Commit bf345441 authored by Jean Mainguy's avatar Jean Mainguy
Browse files

Update doc with new profiles.

#172
parent 376e6fd5
Pipeline #47623 skipped with stage
......@@ -95,7 +95,7 @@ Analyzing your metagenomic data with metagWGS allows you to use all **`nextflow
#### `-profile`
It allows you to choose the configuration profile among:
* `singularity` to analyze **your files** with metagWGS with **singularity containers**. You must have installed Singularity and downloaded the three Singularity containers associated to metagWGS (see [Installation page](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/master/docs/installation.md)). Thus, your results will be reproducible. **NOTE:** there is no definition of the type of cluster (SGE, slurm, etc) you use in this profile.
* `singularity` to analyze **your files** with metagWGS with **singularity containers**. You must have installed Singularity and downloaded the two Singularity containers associated to metagWGS (see [Installation page](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/master/docs/installation.md)). Thus, your results will be reproducible. **NOTE:** there is no definition of the type of cluster (SGE, slurm, etc) you use in this profile.
* `conda` to analyze **your files** with metagWGS with **conda environments** already defined. You must have installed Miniconda (see [here](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html)).
* **NOTE 1:** use of `conda` profile is easier than `singularity` profile but your results will be less reproducible.
* **NOTE 2:** there is no definition of the type of cluster (SGE, slurm, etc) you use in this profile. You can precise it inside of a `nextflow.config` file you can add into your working directory. For example if you are working on a slurm cluster, add this line to your `nextflow.config`:
......@@ -103,14 +103,14 @@ It allows you to choose the configuration profile among:
process.executor = 'slurm'
```
* **NOTE 3:** on [genologin cluster](http://bioinfo.genotoul.fr/) Miniconda is already installed. You can search Miniconda module with `search_module Miniconda` and load it with `module load chosen_miniconda_module`.
* `genotoul` to analyze **your files** with metagWGS **on genologin cluster** with Singularity images `metagWGS.sif` and `eggnog_mapper.sif`.
* `test_genotoul_workq` to analyze **small test data files** (used in [I. Basic Usage](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/master/docs/usage.md#i-basic-usage)) with metagWGS **on genologin cluster** on the **`workq`** queue with Singularity images `metagWGS.sif` and `eggnog_mapper.sif`.
* `test_genotoul_testq` to analyze **small test data files** (used in [I. Basic Usage](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/master/docs/usage.md#i-basic-usage)) with metagWGS **on genologin cluster** on the **`testq`** queue with Singularity images `metagWGS.sif` and `eggnog_mapper.sif`.
* `big_test_genotoul` to analyze **big test data files** (used in [Use case documentation page](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/master/docs/use_case.md)) with metagWGS **on genologin cluster** (on the **`workq`** queue) with Singularity images `metagWGS.sif` and `eggnog_mapper.sif`.
* `test_local` to analyze **small test data files** (used in [I. Basic Usage](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/master/docs/usage.md#i-basic-usage)) with metagWGS **on your computer** with Singularity images `metagWGS.sif` and `eggnog_mapper.sif`.
* `genotoul` to analyze **your files** with metagWGS **on genologin cluster** with Singularity images `metagWGS.sif` and `eggnog_mapper.sif`. This profile include the `singularity` profile.
* `test` to analyze **small test data files** (used in [I. Basic Usage](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/master/docs/usage.md#i-basic-usage)) with metagWGS **on genologin cluster** on the **`workq`** queue with Singularity images `metagWGS.sif` and `eggnog_mapper.sif`.
* `local` to launch the pipeline in local executor.
* `debug` to **debug** metagWGS pipeline.
These profiles are associated to different configuration files developped [in this directory](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/tree/master/conf). The `base.config` file available in this directory is the base configuration load in first which is crushed by indications of the profile you use. See [here](https://genotoul-bioinfo.pages.mia.inra.fr/use-nextflow-nfcore-course/nfcore/profiles.html) for more explanations.
These profiles are associated to different configuration files found [in this directory](../conf). The `base.config` file available in this directory is the base configuration load in first which is crushed by indications of the profile you use. See [here](https://genotoul-bioinfo.pages.mia.inra.fr/use-nextflow-nfcore-course/nfcore/profiles.html) for more explanations.
**NOTE:** Two or more configuration profiles can be specified by separating the profile names with a comma character, for example: `-profile genotoul,test`.
### 2. Useful options
......
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