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feat: v1 #22
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* Add clean step * Use raw bowtie2 rather than wrapper * Added picard reports * Bugfix: release-please has moved * Added gatk4 base recalibrator reports * Remove config.yaml * Reports and enhancements of snpEff * Add reports by sample. Clean
* Fix program versions * Expand tests to devel * feat: bump versions
* Add default profile * Linting * Remove clean * Read adaptors from samples.tsv * Get parameters from file * Use fastp reports * Get parameters from parameters.yml * Cleaning up * Remove redundant target rule * Cleanup * Cleanup more * Add extra params from file * Add extra params from file * Add temptative slurm defaults * Add slurm default profile * Add simple slurm script
* Split analyses by chromosome in picard and gatk * per sample -> per library * Separate rules from functions
…n mice (#8) * Added sommalier steps. Will try to figure it out how it works in mice * Solve snakelint
* Raise latency to 30 sec * Linting
* Document reads * Document reference * Document fastp * Document bowtie2 * Document picard * Document gatk4 * Document snpeff * Document somalier * Solve TODO * Document bcftools * Document samtools * Document reports_per_step * Document reports_per_library * Document the all rule * Document fastqc * Document common functions
* Split analyses by chromosome in picard and gatk * per sample -> per library * Separate rules from functions * Add reports by chromsome
* Set up cache * Cache at the beginning. Set up cache key
* Cache at the beginning. Set up cache key * Add benchmarks to jobs that seem to be big * Use minimizers * Use jobid rather than a hash * Add picard and gatk result to per-library reports
* Cache at the beginning. Set up cache key * Add benchmarks to jobs that seem to be big * In samtools sort, use minimizers * Use jobid rather than a hash in slurm job names * Add picard and gatk result to per-library reports * time -> runtime * yamllint GHA * Stub for caching separtedly * Put bam report variables into a list * Separate between bowtie2 and picard reports * Add reports and rename function * Remove unused variables * Refactor functions * Add snakemake download step and use mamba * Lint precommit and add shellcheck * Download envs with --conda-create-envs-only * Append number of cores in GH action
* Reduce default disk usage * Raise snpeff ann default time * Set up weekly cache * Update super-linter * CRON time as numeric
* Set up weekly cache * Trim poly-G + poly-X * Use Pre-commit on GHA * Refactor fastp
* fix: moved code * feat: conditional ploidy * Import sexy functions * fix: haplotype caller uses ploidy now
* Run fastqc over fastp files * Collect fastp-fastqc reports * fix cache misses * somalier -> bcftools gtcheck * R project * Plot gtcheck heatmap * Environment confinement + linting
* Document all rules * Update README.md
feat: reformat everything
fix: multiple fixes
feat: add somalier
feat: add preliminary bcftools calls for gatk
jlanga
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May 10, 2024
ci: Merge pull request #22 from 3d-omics/devel
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