.. |PipeCraft2_logo| image:: _static/PipeCraft2_icon_v2.png
  :width: 50
  :target: https://github.com/pipecraft2/pipecraft

.. raw:: html

    <style> .red {color:#ff0000; font-weight:bold; font-size:16px} </style>

.. role:: red


.. _releases:

========
Releases 
========

|PipeCraft2_logo|

.. contents:: Contents
   :depth: 2

____________________________________________________


.. _1.2.0:

1.2.0 (28.05.2026)
==================

`DOWNLOAD link for v1.2.0 <https://github.com/pipecraft2/pipecraft/releases/tag/v1.2.0>`_

Software updates:

* added FunBarONT pipeline for Oxford Nanopore ITS sequences (barcoding pipeline)
* In Utilities, added module to add sequences to feature table (add sequences to table)
* BlasCh module for identifying false-positive chimeras (postprocessing panel).
* updated metaMATE to version 0.5.6; added per-sample filtering mode and OTU-mode. Global (find+dump) and per-sample (filter-adaptive) filtering modes are available.
* added swarm clustering to clustering panel.
* updated NextITS pipeline to version 1.1.0.
* ITSx image rebuild — new HMM profiles (ITSx_HMMs 2024.04.05), HMMER 3.4, Ubuntu 24.04 base image.
* Releases will now contain a universal Mac DMG (Intel + Apple Silicon).
* Added auto-update functionality to the PipeCraft2 app (App will automatically check for updates on startup and notify the user).
* Added BOLDigger3 taxonomy assignment tool (QuickTools).
 
General updates:

* speed up the seq_count_summary making
* added workflow for dealing with dataset with thousands of samples for 'merge sequencing runs' in vsearch/unoise pipeline. 
* PipeCraft2 automatically detects the file extensions in the working directory. 
* NextITS: runtime image ``pipecraft/nextits:1.1.0-pc1.2.0`` (extends ``vmikk/nextits:1.1.0``; Nextflow v25.10.4).
* ORF-finder module now automatically filters also the feature table (input table required; can contain "Sequence" column).
* ASV TO OTU module: fasta file can contain a subset of ASVs that are present in the provided table file.
* adjusted vsearch and unoise pre-compiled pipelines so that quality filtering is performed before paired-end merging (consistent with DADA2 ASVs workflow).
* updated similarity score calculation in BLAST results to account for 'alignment len' > qlen. 

Bug fixes:

* SINTAX classifier did not work with UDB files, fixed. 
* bug fix to seq_count_summary making after ITSx for full_ITS/full_and_partial dir
* fix to MetaMATE to work with the default specification0.txt (no abundance filtering) in the Docker container.
* ITSx: fix the issue of reporting ERROR when all sequences had no ITS region detected (i.e., no sequences in no_detection directory)
* only v1.1.0: changing MERGE PAIRS settings in DADA2 ASVs workflow did not have any effect, the run was always using the default settings (THIS IS FINE UNLESS some settings were tuned).
* only v1.1.0: dada2 denoising setting "pool" was effectively always set to FALSE. Now, "pool" = TRUE/pseudo has an effect (more RAM hungry, but more sensitive to rare variants).

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

+------------------------------------------------------------------------+-------------+
| Software/Process                                                       | version     |
+========================================================================+=============+
| :ref:`swarm clustering <clustering_swarm>` :red:`(new)`                | **v3.1.6**  |
+------------------------------------------------------------------------+-------------+
| :ref:`FunBarONT pipeline <funbaront_pipeline>` :red:`(new)`            | 13.03.2026  |
+------------------------------------------------------------------------+-------------+
| :ref:`BlasCh <postprocessing_blasch>` :red:`(new)`                     | v0.1.0      |
+------------------------------------------------------------------------+-------------+
| `OptimOTU <https://github.com/brendanf/optimotu_targets>`_             | 5.1.0       |
+------------------------------------------------------------------------+-------------+
| `metaMATE <https://github.com/tjcreedy/metamate>`_                     | **0.5.6**   |
+------------------------------------------------------------------------+-------------+
| SINTAX (via vsearch)                                                   | v2.30.4     |
+------------------------------------------------------------------------+-------------+
| `NextITS pipeline <https://next-its.github.io/>`_                      | **1.1.0**   |
+------------------------------------------------------------------------+-------------+
| `ORFfinder <https://www.ncbi.nlm.nih.gov/orffinder/>`_                 | **v0.4.3**  |
+------------------------------------------------------------------------+-------------+
| RDP classifier                                                         | v2.13       |
+------------------------------------------------------------------------+-------------+
| `DADA2 <https://benjjneb.github.io/dada2/index.html>`_                 | 1.41        |
+------------------------------------------------------------------------+-------------+
| `vsearch <https://github.com/torognes/vsearch>`_                       | **2.30.4**  |
+------------------------------------------------------------------------+-------------+
| `trimmomatic <http://www.usadellab.org/cms/?page=trimmomatic>`_        | **0.40**    |
+------------------------------------------------------------------------+-------------+
| `BOLDigger3 <https://github.com/Teichlab/BOLDigger3>`_ :red:`(new)`    | **2.2.0**   |
+------------------------------------------------------------------------+-------------+
| Nextflow (NextITS image)                                               | **25.10.4** |
+------------------------------------------------------------------------+-------------+
| BBMap (metaMATE image)                                                 | 39.06       |
+------------------------------------------------------------------------+-------------+
| `seqkit <https://bioinf.shenwei.me/seqkit/>`_                          | **2.13.0**  |
+------------------------------------------------------------------------+-------------+
| `cutadapt <https://cutadapt.readthedocs.io/en/stable/>`_               | **v5.2**    |
+------------------------------------------------------------------------+-------------+
| `mothur <https://github.com/mothur/mothur>`_                           | 1.46.1      |
+------------------------------------------------------------------------+-------------+
| `ITS Extractor <https://microbiology.se/software/itsx/>`_              | 1.1.3       |
+------------------------------------------------------------------------+-------------+
| `fqgrep <https://github.com/indraniel/fqgrep>`_                        | 0.4.4       |
+------------------------------------------------------------------------+-------------+
| `BLAST <https://blast.ncbi.nlm.nih.gov/Blast.cgi>`_                    | **2.16.0+** |
+------------------------------------------------------------------------+-------------+
| `FastQC <https://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_ | 0.11.9      |
+------------------------------------------------------------------------+-------------+
| `MultiQC <https://multiqc.info/>`_                                     | 1.12        |
+------------------------------------------------------------------------+-------------+
| `LULU <https://github.com/tobiasgf/lulu>`_                             | 0.1.0       |
+------------------------------------------------------------------------+-------------+
| `fastp <https://github.com/OpenGene/fastp>`_                           | 0.23.2      |
+------------------------------------------------------------------------+-------------+
| `DEICODE <https://github.com/biocore/DEICODE>`_                        | 0.2.4       |
+------------------------------------------------------------------------+-------------+

__________________________________________________

.. _1.1.0:

1.1.0 (12.03.2025)
==================

`DOWNLOAD link for v1.1.0 <https://github.com/pipecraft2/pipecraft/releases/tag/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-compiled 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

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

=======================================================================  ==========
Software                                                                 version                                                                                       
=======================================================================  ==========
`OptimOTU <https://github.com/brendanf/optimotu_targets>`_ :red:`(new)`  **5.1.0**
SINTAX (via vsearch) :red:`(new)`                                        **2.29.4**
`metaMATE <https://github.com/tjcreedy/metamate>`_ :red:`(new)`          **0.4.3**
`NextITS pipeline <https://next-its.github.io/>`_                        0.5.0
`ORFfinder <https://www.ncbi.nlm.nih.gov/orffinder/>`_                   **v0.4.3**
`RDP classifier`                                                         v2.13
`DADA2 <https://benjjneb.github.io/dada2/index.html>`_                   **1.34**
`vsearch <https://github.com/torognes/vsearch>`_                         **2.29.4**
`trimmomatic <http://www.usadellab.org/cms/?page=trimmomatic>`_          0.39
`seqkit <https://bioinf.shenwei.me/seqkit/>`_                            2.3.0
`cutadapt <https://cutadapt.readthedocs.io/en/stable/>`_                 4.4
`mothur <https://github.com/mothur/mothur>`_                             1.46.1
`ITS Extractor <https://microbiology.se/software/itsx/>`_                1.1.3
`fqgrep <https://github.com/indraniel/fqgrep>`_                          0.4.4
`BLAST <https://blast.ncbi.nlm.nih.gov/Blast.cgi>`_                      2.14.0+
`FastQC <https://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_   0.11.9
`MultiQC <https://multiqc.info/>`_                                       1.12
`LULU <https://github.com/tobiasgf/lulu>`_                               0.1.0
`fastp <https://github.com/OpenGene/fastp>`_                             0.23.2
`DEICODE <https://github.com/biocore/DEICODE>`_                          0.2.4
=======================================================================  ==========

__________________________________________________

.. _1.0.0:

1.0.0 (01.09.2023)
==================

`DOWNLOAD link for v1.0.0 <https://github.com/pipecraft2/pipecraft/releases/tag/v1.0.0>`_

* major updates in the front-end; 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)
* implemented DADA2 denoising sensitivity editing
* all features will get sha1 ID 
* added ASVs to OTUs module (cluster ASVs into OTUs with vsearch)
* added tag-jumps filtering module (UNCROSS2)
* fixed the vsearch_dada2 container issues for MacOS 
  
Implemented software:
*(software version in bold denotes version upgrade)*

=======================================================================  ==========
Software                                                                 version                                                                                       
=======================================================================  ==========
`NextITS pipeline <https://next-its.github.io/>`_ :red:`(new)`           **0.5.0**
`ORFfinder <https://www.ncbi.nlm.nih.gov/orffinder/>`_ :red:`(new)`      **v0.4.3**
RDP classifier :red:`(new)`                                              **v2.13**
`DADA2 <https://benjjneb.github.io/dada2/index.html>`_                   **1.27**
`vsearch <https://github.com/torognes/vsearch>`_                         **2.23**
`trimmomatic <http://www.usadellab.org/cms/?page=trimmomatic>`_          0.39
`seqkit <https://bioinf.shenwei.me/seqkit/>`_                            2.3.0
`cutadapt <https://cutadapt.readthedocs.io/en/stable/>`_                 **4.4**
`mothur <https://github.com/mothur/mothur>`_                             1.46.1
`ITS Extractor <https://microbiology.se/software/itsx/>`_                1.1.3
`fqgrep <https://github.com/indraniel/fqgrep>`_                          0.4.4
`BLAST <https://blast.ncbi.nlm.nih.gov/Blast.cgi>`_                      **2.14.0+**
`FastQC <https://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_   0.11.9
`MultiQC <https://multiqc.info/>`_                                       1.12
`LULU <https://github.com/tobiasgf/lulu>`_                               0.1.0
`fastp <https://github.com/OpenGene/fastp>`_                             0.23.2
`DEICODE <https://github.com/biocore/DEICODE>`_                          0.2.4
=======================================================================  ==========

____________________________________________________

.. _0.1.4:

0.1.4 (15.12.2022)
==================

`DOWNLOAD link for v0.1.4 <https://github.com/pipecraft2/pipecraft/releases/tag/v0.1.4>`_

* 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)*

=======================================================================  ==========  =========================================================================================
Software                                                                 version     Reference                                                                                  
=======================================================================  ==========  =========================================================================================
`DADA2 <https://benjjneb.github.io/dada2/index.html>`_                   1.20        `Callahan et. al 2016 <https://www.nature.com/articles/nmeth.3869>`_                      
`vsearch <https://github.com/torognes/vsearch>`_                         **2.22.1**  `Rognes et. al 2016 <https://peerj.com/articles/2584/>`_                                  
`trimmomatic <http://www.usadellab.org/cms/?page=trimmomatic>`_          0.39        `Bolger et al. 2014 <https://doi.org/10.1093/bioinformatics/btu170>`_                     
`seqkit <https://bioinf.shenwei.me/seqkit/>`_                            **2.3.0**   `Shen et al. 2016 <https://doi.org/10.1371/journal.pone.0163962>`_                        
`cutadapt <https://cutadapt.readthedocs.io/en/stable/>`_                 3.5         `Martin 2011 <https://doi.org/10.14806/ej.17.1.200>`_                                     
`mothur <https://github.com/mothur/mothur>`_                             1.46.1      `Schloss et al. 2009 <https://doi.org/10.1128/AEM.01541-09>`_                             
`ITS Extractor <https://microbiology.se/software/itsx/>`_                1.1.3       `Bengtsson-Palme et al. 2013 <https://doi.org/10.1111/2041-210X.12073>`_                  
`fqgrep <https://github.com/indraniel/fqgrep>`_                          0.4.4       `Indraniel Das 2011 <https://github.com/indraniel/fqgrep>`_                               
`BLAST <https://blast.ncbi.nlm.nih.gov/Blast.cgi>`_                      2.11.0+     `Camacho et al. 2009 <https://doi.org/10.1186/1471-2105-10-421>`_                         
`FastQC <https://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_   0.11.9      `Andrews 2019 <https://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_              
`MultiQC <https://multiqc.info/>`_                                       1.12        `Ewels et al. 2016 <https://doi.org/10.1093/bioinformatics/btw354>`_                      
`LULU <https://github.com/tobiasgf/lulu>`_                               0.1.0       `Froslev et al. 2017 <https://doi.org/10.1038/s41467-017-01312-x>`_
`fastp <https://github.com/OpenGene/fastp>`_                             0.23.2      `Chen et al. 2018 <https://doi.org/10.1093/bioinformatics/bty560>`_
`DEICODE <https://github.com/biocore/DEICODE>`_                          0.2.4       `Martion et al. 2019 <https://journals.asm.org/doi/10.1128/mSystems.00016-19>`_
=======================================================================  ==========  =========================================================================================

____________________________________________________


.. _0.1.3:

0.1.3 (28.07.2022)
==================

`DOWNLOAD link for v0.1.3 <https://github.com/SuvalineVana/pipecraft/releases/tag/v0.1.3>`_

* 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:

0.1.2 (07.06.2022)
==================

`DOWNLOAD link for v0.1.2 <https://github.com/SuvalineVana/pipecraft/releases/tag/v0.1.2>`_

* 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  'version' in bold denotes version upgrade)*

=======================================================================  ========  =========================================================================================
Software                                                                 version   Reference                                                                                  
=======================================================================  ========  =========================================================================================
`DADA2 <https://benjjneb.github.io/dada2/index.html>`_                   **1.20**  `Callahan et. al 2016 <https://www.nature.com/articles/nmeth.3869>`_                      
`vsearch <https://github.com/torognes/vsearch>`_                         2.18.0    `Rognes et. al 2016 <https://peerj.com/articles/2584/>`_                                  
`trimmomatic <http://www.usadellab.org/cms/?page=trimmomatic>`_          0.39      `Bolger et al. 2014 <https://doi.org/10.1093/bioinformatics/btu170>`_                     
`seqkit <https://bioinf.shenwei.me/seqkit/>`_                            2.0.0     `Shen et al. 2016 <https://doi.org/10.1371/journal.pone.0163962>`_                        
`cutadapt <https://cutadapt.readthedocs.io/en/stable/>`_                 3.5       `Martin 2011 <https://doi.org/10.14806/ej.17.1.200>`_                                     
`mothur <https://github.com/mothur/mothur>`_                             1.46.1    `Schloss et al. 2009 <https://doi.org/10.1128/AEM.01541-09>`_                             
`ITS Extractor <https://microbiology.se/software/itsx/>`_                1.1.3     `Bengtsson-Palme et al. 2013 <https://doi.org/10.1111/2041-210X.12073>`_                  
`fqgrep <https://github.com/indraniel/fqgrep>`_                          0.4.4     `Indraniel Das 2011 <https://github.com/indraniel/fqgrep>`_                               
`BLAST <https://blast.ncbi.nlm.nih.gov/Blast.cgi>`_                      2.11.0+   `Camacho et al. 2009 <https://doi.org/10.1186/1471-2105-10-421>`_                         
`FastQC <https://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_   0.11.9    `Andrews 2019 <https://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_              
`MultiQC <https://multiqc.info/>`_                                       1.12      `Ewels et al. 2016 <https://doi.org/10.1093/bioinformatics/btw354>`_                      
`LULU <https://github.com/tobiasgf/lulu>`_ :red:`(new)`                  0.1.0     `Froslev et al. 2017 <https://doi.org/10.1038/s41467-017-01312-x>`_
`fastp <https://github.com/OpenGene/fastp>`_ :red:`(new)`                0.23.2    `Chen et al. 2018 <https://doi.org/10.1093/bioinformatics/bty560>`_
`DEICODE <https://github.com/biocore/DEICODE>`_ :red:`(new)`             0.2.4     `Martion et al. 2019 <https://journals.asm.org/doi/10.1128/mSystems.00016-19>`_
=======================================================================  ========  =========================================================================================

____________________________________________________

.. _0.1.1:

0.1.1 (01.04.2022)
==================

Minor cosmetic changes and bug fixes. 
`DOWNLOAD link for v0.1.1 <https://github.com/SuvalineVana/pipecraft/releases/tag/0.1.1>`_

* 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).

____________________________________________________

.. _0.1.0:

0.1.0 pre-release (14.12.2021)
==============================

`DOWNLOAD link for v0.1.0 <https://github.com/SuvalineVana/pipecraft/releases/tag/0.1.0>`_

* ASV workflow with DADA2 for paired-end data.
* vsearch based OTU workflow.
* QualityCheck module with MultiQC and FastQC

Implemented software:

=======================================================================  ========  =========================================================================================
Software                                                                 version   Reference                                                                                  
=======================================================================  ========  =========================================================================================
`DADA2 <https://benjjneb.github.io/dada2/index.html>`_                   1.14      `Callahan et. al 2016 <https://www.nature.com/articles/nmeth.3869>`_                      
`vsearch <https://github.com/torognes/vsearch>`_                         2.18.0    `Rognes et. al 2016 <https://peerj.com/articles/2584/>`_                                  
`trimmomatic <http://www.usadellab.org/cms/?page=trimmomatic>`_          0.39      `Bolger et al. 2014 <https://doi.org/10.1093/bioinformatics/btu170>`_                     
`seqkit <https://bioinf.shenwei.me/seqkit/>`_                            2.0.0     `Shen et al. 2016 <https://doi.org/10.1371/journal.pone.0163962>`_                        
`cutadapt <https://cutadapt.readthedocs.io/en/stable/>`_                 3.5       `Martin 2011 <https://doi.org/10.14806/ej.17.1.200>`_                                     
`mothur <https://github.com/mothur/mothur>`_                             1.46.1    `Schloss et al. 2009 <https://doi.org/10.1128/AEM.01541-09>`_                             
`ITS Extractor <https://microbiology.se/software/itsx/>`_                1.1.3     `Bengtsson-Palme et al. 2013 <https://doi.org/10.1111/2041-210X.12073>`_                  
`fqgrep <https://github.com/indraniel/fqgrep>`_                          0.4.4     `Indraniel Das 2011 <https://github.com/indraniel/fqgrep>`_                               
`BLAST <https://blast.ncbi.nlm.nih.gov/Blast.cgi>`_                      2.11.0+   `Camacho et al. 2009 <https://doi.org/10.1186/1471-2105-10-421>`_                         
`FastQC <https://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_   0.11.9    `Andrews 2019 <https://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_              
`MultiQC <https://multiqc.info/>`_                                       1.12      `Ewels et al. 2016 <https://doi.org/10.1093/bioinformatics/btw354>`_                      
=======================================================================  ========  =========================================================================================