Releases: pipecraft2/pipecraft
Releases · pipecraft2/pipecraft
Version 1.12
Bug fixes:
Updated Metamate specifications file loading
Updated Docker recognition for all platforms
Improved error logging
NextITS version 1.0.0
Added the BlasCh module for false-positive chimeras detection
v1.1.0
- added Resource Manager to control the resources used by Docker containers
- added OptimOTU pipeline for Fungi and Metazoa
- added metaMATE tool for filtering COI reads
- added SINTAX classifier
- added sim_score (pident * (alignment length / qlen) and adj_qcov (if qlen > slen then ((send-sstart+1)/slen)*100, otherwise equal to qcovs) to BLAST results
- sequences are now also added to the OTU table
- added support to process and merge multiple sequencing runs (runs must be in multiRunDir directory)
- tag-jumps filtering module (UNCROSS2) in now in the pre-defined pipelines (curate table box)
- NextITS in now available in MacOS
- removed read_R1 string input requirement (PE files must contain R1 and R2, then the PE samples will be automatically detected)
- removed HMM search from ORFfinder (now only ORFfinder is available); HMM did not work properly.
- added RAM friendly DADA2 pipeline implementation for denoising ("dada2 Big Data")
- added fix to CUT PRIMERS module to properly clip primers when PE amplicons are shorter than the sequencing cycle
- added fix to UNOISE pipeline to remove chimeras also from the table, not oonly form the final fasta file
- disabled automatic clustering in UNOISE pipeline; zOTUs can be clustered with ASV TO OTU module
- added min_lenght option back to demultiplexing module
- updated and fixed multiQC module to merge fastqc reports
v1.0.0
- major updates in the front-end (GUI); individual tools on the right, pipelines on left.
- added debugging mode and improved log info
- added NextITS pipeline for PacBio ITS sequences (not available for MacOS release)
- added ORFfinder + HMM bsed pseudogene/off-targets filtering for protein coding genes
- added RDP classifier
- added DADA2 pipeline for PacBio data
- added DADA2 pipeline for paired-end mixed oriented amplicons (fwd_orient and rev_orient are denoised separately and then merged)
- all features will get sha1 ID
- added ASVs to OTUs module (cluster ASVs into OTUs with vsearch)
- added tag-jumps filtering module (UNCROSS2)