Skip to content

Commit

Permalink
docs: update google drive link to example slides
Browse files Browse the repository at this point in the history
  • Loading branch information
Katherine Eaton authored and ktmeaton committed Jun 21, 2022
1 parent a37afee commit a0c6ece
Showing 1 changed file with 7 additions and 4 deletions.
11 changes: 7 additions & 4 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ https://docs.google.com/spreadsheets/d/1EH-JmXFTAnzUHavxPOZnNNgHIBZcyhSMRSQJ8J6q

Powerpoint/google slides with acommpanying plots for presenting.

[![powerpoint_output](images/powerpoint_output.png)](https://docs.google.com/presentation/d/1dFKHPaaD8wOHt_4Vde_yfSBlHz8m7XrqDDn0pik_hs4/edit#slide=id.p2)
[![powerpoint_output](images/powerpoint_output.png)](https://docs.google.com/presentation/d/17EDrQk34VUGOfPtpqdNQiBv5OfWPkULpZwgERWeZf-8/edit#slide=id.p2)

### Breakpoints

Expand Down Expand Up @@ -145,6 +145,9 @@ Placement of samples on the latest global phylogeny using [UShER](https://github
snakemake --profile my_profiles/custom
```

> - Note: you can add the param `--controls` to add a `controls` build that will run in parallel.
> - Note: The `controls` build analyzes a dataset of positive and negative recombinant sequences, and adds \~30 min to the runtime.

1. Edit `my_profiles/custom/config.yaml`, so that the `jobs` and `default-resources` match your system.

> Note: For HPC environments, see the [High Performance Computing](https://github.com/ktmeaton/ncov-recombinant#high-performance-computing) section.
Expand Down Expand Up @@ -183,7 +186,7 @@ Placement of samples on the latest global phylogeny using [UShER](https://github
1. Create an HPC-compatible profile to store your build configuration.

```bash
bash scripts/create_profile.sh --data data/custom --hpc
scripts/create_profile.sh --data data/custom --hpc
```

```text
Expand Down Expand Up @@ -223,13 +226,13 @@ Placement of samples on the latest global phylogeny using [UShER](https://github
3. Dispatch the workflow using the slurm wrapper script:

```bash
bash scripts/slurm.sh --profile my_profiles/custom-hpc
scripts/slurm.sh --profile my_profiles/custom-hpc
```

4. Use the `--help` parameter to get additional options for SLURM dispatch.

```bash
bash scripts/slurm.sh --help
scripts/slurm.sh --help
```

```text
Expand Down

0 comments on commit a0c6ece

Please sign in to comment.