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version.txt
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############################
# #
# Q2Pipe Version 0.95.6 #
# January 30, 2024 #
# #
############################
# Latest Qiime2 Version tested : qiime2-2023.9 (Apptainer)
# Changelog since version 0.95.5 (0.95.6)
# BUGFIX: Temporary folder definition changed to prevent disparity with Apptainer + temp checkup at each step to prevent crash
# Changelog since version 0.95.4 (0.95.5)
# MINOR ENHANCEMENT: Number of threads for the classifier now a seperated option
# Qiime2 Recipe updated to new Qiime2 version (2023.9)
# Changelog since version 0.95.1 (0.95.4)
# MINOR ENHANCEMENT: Metrics Generation step now multithreaded (10-fold speed gain on test data)
# MINOR CHANGE: User guide now available in the repository
# DEPRECIATION: Step 5 is now deprecated and will be removed in version 0.96
# Changelog since version 0.95 (0.95.1)
# ENHANCEMENT/BUGFIX: Figaro modified on repo to support multithreading control (was taking all cores on system before)
# ENHANCEMENT: Figaro Sequences trimming now multithreaded (much faster now)
# ENHANCEMENT: Falco MTT version now support multithread and on-the-fly trimming
# ENHANCEMENT: Step 1 now calculate the amount of available thread for each manifest so they can all gain speed on multithreaded processes
# MINOR ENHANCEMENT: New option to control the maximum error rate in primer recognition by CutAdapt step
# Changelog since version 0.94.2 (0.95)
# ENHANCEMENT: Falco now supported in importation step, will scan all samples and raise potential problems
# CHANGE: Dependencies now part of Q2Pipe repo (complete migration to NRCan public repo for publication)
# MINOR ENHANCEMENT: New option to stop denoising step after cutadapt to help evaluate trimming parameters for the DADA2 denoising (issue #24)
# Developpement Apptainer recipe now include Falco support (see issues #29)
# Changelog since version 0.94.0 (0.94.1)
# ENHANCEMENT: Figaro section in step 1 now create a temporary folder in TMPDIR and run the analysis there, following Qiime2's guidelines
# BUGFIX: Running step 1 without specifing a manifest file now return an error instead of stucking the program in an infinite loop
# BUGFIX: Step 2.5 now check if mergecheck folder already exist and exit the program if it is. The fullauto mode also delete the folder automatically (same concept as the metrics folder)
# Qiime2 Recipe updated to new Qiime2 version (2023.2) + small modification to the base runscript to display qiime2 information instead of command list
# Changelog since version 0.93.2 (0.94.0)
# NEW FEATURE : Implementation of Figaro (Denoising trimming parameters prediction)
# Optionfile adjusted for Figaro implementation
# Changelog since version 0.93 (0.93.2)
# New supported option for denoising (p-trunc-q) for auto quality truncation
# Apptainer recipes updated for qiime2-2022.11 (Q2Pipe tested and working correctly)
# BUGFIX : Using Ubuntu 20.04 cause a bug in step 1 and 2 when checking already completed datasets
# Singularity was rebranded Apptainer and is now the open-source branch, every mention of singularity must be replaced by apptainer (should not affect running, but image must be rebuid)
# Now following version numbering standard (X.Y.Z)
# X: Major version where changes makes API incompatible
# Y: Minor version where you add functionnality
# Z: Bugfix without functionnality changes
# Changelog since version 0.92 (0.93)
# Implementation of the results form extraction in step 11, which makes the isolation of specific results file easier
# XLSX form included to complement the results form extraction
# Changelog since version 0.91 (0.92)
# Improvement to the ASV table generation, now generate an ASV Table with DNA Sequences for corresponding ASV
# First dependencies of Q2Pipe, will be distributed from a secondary public repository
# Singularity recipes (regular + Dev) now include dependencies setup
# Changelog since version 0.90 (0.91)
# Metadata filtering incorporated to taxa filtering step + p_where option in optionfile
# Metric generation step no longer crash if alpha-significance fail, now return an error message
# Changelog since version 0.89 (0.90)
# Step1 and Step2 rewritten to support multiple run (the correct way)
# Step1 and Step2 support multijob architecture to accelerate analysis
# Step3 now support multiple run merging
# DELAYED TO FUTURE VERSION New step for Chimera filtering (in case of merged run)
# Changelog since version 0.88 (0.89)
# Rarefaction override now support "both" argument so it can run with and without rarefaction in a single run
# Changelog since version 0.87 (0.88)
# p-confidence now a customisable parameter in classification step (6)
# FUNGuild support (must be installed on PATH using Patrick Gagne's version)
# Changelog since version 0.86 (0.87)
# Create_manifest_direct script now support secondary filter argument (useful to remove _S##)
# Step 2 is now correctly report frequency threshold (typo only, did not have impact on analysis)
# Default optionfile now comply with laboratory guidelines
# Changelog since version 0.85 (0.86)
# Step 11 now generate ASV table (combine feature-table biom with taxonomy)
# Step 2 now generate rep-seqs-dada2.qzv using representative sequences
# Step 1.5 is now more resilient to crash during a test (skipping test instead of cascade crashing)
# Step 1.5 results are now transfered in a folder to prevent folder cluttering
# New option for step 1.5 'DRY_RUN' to stop the program after generating the temp file, but before importation
# Changelog since Version 0.84 (0.85)
# Support for Phylogeny in step 7, 8 and 10
# Step 7 now mandatory, but can be bypassed with a parameter
# Step 1.5 generate a feature table summarize
# Step 2 generate a metadata tabulate
# Step 11 now support ANCOM analysis
# Support for ANCOM differential abundancy tests
# Optionfile now tagged with the pipeline version (for future reference)
# Version file (this one) now available