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Merge pull request #9 from Sage-Bionetworks-Workflows/dev
[IBCDPE-589] Catch up `main` with `dev`
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Original file line number | Diff line number | Diff line change |
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@@ -1,15 +1,15 @@ | ||
repository_type: pipeline | ||
lint: | ||
files_exist: | ||
- CODE_OF_CONDUCT.md | ||
- assets/nf-core-dcqc_logo_light.png | ||
- docs/images/nf-core-dcqc_logo_light.png | ||
- docs/images/nf-core-dcqc_logo_dark.png | ||
- .github/ISSUE_TEMPLATE/config.yml | ||
- .github/workflows/awstest.yml | ||
- .github/workflows/awsfulltest.yml | ||
- CODE_OF_CONDUCT.md | ||
- assets/nf-core-dcqc_logo_light.png | ||
- docs/images/nf-core-dcqc_logo_light.png | ||
- docs/images/nf-core-dcqc_logo_dark.png | ||
- .github/ISSUE_TEMPLATE/config.yml | ||
- .github/workflows/awstest.yml | ||
- .github/workflows/awsfulltest.yml | ||
nextflow_config: | ||
- manifest.name | ||
- manifest.homePage | ||
- manifest.name | ||
- manifest.homePage | ||
multiqc_config: | ||
- report_comment | ||
- report_comment |
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[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) | ||
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[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) | ||
[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.4-23aa62.svg)](https://www.nextflow.io/) | ||
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) | ||
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) | ||
[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) | ||
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@@ -27,7 +27,7 @@ On release, automated continuous integration tests run the pipeline on a full-si | |
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## Quick Start | ||
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1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`) | ||
1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.4`) | ||
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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))_. | ||
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@@ -52,6 +52,16 @@ On release, automated continuous integration tests run the pipeline on a full-si | |
nextflow run sage/dcqc --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> | ||
``` | ||
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## Special Considerations for Running `nf-dcqc` on Nextflow Tower | ||
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`nf-dcqc` leverages the reports feature when executed on Tower. This is done by pointing Tower to the generated `output.csv` file which is saved to `params.outdir` after a successful run. By default, the `outdir` for the workflow is set to a local directory called `results`. This does not work on Nextflow Tower runs, as you will not have access to the `results` directory once the job has completed. Thus, the `outdir` should be set to an S3 bucket location that the Tower workspace you are using has access to. For example, in the `pipeline parameters` for a Tower run, you can provide YAML such as: | ||
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```yaml | ||
outdir: s3://example-project-tower-bucket/dcqc_output | ||
``` | ||
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From the reports tab within your workflow run, you can view and download the generated `output.csv` file. | ||
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## Credits | ||
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sage/dcqc was originally written by Bruno Grande <[email protected]>. | ||
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