Merge pull request #2279 from drpatelh/cleanup

Remove cleanup=true from test_full.config

CHANGELOG.md

@@ -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))

nf_core/pipeline-template/conf/test_full.config

@@ -10,8 +10,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-cleanup = true
-
 params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'

nf_core/pipeline-template/docs/usage.md

@@ -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.
@@ -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
@@ -92,7 +93,6 @@ with `params.yaml` containing:
 input: './samplesheet.csv'
 outdir: './results/'
 genome: 'GRCh37'
-input: 'data'
 <...>
 ```