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Move nfcore info into nf-core run page

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#Chap III. nf-core on Genotoul
---
![image](../assets/img/logo/nf-core-logo.svg.png)
## What is [nf-core](https://nf-co.re/) ?
* a community
* a set of pipelines
* a helper tools
## Loading environment
On `genobioinfo` server, each time you want to use nf-core workflows, you will have to load one of the following module:
```bash
$ search_module nfcore
bioinfo/nfcore-Nextflow-v19.04.0
bioinfo/nfcore-Nextflow-v20.01.0
bioinfo/nfcore-Nextflow-v20.11.0-edge
```
The nf-core module depends on the Nextflow module, you can choose the nextflow version you want to use.
```bash
module load bioinfo/nfcore-Nextflow-v20.11.0-edge
```
This will load :
* Nextflow module,
* singularity module,
* set the path to access to the local singularity images available in `/usr/local/bioinfo/src/NextflowWorkflows/singularity-img/`
## Listing available nf-core pipelines
The tool `nf-core` has a range of subcommands. The most useful is `nf-core list`, which lists all available _nf-core_ pipelines. The output shows the latest version number and when it was released. If the pipeline has been pulled locally using Nextflow, it tells you when that was and whether you have the latest version.
If you supply additional keywords after the command, the listed pipeline will be filtered. Note that this searches more than just the displayed output, including keywords and description text.
```bash
$ nf-core list rna
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
ERROR: Could not fetch status of local Nextflow copy of nf-core/sarek:
HEAD is a detached symbolic reference as it points to '7ccfb36509d8380946c048065129b29d69c8443b'
It's probably a good idea to delete this local copy and pull again:
rm -rf /home/cnoirot/.nextflow/assets/nf-core/sarek
nextflow pull nf-core/sarek
ERROR: Could not fetch status of local Nextflow copy of nf-core/rnaseq:
HEAD is a detached symbolic reference as it points to '3643a94411b65f42bce5357c5015603099556ad9'
It's probably a good idea to delete this local copy and pull again:
rm -rf /home/cnoirot/.nextflow/assets/nf-core/rnaseq
nextflow pull nf-core/rnaseq
Name Version Released Last Pulled Have latest release?
------------------ --------- ------------ ------------- ----------------------
nf-core/dualrnaseq 1.0.0 1 months ago - -
nf-core/ampliseq 1.2.0 2 months ago - -
nf-core/cageseq 1.0.2 2 months ago - -
nf-core/rnaseq 3.0 3 months ago Yes
nf-core/hlatyping 1.2.0 7 months ago - -
nf-core/rnafusion 1.2.0 8 months ago - -
nf-core/scrnaseq 1.0.0 1 years ago - -
nf-core/smrnaseq 1.0.0 2 years ago 7 months ago No
nf-core/nascent 1.0 2 years ago - -
nf-core/circrna dev - - -
nf-core/clipseq dev - - -
nf-core/lncpipe dev - - -
nf-core/scflow dev - - -
```
### Fetching pipeline code
Unless you are actively developing pipeline code, we recommend using the Nextflow [built-in functionality](https://www.nextflow.io/docs/latest/sharing.html) to fetch _nf-core_ pipelines. Nextflow will automatically fetch the pipeline code when you run `nextflow run nf-core/PIPELINE`. For the best reproducibility, it is good to explicitly reference the pipeline version number that you wish to use with the `-revision`/`-r` flag. For example:
```bash
nextflow run nf-core/rnaseq -revision 3.0
```
If not specified, Nextflow will fetch the `master` branch - for _nf-core_ pipelines this will be the latest release. If you would like to run the latest development code, use `-r dev`.
**Note that once pulled, Nextflow will use the local cached version for subsequent runs**. Use the `-latest` flag when running the pipeline to always fetch the latest version. Alternatively, you can force Nextflow to pull a pipeline again using the `nextflow pull` command:
```bash
nextflow pull nf-core/rnaseq
```
### Exercise 8
* Load latest version of nf-core module
* List all pipelines
* Fetch one of the pipelines using `nextflow pull nf-core/PIPELINE`
* Use `nf-core list` to see if the pipeline you pulled is up to date
* Get info on this pipeline with `nextflow info` command
[View correction](./correction.md)
docs/pages/nfcore_run.md
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# nf-core workflows
# nf-core
---
## Software requirements
In order to run _nf-core_ workflows, you need to have Nextflow installed ([https://www.nextflow.io](https://www.nextflow.io/)). The only other requirement is a software packaging tool: [Conda](https://docs.conda.io/en/latest/miniconda.html), [Docker](https://www.docker.com) or [Singularity](https://sylabs.io/singularity/). **On Genotoul, we use Singularity.**
## What is [nf-core](https://nf-co.re/) ?![image](../assets/img/logo/nf-core-logo.svg.png)
* a community
* a set of workflows
* a helper tools
## Usage instructions and documentation
## Loading environment
On `genobioinfo` server, each time you want to use nf-core workflows, you will have to load one of the following module:
```bash
search_module nfcore
```
```
bioinfo/NextflowWorkflows/nfcore-Nextflow-v20.11.0-edge
bioinfo/NextflowWorkflows/nfcore-Nextflow-v21.10.6
bioinfo/NextflowWorkflows/nfcore-Nextflow-v22.12.0-edge
bioinfo/NextflowWorkflows/nfcore-Nextflow-v23.04.3
bioinfo/NextflowWorkflows/nfcore-Nextflow-v23.10.0
bioinfo/NextflowWorkflows/nfcore-Nextflow-v24.04.2
```
The nf-core module depends on the Nextflow module, you can choose the nextflow version you want to use.
```bash
module load bioinfo/NextflowWorkflows/nfcore-Nextflow-v24.04.2
```
!!! Tips
To know what is contain in a module you can use the following command `module show`
```
module show bioinfo/NextflowWorkflows/nfcore-Nextflow-v24.04.2
-------------------------------------------------------------------
/tools/modulefiles/bioinfo/NextflowWorkflows/nfcore-Nextflow-v24.04.2:
module-whatis {loads the bioinfo/NextflowWorkflows/nfcore-Nextflow-v24.04.2 environment}
module load devel/java/17.0.6
module load containers/singularity/3.9.9
module load bioinfo/Nextflow/24.04.2
module load devel/python/Python-3.11.1
setenv NXF_SINGULARITY_CACHEDIR /usr/local/bioinfo/src/NextflowWorkflows/singularity-img/
-------------------------------------------------------------------
```
This will load :
* Nextflow module,
* singularity module,
* set the path to access to the local singularity images available in `/usr/local/bioinfo/src/NextflowWorkflows/singularity-img/`
## List all available pipeline
### By command line :
```
nf-core list
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.13 - https://nf-co.re
There is a new version of nf-core/tools available! (2.14.1)
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Pipeline Name ┃ Stars ┃ Latest Release ┃ Released ┃ Last Pulled ┃ Have latest release? ┃
┡━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━┩
│ sarek │ 345 │ 3.4.2 │ 4 weeks ago │ - │ - │
│ funcscan │ 58 │ 1.1.5 │ 3 months ago │ - │ - │
│ scrnaseq │ 174 │ 2.6.0 │ 4 weeks ago │ - │ - │
│ crisprseq │ 22 │ 2.1.1 │ 6 months ago │ - │ - │
│ oncoanalyser │ 15 │ dev │ yesterday │ - │ - │
│ phaseimpute │ 15 │ dev │ yesterday │ - │ - │
│ raredisease │ 74 │ 2.1.0 │ 1 week ago │ - │ - │
│ proteinfold │ 41 │ 1.0.0 │ 1 years ago │ - │ - │
│ bacass │ 55 │ 2.2.0 │ 2 months ago │ - │ - │
│ bamtofastq │ 13 │ 2.1.1 │ 4 weeks ago │ - │ - │
│ airrflow │ 44 │ 4.1.0 │ 4 days ago │ - │ - │
│ reportho │ 4 │ dev │ 4 days ago │ - │ - │
│ rnavar │ 31 │ 1.0.0 │ 2 years ago │ 2 weeks ago │ No (master - 222d7a1) │
```
## On https://nf-co.re/
Each pipeline has its own webpage at `https://nf-co.re/PIPELINE`.
![image](../assets/img/nfcore_rnaseq.png)
See online documentation for [rnaseq pipeline](https://nf-co.re/rnaseq/)
......@@ -23,6 +101,26 @@ nextflow run nf-core/rnaseq --help
!!! exercice
Visit the page of the workflow [rnaseq ](https://nf-co.re/rnaseq). Check which analyses are performed by default and what are the required parameters ?
## Fetching pipeline code
Unless you are actively developing pipeline code, we recommend using the Nextflow [built-in functionality](https://www.nextflow.io/docs/latest/sharing.html) to fetch _nf-core_ pipelines. Nextflow will automatically fetch the pipeline code when you run `nextflow run nf-core/PIPELINE`. For the best reproducibility, it is good to explicitly reference the pipeline version number that you wish to use with the `-revision`/`-r` flag. For example:
```bash
nextflow run nf-core/rnaseq -revision 3.0
```
If not specified, Nextflow will fetch the `master` branch - for _nf-core_ pipelines this will be the latest release. If you would like to run the latest development code, use `-r dev`.
**Note that once pulled, Nextflow will use the local cached version for subsequent runs**. Use the `-latest` flag when running the pipeline to always fetch the latest version. Alternatively, you can force Nextflow to pull a pipeline again using the `nextflow pull` command:
```bash
nextflow pull nf-core/rnaseq
```
!!! Tips
Get info on this pipeline with `nextflow info` command such as where is store the workflow code?
## Test a workflow
Each workflow come with test data. The first thing to do, is to try your favorite workflow with option '-profile test', as you are on genotoul you can add '-profile test,genotoul'. We will see later the content of those profiles.
......@@ -121,3 +219,8 @@ Succeeded : 194
!!! success
Thus you can see if the workflow run correctly on our infrastructure. This is a good news and the first thing to do before trying with you data.
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