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Merge pull request #43 from gymrek-lab/feat/multiple-testing
feat: finish running on geuvadis
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| // For format details, see https://aka.ms/devcontainer.json. For config options, see the | ||
| // README at: https://github.com/devcontainers/templates/tree/main/src/ubuntu | ||
| { | ||
| "name": "Ubuntu", | ||
| // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile | ||
| "image": "mcr.microsoft.com/devcontainers/base:jammy", | ||
| "features": { | ||
| "ghcr.io/rocker-org/devcontainer-features/miniforge:1": { | ||
| "version": "latest", | ||
| "variant": "Mambaforge" | ||
| } | ||
| }, | ||
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| // Features to add to the dev container. More info: https://containers.dev/features. | ||
| // "features": {}, | ||
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| // Use 'forwardPorts' to make a list of ports inside the container available locally. | ||
| // "forwardPorts": [], | ||
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| // Use 'postCreateCommand' to run commands after the container is created. | ||
| "postCreateCommand": "mamba env create -n happler -f dev-env.yml && conda run -n happler poetry install", | ||
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| // Configure tool-specific properties. | ||
| "customizations": { | ||
| "vscode": { | ||
| "extensions": ["ms-python.python"], | ||
| "settings": { | ||
| "python.condaPath": "/opt/conda/condabin/conda", | ||
| "python.defaultInterpreterPath": "/opt/conda/envs/happler/bin/python", | ||
| "python.terminal.activateEnvironment": true, | ||
| "python.terminal.activateEnvInCurrentTerminal": true, | ||
| "python.venvFolders": ["/home/vscode/.cache/pypoetry/virtualenvs"], | ||
| "terminal.integrated.environmentChangesRelaunch": true, | ||
| "terminal.integrated.hideOnStartup": "always" | ||
| } | ||
| } | ||
| } | ||
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| // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root. | ||
| // "remoteUser": "root" | ||
| } |
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| ## Checklist | ||
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| * [ ] I've checked to ensure there aren't already other open [pull requests](../../../pulls) for the same update/change | ||
| * [ ] I've prefixed the title of my PR according to [the conventional commits specification](https://www.conventionalcommits.org/). If your PR fixes a bug, please prefix the PR with `fix: `. Otherwise, if it introduces a new feature, please prefix it with `feat: `. If it introduces a breaking change, please add an exclamation before the colon, like `feat!: `. If the scope of the PR changes because of a revision to it, please update the PR title, since the title will be used in our CHANGELOG. | ||
| * [ ] At the top of the PR, I've [listed any open issues that this PR will resolve](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue#linking-a-pull-request-to-an-issue-using-a-keyword). For example, "resolves #0" if this PR resolves issue #0 | ||
| - [ ] I've explained my changes in a manner that will make it possible for both users and maintainers of happler to understand them | ||
| * [ ] I have followed the [contributing guidelines](https://happler.readthedocs.io/en/stable/project_info/contributing.html#how-to-fix-a-bug-or-implement-a-new-feature) | ||
| * [ ] I have adhered to the [style guidelines](https://happler.readthedocs.io/en/stable/project_info/contributing.html#style) | ||
| * [ ] I've added tests for any new functionality. Or, if this PR fixes a bug, I've added test(s) that replicate it | ||
| * [ ] I've updated the relevant documentation and checked that the newly built documentation is formatted properly | ||
| * [ ] All functions, modules, classes etc. still conform to [numpy docstring standards](https://numpydoc.readthedocs.io/en/latest/format.html) | ||
| * [ ] (if applicable) I've updated the pyproject.toml file with any changes I've made to happler's dependencies, and I've run `poetry lock --no-update` to ensure the lock file stays up to date and that our dependencies are locked to their minimum versions | ||
| * [ ] In the body of this PR, I've included a short address to the reviewer highlighting one or two items that might deserve their focus |
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| # This is the Snakemake configuration file that specifies paths and | ||
| # and options for the pipeline. Anybody wishing to use | ||
| # the provided snakemake pipeline should first fill out this file with paths to | ||
| # their own data, as the Snakefile requires it. | ||
| # Every config option has reasonable defaults unless it is labeled as "required." | ||
| # All paths are relative to the directory that Snakemake is executed in. | ||
| # Note: this file is written in the YAML syntax (https://learnxinyminutes.com/docs/yaml/) | ||
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| # Paths to a SNP-STR haplotype reference panel | ||
| # You can download this from http://gymreklab.com/2018/03/05/snpstr_imputation.html | ||
| # If the VCFs are per-chromosome, replace the contig name in the file name with "{chr}" | ||
| # The VCF(s) must be sorted and indexed (with a .tbi file in the same directory) | ||
| # required! | ||
| # ref_panel: "/projects/ps-gymreklab/resources/datasets/snpstr/1kg.snp.str.chr{chr}.vcf.gz" | ||
| # snp_panel: "/projects/ps-gymreklab/resources/datasets/ukbiobank/array_imputed/pfile_converted/chr{chr}.pgen" | ||
| snp_panel: "data/geuvadis/geuvadis_ensemble_phasing.pgen" | ||
| # str_panel: "/tscc/projects/ps-gymreklab/jmargoli/ukbiobank/str_imputed/runs/first_pass/vcfs/annotated_strs/chr{chr}.vcf.gz" | ||
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| # Path to a list of samples to exclude from the analysis | ||
| # There should be one sample ID per line | ||
| # exclude_samples: data/ukb_random_samples_exclude.tsv | ||
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| # If SNPs are unphased, provide the path to a SHAPEIT4 map file like these: | ||
| # https://github.com/odelaneau/shapeit4/tree/master/maps | ||
| # The map file should use the same reference genome as the reference panel VCFs | ||
| # phase_map: data/genetic_maps/chr{chr}.b37.gmap.gz | ||
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| # A "locus" is a string with a contig name, a colon, the start position, a dash, and | ||
| # the end position or a BED file with a ".bed" file ending | ||
| # There are different simulation modes that you can use: | ||
| # 1. "str" - a tandem repeat is a string with a contig name, a colon, and the start position | ||
| # 2. "snp" - a SNP follows the same format as "str" | ||
| # 3. "hap" - a haplotype | ||
| # 4. "ld_range" - creates random two-SNP haplotypes with a range of LD values between the alleles of each haplotype | ||
| # 5. "run" - execute happler on a locus without simulating anything | ||
| # The STR and SNP positions should be contained within the locus. | ||
| # The positions should be provided in the same coordinate system as the reference | ||
| # genome of the reference panel VCFs | ||
| # The contig should correspond with the contig name from the {chr} wildcard in the VCF | ||
| # required! and unless otherwise noted, all attributes of each mode are required | ||
| # locus: 19:45401409-46401409 # center: 45901409 (APOe4) | ||
| locus: data/geuvadis/geuvadis_eqtl_genes.full.liftover.bed | ||
| modes: | ||
| str: | ||
| pos: 19:45903857 # STR_691361 | ||
| snp: | ||
| pos: 19:45910672 # rs1046282 | ||
| hap: | ||
| alleles: [rs36046716:G, rs1046282:G] # 45892145, 45910672 | ||
| beta: [0.05, 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45] | ||
| ld_range: | ||
| reps: 1 | ||
| min_ld: 0 | ||
| max_ld: 1 | ||
| step: 0.1 | ||
| min_af: 0.25 | ||
| max_af: 0.75 | ||
| # beta: [0.35] | ||
| beta: [0.05, 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45] | ||
| alpha: [0.05] | ||
| random: false # whether to also produce random haplotypes | ||
| run: | ||
| pheno: data/geuvadis/phenos/{trait}.pheno | ||
| SVs: data/geuvadis/pangenie_hprc_hg38_all-samples_bi_SVs-missing_removed.pgen | ||
| # pheno_matrix: data/geuvadis/EUR_converted_expr_hg38.csv # optional | ||
| mode: run | ||
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| # Covariates to use if they're needed | ||
| # Otherwise, they're assumed to be regressed out of the phenotypes | ||
| # Note: the finemapping methods won't be able to handle these covariates | ||
| # covar: data/geuvadis/5PCs_sex.covar | ||
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| # Discard rare variants with a MAF below this number | ||
| # Defaults to 0 if not specified | ||
| min_maf: 0.1 | ||
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| # Sample sizes to use | ||
| # sample_size: [500, 1000, 1500, 2000, 2500] | ||
| # sample_size: 777 | ||
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| # Whether to include the causal variant in the set of genotypes provided to the | ||
| # finemapping methods. Set this to true if you're interested in seeing how the | ||
| # methods perform when the causal variant is absent from the data. | ||
| # Defaults to false if not specified | ||
| # You can also provide a list of booleans, if you want to test both values | ||
| exclude_causal: [true, false] |
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