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feat: v1 #22

Merged
merged 122 commits into from
May 10, 2024
Merged

feat: v1 #22

merged 122 commits into from
May 10, 2024

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jlanga
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@jlanga jlanga commented May 2, 2024

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jlanga and others added 30 commits May 2, 2023 16:09
* 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
@jlanga jlanga changed the title v1 feat: v1 May 2, 2024
@jlanga jlanga merged commit 8999c4c into main May 10, 2024
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jlanga added a commit that referenced this pull request May 10, 2024
ci: Merge pull request #22 from 3d-omics/devel
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