Analyses have been completed.
+data/deliveries.data/raw-data on rackham.data/intermediates on rackham.data/finalized on rackham.analyses/Roadmap.md is upto date with the relationship between analyses.docs/report.New Repository on Github from the + symbol in the top right corner.NBISweden/assembly_project_template in Repository template.owner to NBISweden.<project>-<species>-<year>-<short_description> where
+<project>:
+VREBP: For VR-EBP projectsERGA: For ERGA projectsBGE: For BGE projectsSMS: For NBIS short term projects<species>: Species name<year>: Year project started<short_description>: Short project description.bash cd /proj/snic2021-6-194 git clone git@github.com:NBISweden/<repo>.gitdata/raw-data.assembly_parameters.yml to point to files in data/raw-data.The template provides an organised folder structure, and skeleton files to quickly start analyzing.
+Analyses are primarily run on Uppmax. Github is used as the primary repository, and analysis files should be tracked and pushed regularly.
+ + +What happens when a new species is to be assembled?
+Sequence data has arrived. What next?
+All data should be structured in the data/ folder as follows to make data findable.
data/
+ | - deliveries
+ | - raw-data
+ | - intermediates
+ \ - finalizeddata/deliveries contains read-only folders of deliveries from the sequencing centers.
data/raw-data contains subfolders that indicate the sequence data type, e.g. PacBio-Revio-WGS and within those folders are symlinks to data in subfolders of data/deliveries. Additional data downloaded from other locations should also be in subfolders and include a shell script that can redownload the file from the original location. e.g.,
#! /usr/bin/env bash
+curl -O ftp://path/to/public/archive/file.extdata/intermediates contains the results from tools lauched in the analyses folders using the same label as the launching folder. e.g., analyses/01_assembly-workflow_initial-run_rackham puts results in data/intermediates/01_assembly-workflow_initial-run_rackham.
data/finalized contains symlinks to folders in data/intermediates which are stage end-points, e.g. the raw-reads have been processed in various ways, and after looking at QC controls, one folder is selected to be used for assembly. This is symlinked in finalized.
code/scripts, code/snakemake, code/nextflow, and launch scripts under code/launch_templates.Assembly, annotation, and pop gen analyses are in progress.
+Who is responsible?
What happens when someone else is made responsible?
How do we notify project progress?
What happens when the data is insufficient?
What happens when the data is too contaminated?
How to monitor stages?
+Keep report up to date.
Here you can find instructions on how to run assembly projects for the VR-EBP, ERGA, and BGE projects.
+A Github account is needed. A new member needs to added to the NBISweden Github organisation (Responsible: FIXME), and then to the ERGA assemblies team (Responsible: Martin P.) to access this webpage and template.
+New members also need to be added to the NAISS compute and storage allocations in SUPR (Responsible: Henrik).
+Life-cyle:
+graph LR + onboard[onboarding] --> project + subgraph project + direction LR + initialize --> launch + launch --> monitor + monitor --> launch + monitor --> closing + end ++
## Roles:
+sequenceDiagram + actor Lead + actor Sequencer + actor Assembler + actor Annotator + actor Steward + actor Analyst + actor Developer + Lead ->> Sequencer: Sequence this species + Sequencer ->> Assembler: Sequence data delivered + Sequencer ->> Steward: Submit read data + Assembler ->> Annotator: Assembly finished. Annotate please. + Annotator ->> Analyst: Annotation complete. Analyse please. + Annotator ->> Steward: Assembly and Annotation complete. Submit it. ++