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boulund / adapter_benchmark Public

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Add fasten and some of lskatz improvements#7

Merged

boulund merged 38 commits into

masterboulund/adapter_benchmark:masterfrom

pull_6boulund/adapter_benchmark:pull_6Copy head branch name to clipboard

Jun 13, 2025

Conversation Commits38 (38)Checks Files changed

Merged

Add fasten and some of lskatz improvements#7
boulund merged 38 commits into
masterfrom
pull_6

Commits

Commits on Apr 7, 2025

fasten and github actions
lskatz
committed
bioconda
lskatz
committed
conda-forge
lskatz
committed
better snakemake checks
lskatz
committed
use snakemake workflow in github actions
lskatz
committed
m
lskatz
committed
hardcode for now
lskatz
committed
softcode
lskatz
committed
trying advanced syntax with json
lskatz
committed
back to conda
lskatz
committed
avoid pulp solver
lskatz
committed
I'm being told that simple isn't correct. Greedy it is.
lskatz
committed
hardcode 1 core in case it's resource limited
lskatz
committed
trying with compressed dirty file. DEBUG: taking percentage of file
lskatz
committed
m
lskatz
committed
m
lskatz
committed

Commits on Apr 8, 2025

back to basics and fix fasten command
lskatz
committed
limit the size of the input file
lskatz
committed
zcat -> gunzip -c
lskatz
committed
2442190 \
lskatz
committed
tmpfile param
lskatz
committed
tmpfile param
lskatz
committed
random fastq instead of downloading
lskatz
committed
copying seems to work
lskatz
committed
local fastq.gz
lskatz
committed

Commits on Jun 4, 2025

Refactor a little bit, add config file
boulund
committed
Clean up envs, remove defaults
boulund
committed
Try snakemake-minimal and rearranging channels
boulund
committed
create separate env
boulund
committed
activate
boulund
committed
Activate when needed, sed config
boulund
committed
use conda-incubator/setup-miniconda
boulund
committed
Only run 1 replicate in CI
boulund
committed
Improve variable naming
boulund
committed
Update README
boulund
committed

Commits on Jun 5, 2025

Move CI env to envs dir to get rid of errors
boulund
committed
Update all tools to latest versions
boulund
committed
Add latest plots
boulund
committed

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