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Remove cleanup=true from test_full.config #2279

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May 4, 2023
Merged

Remove cleanup=true from test_full.config #2279

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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -4,6 +4,9 @@

### Template

- Remove `cleanup = true` from `test_full.config` in pipeline template
- Fix usage docs for specifying `params.yaml`

### Linting

- Warn if container access is denied ([#2270](https://github.com/nf-core/tools/pull/2270))
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2 changes: 0 additions & 2 deletions nf_core/pipeline-template/conf/test_full.config
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Expand Up @@ -10,8 +10,6 @@
----------------------------------------------------------------------------------------
*/

cleanup = true

params {
config_profile_name = 'Full test profile'
config_profile_description = 'Full test dataset to check pipeline function'
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6 changes: 3 additions & 3 deletions nf_core/pipeline-template/docs/usage.md
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Expand Up @@ -61,7 +61,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
The typical command for running the pipeline is as follows:

```bash
nextflow run {{ name }} --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile docker
nextflow run {{ name }} --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker
```

This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
Expand All @@ -80,7 +80,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.

> ⚠️ Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
> The above pipeline run specified with a params file in yaml format:

The above pipeline run specified with a params file in yaml format:

```bash
nextflow run {{ name }} -profile docker -params-file params.yaml
Expand All @@ -92,7 +93,6 @@ with `params.yaml` containing:
input: './samplesheet.csv'
outdir: './results/'
genome: 'GRCh37'
input: 'data'
<...>
```

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