- Feb 07, 2024
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Alexis Mergez authored
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Alexis Mergez authored
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Alexis Mergez authored
Moved from wfmash to ragtag in clustering step See merge request !3
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Alexis Mergez authored
Updated regex pattern to search for required pattern (<haplotype>#<chromosome|ctg id>). Updated README
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Alexis Mergez authored
Moved ragtag scaffolding to standalone script (ragtagChromInfer.sh). Snakemake now call this script. Fixed missing library in inputClustering.py. Updated Snakefile accordingly
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Alexis Mergez authored
Changed clustering tool from wfmash to ragtag. Test phase ahead.
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Alexis Mergez authored
v1.1 See merge request !2
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Alexis Mergez authored
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Alexis Mergez authored
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Alexis Mergez authored
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Alexis Mergez authored
Fixed missing apptainer image name Fixed awk commands (creating temp files instead of editing the file inplace)
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- Feb 06, 2024
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Alexis Mergez authored
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Alexis Mergez authored
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Alexis Mergez authored
Added PAV matrix generation in output/pav. It can be directly used in Panache
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- Feb 05, 2024
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Alexis Mergez authored
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Alexis Mergez authored
Moved reference haplotype to data/haplotypes folder. Removing reference folder
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- Feb 02, 2024
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Alexis Mergez authored
Added data prep section Updated Usage section Still more documentation to do
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Alexis Mergez authored
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Alexis Mergez authored
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- Feb 01, 2024
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Alexis Mergez authored
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Alexis Mergez authored
Added a rule to create 1D and path coverage firgures of each chromosomes in output/figures Added parameters to config.yml accordingly
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- Jan 31, 2024
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Alexis Mergez authored
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Alexis Mergez authored
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Alexis Mergez authored
Added param fileds in several rules Added keys in config.yml
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- Jan 30, 2024
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Alexis Mergez authored
Added missing library (os)
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Alexis Mergez authored
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Alexis Mergez authored
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