added 2nd round of cut primers to properly remove fwd and rev primers form the paired-end data set
added UNOISE3 module to generate zOTUs (under clustering)
added uchime3 chimera filtering (for denoised amplicons)
edited sequence count statistics process after the process (using seqkit)
only fasta (fa, fas) format is accepted for clustering
edited OTU table making strategy for OTU clustering (was –usearch_global before)
added table filtering options for DADA2 ASV table (collapse mismatch, filter by length)
added ASV to OTU module (clustering DADA2 ASVs into OTUs)
select region to cluster after ITSx in OTUs workflow
automatically saves the PipeCraft workflow settings into loadable JSON file
outputs log file (in development)
merged vsearch and dada2 containers (had a lot in common)

Implemented software: (software version in bold denotes version upgrade)

0.1.3 (28.07.2022)

updated BLAST 2.11.0+ to BLAST 2.12.0+ and added biopython to BLAST container (fixed the coverage% calculation)
fixed the megaBLAST, when gapextend=undefined
quality Check module edit (does not stop when browsing around)
fixed ASVs workflow error message when using <2 samples
added lock panels when starting a process
few cosmetic front-end adds

0.1.2 (07.06.2022)

added LULU post-clustering
added DEICODE (postprocessing)
added fastp quality filtering
added DADA2 quality filtering under ‘ADD STEP’ -> ‘QUALITY FILTERING’ panel
added DADA2 denoise and assemble paired-end data under ‘ADD STEP’ -> ‘ASSEMBLE PAIRED-END’ panel
added DADA2 assignTaxonomy under ‘ADD STEP’ -> ‘ASSIGN TAXONOMY’ panel
added trunc_length option for vsearch quality filtering
python3 module fix for ITSx for removing empty sequeces

Implemented software: (software in red font denote new additions; ‘version’ in bold denotes version upgrade)

Minor cosmetic changes and bug fixes. DOWNLOAD link for v0.1.1

separate output forlder for unused index combinations in demultiplexing.
resolved issues with sample renaiming when using dual combinational indexes for paired-end data (DEMULTIPLEX)
minBoot option fixed in DADA2 taxonomy annotation
vsearch quality filtering “minsize” not working (option currently removed).

Implemented software: