From a0ca7b173871af175e319c92d359be8a0c440d24 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Thu, 6 Aug 2020 16:30:32 +0100 Subject: [PATCH] Update meta.yml link --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index f8563fcc..37142ec6 100644 --- a/README.md +++ b/README.md @@ -190,7 +190,7 @@ The [Nextflow `publishDir`](https://www.nextflow.io/docs/latest/process.html#pub saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } ``` -The `saveFiles` function can be found in the [`functions.nf`](software/fastqc/functions.nf) file of utility functions that will be copied into all modules directories. It uses the various publishing `options` specified as input to the module to construct and append the relevant output path to `params.outdir`. +The `saveFiles` function can be found in the [`functions.nf`](software/fastqc/functions.nf) file of utility functions that will be copied into all module directories. It uses the various publishing `options` specified as input to the module to construct and append the relevant output path to `params.outdir`. We also use a standardised parameter called `params.publish_dir_mode` that can be used to alter the file publishing method (default: `copy`). @@ -200,15 +200,15 @@ We also use a standardised parameter called `params.publish_dir_mode` that can b - Test files MUST be kept as tiny as possible. -- It is RECOMMENDED to re-use generic files from `tests/data/` by symlinking them into the `test/` directory of the module. +- It is RECOMMENDED to re-use generic files from [`tests/data/`](tests/data/) by symlinking them into the [`test/`](software/fastqc/test) directory of the module. - If the appropriate test data doesn't exist for your module then it MUST be added to [`tests/data`](tests/data/). -- Every module MUST be tested by adding a test workflow with a toy dataset in the `test/` directory of the module. +- Every module MUST be tested by adding a test workflow with a toy dataset in the [`test/`](software/fastqc/test) directory of the module. ### Documentation -- A module MUST be documented in the `meta.yml` file. It MUST document `params`, `input` and `output`. `input` and `output` MUST be a nested list. +- A module MUST be documented in the [`meta.yml`](software/fastqc/meta.yml) file. It MUST document `params`, `input` and `output`. `input` and `output` MUST be a nested list. ### Uploading to `nf-core/modules`