULE and MultiQC

  mberacochea

  committed
  14ae4ee

• Added UniFire memory requirements

  tgurbich

  committed
  af6ff56

• Fixed typo

  tgurbich

  committed
  07b5f86

• Add tower.yml

  mberacochea

  committed
  4446eeb

• Merge branch 'extend-annotations' of github.com:EBI-Metagenomics/mettannotator into extend-annotations

  mberacochea

  committed
  ddafcc5

• Patch rRNA detection step with tmp folder fix.

  Show description for dd81bce
  mberacochea

  committed
  dd81bce

• Rename tower.yml

  mberacochea

  committed
  b3e5d4f

Commits on Nov 23, 2023

• Added UniRule post-processing script - WIP

  tgurbich

  committed
  8026915

• Combined parsing functions

  tgurbich

  committed
  4bf4054

Commits on Nov 24, 2023

• Add antiSMASH 7.1

  mberacochea

  committed
  a147b65

• Merge branch 'extend-annotations' of github.com:EBI-Metagenomics/mettannotator into extend-annotations

  mberacochea

  committed
  8da6072

Commits on Nov 27, 2023

• Adjust antiSMASH outdir results structure

  mberacochea

  committed
  0c77757

• Adjust the outdir results structure

  mberacochea

  committed
  ddb8903

• Typo on process selector

  mberacochea

  committed
  38f08f6

Commits on Nov 29, 2023

• Added dbcan

  tgurbich

  committed
  2fa0916

• Merge branch 'extend-annotations' of https://github.com/EBI-Metagenomics/mettannotator into extend-annotations

  tgurbich

  committed
  9fb11ba

• Bug fix

  tgurbich

  committed
  f0f0f56

• Bug fix

  tgurbich

  committed
  b606043

• Input format change

  tgurbich

  committed
  f92bb13

Commits on Nov 30, 2023

• Fixed typos and removed testing edits

  tgurbich

  committed
  ac6719b

• Bug fix and typo fixes

  tgurbich

  committed
  7b0aca6

• Added GO-terms to the annotate_gff script

  tgurbich

  committed
  8ce9bc6

• Removed reporting of empty IPS

  tgurbich

  committed
  8f05c94

• Removed empty values from GFF

  tgurbich

  committed
  7b2df5e

• Bug fix in annotate_gff

  tgurbich

  committed
  d679dbe

Commits on Dec 1, 2023

• Added dbcan post-processing

  tgurbich

  committed
  566de3d

• dbCAN GFF format edits

  tgurbich

  committed
  efba874

• Tweak the results folder structure.

  mberacochea

  committed
  b541105

• Annotate GFF versions fix

  mberacochea

  committed
  2180c9f

• Format edits for dbcan processing script

  tgurbich

  committed
  b323010

• Added unifire post-processing

  tgurbich

  committed
  725665b

• WIP

  tgurbich

  committed
  7ec709b

• WIP

  tgurbich

  committed
  ce7a245

• Added join to arguments

  tgurbich

  committed
  3b5f16a

• WIP

  tgurbich

  committed
  af84985

• WIP

  tgurbich

  committed
  18c7333

Commits on Dec 5, 2023

• Bug fix

  tgurbich

  committed
  f484ef1

• Bug fix

  tgurbich

  committed
  6387305

Commits on Dec 6, 2023

• GFF format changes

  tgurbich

  committed
  0825e45

Commits on Dec 7, 2023

• Added defense finder post-processing script

  tgurbich

  committed
  3033c5e

• Added DefenseFinder post-processing to nf

  tgurbich

  committed
  fd053c6

• Added duplicate resolution script - WIP

  tgurbich

  committed
  1b0c9ca

• Format edit

  tgurbich

  committed
  c3c70ee

• Changed dbcan output name format

  tgurbich

  committed
  2b7389a

• Added AMRFinderPlus processing script

  tgurbich

  committed
  5024ed0

• Added AMR post-processing to the AMR module

  tgurbich

  committed
  db27d87

• Fixed unifire post-processing script

  tgurbich

  committed
  86b6021

• Temporarily removed amrfinder post-processing

  tgurbich

  committed
  3b11069

• Fixed typo

  tgurbich

  committed
  7e22e4b

• Fixed typo

  tgurbich

  committed
  8a4726c

• Removed post-processing

  tgurbich

  committed
  4037c7d

• Add an antismash to gff script

  mberacochea

  committed
  699e42e

• Move PROKKA results to the functional annotation folder.

  mberacochea

  committed
  150b35e

• Move sanntis to the bgc results folder

  mberacochea

  committed
  3af5a9f

Commits on Dec 8, 2023

• Changed antismash GFF name

  tgurbich

  committed
  0d721f3

• Text edits

  tgurbich

  committed
  6f036db

• Format edits

  tgurbich

  committed
  9d4bde2

• Merge pull request #2 from EBI-Metagenomics/feature/antismash-gff

  Show description for 18549fe
  tgurbich

  authored
  18549fe

• Bug fix

  tgurbich

  committed
  c74a36c

• Added an extra GFF processing script to the annotate_gff process

  mberacochea

  committed
  12e7f86

• Fixed the schema

  Show description for e039cf2
  mberacochea

  committed
  e039cf2

• Fix nf-core pipeline linting issues

  mberacochea

  committed
  93a0f72

• convert_cds_into_multiple_lines correction

  mberacochea

  committed
  d4956be

• CRISPR fix for correct visualisation

  tgurbich

  committed
  d9c49de

• Added protein component filter

  tgurbich

  committed
  e9d4b9e

• Removed uniprot fields that are not in the existing dictionary

  tgurbich

  committed
  b94715f

• Add an AMRFinderPlus GFF generation step

  mberacochea

  committed
  4fc6da8

• Fixed crispr naming

  tgurbich

  committed
  a513267

• Typo in convert_cds script. Added tag to IPS

  mberacochea

  committed
  b891c33

• Typos in amrfinder post processing

  mberacochea

  committed
  9d90096

• AMRFINDER_PLUS_TO_GFF add required -v param

  mberacochea

  committed
  836227d

• Removed parent field from flank sequence in CRISPRCas results

  tgurbich

  committed
  6aa4bcc

• Tweak DBCan outputfolder

  mberacochea

  committed
  1b2b761

• Remove the structure annotation folder.

  Show description for bd873c2
  mberacochea

  committed
  bd873c2

• Merge pull request #3 from EBI-Metagenomics/feature/gff_post_processing_split_cds

  Show description for abd9e22
  tgurbich

  authored
  abd9e22

• Mobilome merger script added

  Ales-ibt

  authored
  d5526d3

• Finished GECCO addition to annotate_gff script

  tgurbich

  committed
  dad4d02

• Resolved

  tgurbich

  committed
  f371d33

• Added antismash to annotate_gff

  tgurbich

  committed
  bbb596c

• Removed extra spaces from dbcan protein fams

  tgurbich

  committed
  1c18835

• Added dbCAN to the annotate_gff script

  tgurbich

  committed
  7b76e63

• Added defense finder to annotate_gff

  tgurbich

  committed
  c1f98b9

Commits on Dec 11, 2023

• Added arguments to annotate_gff

  tgurbich

  committed
  62c3f8a

• Added combined unifire output

  tgurbich

  committed
  574dd1e

• Format

  tgurbich

  committed
  a960896

• Removed gff line splitting

  tgurbich

  committed
  d634e08

Commits on Jan 15, 2024

• Removed mmseqs from the duplicate resolution script

  tgurbich

  committed
  ae7e2fa

• Fixed integer checked in duplicate gene names

  tgurbich

  committed
  bfd2174

• Moved duplicate loading into a separate function

  tgurbich

  committed
  d3bc930

Commits on Jan 16, 2024

• Refactored the duplicate resolution script

  tgurbich

  committed
  4813b3f

Commits on Jan 19, 2024

• WIP

  tgurbich

  committed
  c15f62a