iarcbioinfo / template-nf

Empty template for nextflow pipelines

Name

Empty template for nextflow pipelines (short description)

Description

...

Dependencies

1. This pipeline is based on nextflow. As we have several nextflow pipelines, we have centralized the common information in the IARC-nf repository. Please read it carefully as it contains essential information for the installation, basic usage and configuration of nextflow and our pipelines.
2. External software:

• ...
• ...

You can avoid installing all the external software by only installing Docker. See the IARC-nf repository for more information.

Input

Type	Description
input1	......
input2	......

Specify the test files location

Parameters

• Mandatory

Name	Example value	Description
--param1	xx	......
--param2	xx	......

• Optional

Name	Default value	Description
--param3	xx	......
--param4	xx	......

• Flags

Flags are special parameters without value.

Name	Description
--help	Display help
--flag2	....

Usage

...

Output

Type	Description
output1	......
output2	......

Detailed description (optional section)

...

Directed Acyclic Graph

Contributions

Name	Email	Description
contrib1*	xx	Developer to contact for support (link to specific gitter chatroom)
contrib2	xx	Developer
contrib3	xx	Tester

References (optional)

FAQ (optional)

template-nf's Issues

improve SingularityHub deployment

At the moment, the deployment on SingularityHub is done only for github pushes on the Singularity file. Since our container depends on two files (environment.yml and the singularity), this means that triggers are not well defined.
See this discussion:
singularityhub/singularityhub.github.io#142 (comment)

make the pipeline citable

Archive the GitHub repo and assign a DOI with the data archiving tool Zenodo.
Look at this tutorial:
https://guides.github.com/activities/citable-code/

For that we need to release the code.
Then we could also post a DOI badge on the readme.

Singularity Hub

hey IARCbioinfo! ! I'm really glad to see that you guys are taking advantage of Singularity Hub! :) Would you mind deleting builds that you no longer need? It looks like you just hit 20 (all successful) and since we are storing (and paying for) each build, it's good container hygiene to keep this sort of thing in mind. If needed, you can also disable building for times when you anticipate high levels of commits, or just use a different branch for releases / Singularity Hub. Thank you!