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
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@@ -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.
