From 5e054c260228e25f0848da30af0491b4b90e073d Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 4 May 2023 21:28:56 +0100 Subject: [PATCH] Remove cleanup=true from test_full.config --- CHANGELOG.md | 3 +++ nf_core/pipeline-template/conf/test_full.config | 2 -- nf_core/pipeline-template/docs/usage.md | 6 +++--- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d3c0792519..fb5e81e6e2 100644 --- a/CHANGELOG.md +++ b/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)) diff --git a/nf_core/pipeline-template/conf/test_full.config b/nf_core/pipeline-template/conf/test_full.config index 46b165a910..d92692fa94 100644 --- a/nf_core/pipeline-template/conf/test_full.config +++ b/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' diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md index 73e1132541..e89c2a7332 100644 --- a/nf_core/pipeline-template/docs/usage.md +++ b/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 --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 `. > ⚠️ Do not use `-c ` 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' <...> ```