NBIS project template

This is a personal template for National Bioinformatics Infrastructure Sweden (NBIS) support projects. It is an evolving method of working as I gain experience and find better ways of working. See the template website for how I use this template.

<Title>

• NBIS Project ID:
• NBIS experts: Mahesh Binzer-Panchal (mahesh.binzer-panchal@nbis.se)
• Request by: ()
• Principal Investigator: ()

Expert Affiliation:

Mahesh Binzer-Panchal
Department of Medical Biochemistry and Microbiology,
National Bioinformatics Infrastructure Sweden (NBIS),
Science for Life Laboratory,
Uppsala Universitet,
Uppsala,
Sweden
ORCID = https://orcid.org/0000-0003-1675-0677

NBIS Support Request.

NBIS Project support request:

NBIS Agreement: ( XX hrs)

• <Agreed outcome 1>
• <Agreed outcome 2>

Directories

/proj/naiss20XX-YY-ZZ/NBIS_support_<id>/       (NAISS Compute Allocation)
 |
 | - README.md                                 Project details summary
 |
 | - analyses/                                 Analysis launch scripts
 | - conda/                                    Shared conda environments
 | - docs/                                     Project documentation
 \ - workflow/                                 Nextflow workflow

/proj/naiss20xx-yy-zz/                         (NAISS Storage Allocation)
 |
 | - nobackup/nxf-work                         Intermediate computations
 \ - NBIS_support_<id>_data/                   Project data
     | - deliveries                              Sequence deliveries
     | - raw-data                                Reorganised input data
     | - outputs                                 Analysis/workflow outputs
     \ - frozen                                  Data to publish

Workflow instructions

Quickstart:

cd /proj/naiss20XX-YY-ZZ/NBIS_support_<id>/analyses/<analysis>/
./run_nextflow.sh

A description of the workflow stages is provided in the Project Report.

Workflow parameter options and outputs are detailed in the workflow README.