Mercury Spider

Added

• #143
  • Added the cmaple module for optional phylogenetic tree inference for final family full MSAs. (by @vagkaratzas)
  • Added extra nf-tests for the REMOVE_REDUNDANCY subworkflow. (by @vagkaratzas)
• #140 - Using the new workflow output syntax to publish the downstream nf-core/proteinannotator samplesheet. (by @vagkaratzas)

Changed

• #143 - Updated metro-maps, citations, README.md and output.md to include cmaple phylogenetic trees. (by @vagkaratzas)
• #141 - Aligning the default output directory of the new output syntax with the publishing directory of the pipeline. (by @vagkaratzas)
• #140
  • Updated metro-map to also depict the optional creation of downstream samplesheets for nf-core/proteinfold and nf-core/proteinannotator. Also swapped seqkit/rmdup and seqkit/replace modules to their proper execution sequence. (by @vagkaratzas)
  • Updated the test_full profile time and memory requirements to avoid AWS failures on release. (by @vagkaratzas)

Fixed

• #143
  • Fixed a bug in REMOVE_REDUNDANCY subworkflow, where the combination of these skip flags --skip_sequence_redundancy_removal true, --skip_additional_sequence_recruiting true and --skip_additional_sequence_recruiting false, would execute HHSUITE_REFORMAT_FILTERED to reformat Stockholm alignments while they were already in fasta (or clipkit) format. (by @vagkaratzas)
  • Fixed a bug in REMOVE_REDUNDANCY subworkflow, where unmerged similar families would be removed along with redundant ones, when --skip_family_merging was true and --skip_family_redundancy_removal was false. (by @vagkaratzas)

Dependencies

Tool	Previous version	New version
multiqc	1.32	1.33
cmaple	-	1.1.0