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Releases: nf-core/proteinfamilies

Aluminium Frog

16 Jun 08:06
@vagkaratzas vagkaratzas
1.2.0
58e1574
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Aluminium Frog

Added

  • #93
    • Added nf-test and meta.yml file for local subworkflow GENERATE_FAMILIES.
    • Added nf-test and meta.yml file for local subworkflow REMOVE_REDUNDANCY.
    • Added nf-test and meta.yml file for local subworkflow UPDATE_FAMILIES.
  • #88
    • Added nf-test and meta.yml file for local module BRANCH_HITS_FASTA.
    • Added nf-test and meta.yml file for local module FILTER_NON_REDUNDANT_FAMS.
    • Added nf-test and meta.yml file for local module IDENTIFY_REDUNDANT_FAMS.
    • Added nf-test and meta.yml file for local module EXTRACT_FAMILY_REPS.
    • Added the default pipeline end-to-end nf-test.

Changed

  • #81 - nf-core tools template update to 3.3.1.

Fixed

  • #80 - Fixed a bug where, due to a missing check for equal family sizes, non-redundant families were erroneously marked as redundant through transitive relationships and were removed
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Lead Sparrow

20 May 10:20
@vagkaratzas vagkaratzas
1.1.1
f862501
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Lead Sparrow Latest
Latest

Changed

  • #77 - Default branch changed from master to main.
  • #73 - Changed the fasta parsing library of the CHUNK_CLUSTERS local module, from pyfastx back to the latest version of biopython, and parallelized its writing mechanism, achieving decreased execution time.

Dependencies

Tool Previous version New version
biopython 1.84 1.85
pyfastx 2.2.0

Removed

  • #73 - Deprecated pyfastx module version of CHUNK_CLUSTERS, since it was struggling performance-wise with larger datasets.
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Nickel Elephant

09 May 11:15
@vagkaratzas vagkaratzas
1.1.0
c671acf
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Nickel Elephant

Added

  • #69 - Added the hhsuite/reformat nf-core module to reformat .sto alignments to .fas when in-family sequence redundancy is not removed.
    Also added the option to save intermediate and final family fasta files throughout the workflow with various save parameters.
  • #58 - Added nf-test and meta.yml file for local module REMOVE_REDUNDANCY_SEQS (Hackathon 2025)
  • #56 - Added nf-test and meta.yml file for local module FILTER_RECRUITED (Hackathon 2025)
  • #55 - Added nf-test and meta.yml file for local module CHUNK_CLUSTERS (Hackathon 2025)
  • #54 - Added nf-test for local subworkflow ALIGN_SEQUENCES (Hackathon 2025)
  • #53 - Added nf-test for local subworkflow EXECUTE_CLUSTERING (Hackathon 2025)
  • #51 - Added nf-test and meta.yml file for local module CALCULATE_CLUSTER_DISTRIBUTION (Hackathon 2025)
  • #34 - Added the EXTRACT_UNIQUE_CLUSTER_REPS module, that calculates initial MMseqs clustering metadata, for each sample, to print with MultiQC (Id,Cluster Size,Number of Clusters)

Fixed

  • #69 - Fixed a bug where redundant family alignments were not published properly, if intra-family redundancy removal mechanism was switched off #68
  • #65 - Fixed a bug in CHUNK_CLUSTERS, where pipeline would crash if the module filtered out all clusters, due to a high membership threshold #64
  • #35 - Fixed a bug in remove_redundant_fams.py, where comparison was between strings instead of integers to keep larger family
  • #33 - Fixed an always-true condition at the filter_non_redundant_hmms.py script, by adding missing parentheses
  • #29 - Fixed hmmalign empty input crash error, by preventing the FILTER_RECRUITED module from creating an empty output .fasta.gz file, when there are no remaining sequences after filtering the hmmsearch results #28

Changed

  • #69 - Changed the publish directory architecture for HMMs, seed MSAs, full MSAs and family FASTA files, to make it more intuitive.
    REMOVE_REDUNDANT_FAMS local module converted to IDENTIFY_REDUNDANT_FAMS to extract redundant family ids which will then be used downstream.
    FILTER_NON_REDUNDANT_HMMS local module converted to FILTER_NON_REDUNDANT_FAMS and reused four times (HMM, seed MSA, full MSA, FASTA).
    Changed the output format of the EXTRACT_FAMILY_REPS and REMOVE_REDUNDANT_SEQS local modules from .fa to .faa.
    Metro map updated with new hhsuite/reformat module.
  • #57 - slight improvements of nextflow_schema.json (Hackathon 2025)
  • #57 - slight improtmenets of assets/schema_input.json (Hackathon 2025)
  • #34 - Swapped the SeqIO python library with pyfastx for the CHUNK_CLUSTERS module, quartering its duration
  • #32 - Updated ClipKIT 2.4.0 -> 2.4.1, that now also allows ends-only trimming, to completely replace the custom CLIP_ENDS module. Users can now also define its output format by setting the --clipkit_out_format parameter (default: clipkit)

Dependencies

Tool Previous version New version
ClipKIT 2.4.0 2.4.1
pyfastx 2.2.0
hhsuite 3.3.0
multiqc 1.27 1.28

Deprecated

  • #32 - Deprecated CLIP_ENDS module and --clipping_tool parameter. The only option now is ClipKIT, covering both previous modes, via setting --trim_ends_only
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Iron Rhinoceros

17 Feb 09:22
@vagkaratzas vagkaratzas
1.0.0
dcb9338
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Iron Rhinoceros

Initial release of nf-core/proteinfamilies, created with the nf-core template.

Added

  • Amino acid sequence clustering (mmseqs)
  • Multiple sequence alignment (famsa, mafft, clipkit)
  • Hidden Markov Model generation (hmmer)
  • Between families redundancy removal (hmmer)
  • In-family sequence redundancy removal (mmseqs)
  • Family updating (hmmer, seqkit, mmseqs, famsa, mafft, clipkit)
  • Family statistics presentation (multiqc)

By @vagkaratzas and @mberacochea.

Contributors

mberacochea and vagkaratzas
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