diff --git a/.nojekyll b/.nojekyll new file mode 100644 index 0000000..e69de29 diff --git a/404.html b/404.html new file mode 100644 index 0000000..c9d33ed --- /dev/null +++ b/404.html @@ -0,0 +1,1003 @@ + + + +
+ + + + + + + + + + + + + + + + + + +Fixing fix
+Fixing some issues with blast report generation when using newer BLAST databases. Source of the problemis still unclear but appears to be linked to new realeses of the BLAST db and concerns only specific taxids or sequences.
+Older configuration files are not compatible anymore. Update the files by adding the following line +should yield the same results as before:
+ +It is now possible to desactivate the defualt low-complexity filter of the BLAST search.
+This can be advantageous if you expect your barcode to contain low-complexity sequences which could
+prevent getting any match at all.
+This behaviour can be activated/deactivated by changing the blast_filter_low_complexity
from True
to False
.
The default behaviour (False
) uses the default 'DUST' filter of the blast tool:
+-dust 20 64 1 -soft_masking true
.
trim_primers_3end
parameter (#64)threads_sample
parameter instead of threads
. This results in better ressource management for the BLAST rule.Benchmarking paper for 16S Metabarcoding of meat products is online:
+Denay, G.; Preckel, L.; Petersen, H.; Pietsch, K.; Wöhlke, A.; Brünen-Nieweler, C. +Benchmarking and Validation of a Bioinformatics Workflow for Meat Species Identification Using 16S rDNA Metabarcoding. +Foods 2023, 12, 968. https://doi.org/10.3390/foods12050968
+seq_blocklist
parameter (#60).-s path/to/FooDMe/woorkflow/benchmark
argument.
+ This has no impact on the basic analysis (no -s
argument) or the paramspace analysis (-s path/to/FooDMe/woorkflow/paramspace
).config.yaml
commentsbenchmark
moduleThis update is not backwards compatible. +A configuration file update is nescessary.
+Paramspcae
utility.--config
CLI argument and
+ was required for the implementation of the parameter space exploration workflow.
+ This requires users to update their configurations.paramspace
workflow.This update is not backwards compatible. +A configuration file update is nescessary.
+snakemake benchmark
rmarkdown
environmentpandas
dependency in taxidTools
environmentbc
callsby printf
statements in vsearch.smk
(#52)consensus-table.tsv
taxid_filter
now only accepts integers, default config values have been changed (#42).tests
was renamed .tests
--report
argument (snakemake CLI only)--min_consensus
. The value be be in the interval (0.5;1], 1 being a last common ancestro behavior and 0.51 a simple majority vote.--blocklist
parameter.snakemake --cores 1 --use-conda
Maintaining a repository is a lot of work and it is only possible with the +input for its users. That's why we love to get your feedback and continuously +improve! We want to contibuting to this project as easy and transparent as +possible. That's why we ask all contributions to go through a GitHub workflow.
+Wether you wish to report a bug, discuss the current state of the code, +how to use it, or propose new features, the GitHub repository is the place to +start.
+Go to 'Issues' in the repository's menu and use the search bar to look for your +issue/question, maybe the discussion already exists! if you don't find what +you are looking for, use the green button +'New Issue' +and select the correct template (Question, Bug report or New feature).
+Solving Bugs is not always easy and usually requires to be able to precisely +understand what happened. Try to include the following in your report, so we +can solve the problems quickly:
+Writting a documentation is a big task and we are gratefull for any help +to expand and improve it.
+If you find a specific section of the documentaiton unclear, or would like to +see it in other languages, we would love to hear about it, or if you feel like +it, try suggesting modifications.
+The critical parts of the workflow are currently verified by unit tests.
+These could always be improved and/or expanded. If you like to write tests,
+check the .tests/unit
folder and suggest changes.
All changes in the repository are made through pull requests.
+To submitt a pull request:
+main
Please provide precise and sufficient information on the changes you +performed when you submit your pull request.
+It is a good idea to locally run tests before submitting your pull request.
+We use pytest for running unit tests. Make sure your current environment supports +a recent version of python (3.9 or 3.10).
+python -m pip install --upgrade pip
+pip install pytest
+pip install -r .tests/unit/requirements.txt # Install tests dependencies
+pytest .tests/unit
+
It is always a good idea to verify that the workflow runs properly as a whole. +For this activate a conda enviroment with a recent version of snakemake (see the +documentation) and run the following test:
+ +By submitting changes to this repository, you agree that your contributions +will be licensed under its BSD-3 Clauses License.
+ + + + + + + + + + + + + + + + + +Copyright 2020-2023, Gregoire Denay.
+Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met:
+Redistributions of source code must retain the above copyright notice, this +list of conditions and the following disclaimer.
+Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution.
+Neither the name of the copyright holder nor the names of its contributors +may be used to endorse or promote products derived from this software without +specific prior written permission.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE.
+ + + + + + + + + + + + + + + + + +This pipeline uses several tools and external ressources. +Documentation for these can be found at the links below:
+Tool | +Link | +
---|---|
BLAST | +https://blast.ncbi.nlm.nih.gov/Blast.cgi | +
Conda | +https://docs.conda.io/en/latest/ | +
Cutadapt | +https://cutadapt.readthedocs.io/en/stable/ | +
create_sampleSheet | +https://gitlab.com/bfr_bioinformatics/AQUAMIS | +
DADA2 | +https://benjjneb.github.io/dada2/ | +
DT | +https://rstudio.github.io/DT/ | +
fastp | +https://github.com/OpenGene/fastp | +
Krona | +https://bio.tools/krona | +
Pandas | +https://pandas.pydata.org/ | +
RMarkdown | +https://rmarkdown.rstudio.com/ | +
SeqTK | +https://github.com/lh3/seqtk | +
Snakemake | +https://snakemake.readthedocs.io/en/stable/ | +
scikit-learn | +https://scikit-learn.org/stable/ | +
taxidTools | +https://cvua-rrw.github.io/taxidTools/ | +
Tidyverse | +https://www.tidyverse.org/ | +
VSEARCH | +https://github.com/torognes/vsearch | +