From 46bc25248762a998fb50addf661d127ddf519cfe Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 15 Apr 2021 17:50:10 +0200
Subject: [PATCH] CONTRIBUTING.md: fix typo
---
CONTRIBUTING.md | 24 ++++++++++++------------
1 file changed, 12 insertions(+), 12 deletions(-)
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 1f341df9..e3d61628 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -1,26 +1,26 @@
# Contributing
-When contributing to this repository, please first discuss the change you wish to make via issue,
+When contributing to this repository, please first discuss the change you wish to make via issues,
email, or on the [ENS-Bioinfo channel](https://matrix.to/#/#ens-bioinfo:matrix.org) before making a change.
-## Project organisation
+## Project organization
-The `LBMC/nextflow` project is structured as follow:
+The `LBMC/nextflow` project is structured as follows:
- all the code is in the `src/` folder
- scripts downloading external tools should download them in the `bin/` folder
- all the documentation (including this file) can be found int he `doc/` folder
-- the `data` and `results` folders contain the data and results of your piplines and are ignored by `git`
+- the `data` and `results` folders contain the data and results of your pipelines and are ignored by `git`
## Code structure
-The `src/` folder is where we want to save the pipline (`.nf`) script. This folder also contains:
+The `src/` folder is where we want to save the pipeline (`.nf`) script. This folder also contains
- the `src/install_nextflow.sh` to install the nextflow executable at the root of the project.
- some pipelines examples (like the one build during the nf_pratical)
- the `src/nextflow.config` global configuration file which contains the `docker`, `singularity`, `psmn` and `ccin2p3` profiles.
-- the `src/nf_modules` folder contains per tools `main.nf` modules with predefined process that users can imports in their projects with the [DSL2](https://www.nextflow.io/docs/latest/dsl2.html)
+- the `src/nf_modules` folder contains per tools `main.nf` modules with predefined process that users can import in their projects with the [DSL2](https://www.nextflow.io/docs/latest/dsl2.html)
But also some hidden folders that users don't need to see when building their pipeline:
-- the `src/.docker_modules` contains the recipies for the `docker` containers used in the `src/nf_modules/<tool_names>/main.nf` files
+- the `src/.docker_modules` contains the recipes for the `docker` containers used in the `src/nf_modules/<tool_names>/main.nf` files
- the `src/.singularity_in2p3` and `src/.singularity_psmn` are symbolic links to the shared folder where the singularity images are downloaded on the PSMN and CCIN2P3
# Proposing a new tool
@@ -61,9 +61,9 @@ process fastp {
### process options
-Before each process, you shoud declare at least two `params.` variables:
-- A `params.<process_name>` defaulting to `""` (empty string) to allow user to add more commmand line option to your process without rewritting the process definition
-- A `params.<process_name>_out` defaulting to `""` (empty string) that define the `results/` subfolder where the process output should be copied if the user want to save the process output
+Before each process, you should declare at least two `params.` variables:
+- A `params.<process_name>` defaulting to `""` (empty string) to allow user to add more command line option to your process without rewriting the process definition
+- A `params.<process_name>_out` defaulting to `""` (empty string) that define the `results/` subfolder where the process output should be copied if the user wants to save the process output
```
params.fastp = ""
@@ -136,7 +136,7 @@ This also means that channel emitting `path` item should be transformed with at
.map { it -> [it.simpleName, it]}
````
-for example:
+for example
```
channel
@@ -147,7 +147,7 @@ channel
```
-The rational behind taking a `file_id` and emitting the same `file_id` is to facilitate complex channel operations in pipelines without having to rewrite the `process` blocks.
+The rationale behind taking a `file_id` and emitting the same `file_id` is to facilitate complex channel operations in pipelines without having to rewrite the `process` blocks.
### dealing with paired-end and single-end data
--
GitLab