A bash script to rebuilt the singularity images for nf-core pipelines.
Introduction
A bash script to rebuild the singularity containers for the nf-core/mag pipeline with same name as required.
This is useful in a scenario when a user have singularity v2 instead v3 installed on their local machine and
cannot upgrade. At the moment its only tested for nf-core/mag pipeline. The background information required
for developing this script was obtained from https://nf-co.re/tools/#downloading-pipelines-for-offline-use
For further information on the different nf-core pipelines refer to citation section below.
To rebuiltd the singularity images
bash rebuilt.sh $tool_name ($tool_name=mag)
bash rebuilt.sh mag
Expected output
$PWD
|
|---configs/
| |---configtest.nf
| |---nexftlow.config
| |---nfcore_custom.config
| .
| .
|---singularity-images/
| |---tool1.img
| |---tool2.img
| |---tool3.img
| .
| .
|---workflow/
| |---assets/
| |---bin/
| |--main.nf
| .
| .
Note
Edit the ./workflows/nextflow.config
Add the following statement at the bottom in the nextflow.config
singularity.cacheDir = "${projectDir}/../singularity-images/"
For citation
Please refer to their nfc-core home page