-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #177 from nf-cmgg/dev
v1.6.0 release PR
- Loading branch information
Showing
105 changed files
with
5,277 additions
and
4,346 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| name: build docs | ||
| on: | ||
| push: | ||
| branches: | ||
| - master | ||
| - main | ||
| - dev | ||
| permissions: | ||
| contents: write | ||
| jobs: | ||
| deploy: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| with: | ||
| fetch-depth: 0 # fetch all commits/branches | ||
| - uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: 3.x | ||
| - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV | ||
| - name: Obtain version from nextflow config | ||
| run: | | ||
| version=$(grep "version" nextflow.config | tail -1 | sed -e s'/[^=]*= //' | cut -d "'" -f 2) | ||
| [[ $version == *"dev"* ]] && pipeline_version="dev" || pipeline_version=$version | ||
| echo "pipeline_version=$pipeline_version" >> $GITHUB_ENV | ||
| - name: Setup git user | ||
| run: | | ||
| git config --global user.name "${{github.actor}}" | ||
| git config --global user.email "${{github.actor}}@users.noreply.github.com" | ||
| - uses: actions/cache@v3 | ||
| with: | ||
| key: mkdocs-material-${{ env.cache_id }} | ||
| path: .cache | ||
| restore-keys: | | ||
| mkdocs-material- | ||
| - name: Install dependencies | ||
| run: pip install mkdocs-material pymdown-extensions pillow cairosvg mike | ||
| - name: Build docs | ||
| run: | | ||
| [[ ${{ env.pipeline_version }} == "dev" ]] && mike deploy --push ${{ env.pipeline_version }} || mike deploy --push --update-aliases ${{ env.pipeline_version }} latest | ||
| - name: Set default docs | ||
| run: mike set-default --push latest |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,62 +1,14 @@ | ||
| # nf-cmgg/germline | ||
|
|
||
| [](https://www.nextflow.io/) | ||
| [](https://www.nextflow.io/) | ||
| [](https://www.docker.com/) | ||
| [](https://sylabs.io/docs/) | ||
| [](https://github.com/askimed/nf-test) | ||
|
|
||
| ## Introduction | ||
|
|
||
| **germline** is a bioinformatics best-practice analysis pipeline for calling, joint-genotyping and annotating small variants variants for WGS and WES data. It uses HaplotypeCaller and/or Vardict to call variants, GenotypeGVCFs to genotype and EnsemblVEP to annotate. | ||
| **nf-cmgg/germline** is a nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data. | ||
|
|
||
| The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! | ||
|
|
||
| ## Pipeline summary | ||
|
|
||
|  | ||
|
|
||
| :::note | ||
| If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how | ||
| to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) | ||
| with `-profile test` before running the workflow on actual data. | ||
| ::: | ||
|
|
||
| ## Quick Start | ||
|
|
||
| 1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=23.04.0`) | ||
| 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_. | ||
|
|
||
| `samplesheet.csv`: | ||
|
|
||
| ```csv | ||
| sample,family,cram,crai | ||
| SAMPLE_1,FAMILY_1,SAMPLE_1.cram,SAMPLE_1.crai | ||
| ``` | ||
|
|
||
| Each row represents a single sample to be analysed. More information can be found in the [usage](docs/usage.md) documentation. | ||
|
|
||
| --> | ||
|
|
||
| Now, you can run the pipeline using: | ||
|
|
||
| ```bash | ||
| nextflow run nf-cmgg/germline --input samplesheet.csv --outdir <OUTDIR> --genome GRCh38 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> | ||
| ``` | ||
|
|
||
| > [!WARNING] | ||
| > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; | ||
| > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). | ||
| ## Credits | ||
|
|
||
| germline was originally written and is maintained by [@nvnieuwk](https://github.com/nvnieuwk). | ||
|
|
||
| Special thanks to [@matthdsm](https://github.com/matthdsm) for the many tips and feedback and to [@mvheetve](https://github.com/mvheetve) for testing the pipeline. | ||
|
|
||
| ## Contributions and Support | ||
|
|
||
| If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). | ||
|
|
||
| ## Citations | ||
|
|
||
| An extensive list of references can be found in the [`CITATIONS.md`](CITATIONS.md) file. | ||
| Please have a look at the [documentation](https://nf-cmgg.github.io/germline/latest/) on how to run the pipeline. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,4 @@ | ||
| sample,family,cram,crai,roi,ped,truth_vcf,truth_tbi,truth_bed,vardict_min_af | ||
| DNA049572,Proband_12345,https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test.cram,,,https://raw.githubusercontent.com/nf-cmgg/germline/dev/assets/test.ped,https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/data/genomics/homo_sapiens/illumina/vcf/test.vcf.gz,https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/data/genomics/homo_sapiens/illumina/vcf/test.vcf.gz.tbi,https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/data/genomics/homo_sapiens/illumina/regions/roi.bed,0.01 | ||
| NA24385D2_NVQ_034,Proband_12345,https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram,https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram.crai,https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/data/genomics/homo_sapiens/illumina/regions/roi.bed,,https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/data/genomics/homo_sapiens/illumina/vcf/test2.vcf.gz,,, | ||
| NA24143,Proband_12345,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24143.cram,,,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/genome/test.ped,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24143.vcf.gz,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24143.vcf.gz.tbi,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/regions/roi.bed,0.01 | ||
| NA24149,Proband_12345,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24149.cram,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24149.cram.crai,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/regions/roi.bed,,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24149.vcf.gz,,, | ||
| NA24385,Proband_12345,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24385.cram,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24385.cram.crai,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/regions/roi.bed,,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24385.vcf.gz,,, |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file was deleted.
Oops, something went wrong.
Oops, something went wrong.