Skip to content

Commit

Permalink
Adding base workflow for ONT pipeline
Browse files Browse the repository at this point in the history
  • Loading branch information
skchronicles committed Jan 17, 2023
1 parent 11abf2c commit 7ca73c5
Show file tree
Hide file tree
Showing 22 changed files with 3,572 additions and 0 deletions.
9 changes: 9 additions & 0 deletions config/cluster.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
{
"__default__": {
"threads": "2",
"mem": "8g",
"partition": "norm",
"gres": "lscratch:32",
"time": "0-04:00:00"
}
}
4 changes: 4 additions & 0 deletions config/config.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
{
"options": {
}
}
5 changes: 5 additions & 0 deletions config/containers.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
{
"images": {

}
}
5 changes: 5 additions & 0 deletions config/genome.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
{
"references": {

}
}
7 changes: 7 additions & 0 deletions config/install.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
{
"install": {
"resource_bundle": {

}
}
}
8 changes: 8 additions & 0 deletions config/modules.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
{
"modules": {

},
"conda":{

}
}
35 changes: 35 additions & 0 deletions docker/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
## Steps for Building Docker Images

Directly below are instructions for building an image using the provided Dockerfile:

```bash
# See listing of images on computer
docker image ls

# Build from Dockerfile
docker build --no-cache -f example.dockerfile --tag=example:v0.1.0 .

# Testing, take a peek inside
docker run -ti example:v0.1.0 /bin/bash

# Updating Tag before pushing to DockerHub
docker tag example:v0.1.0 skchronicles/example:v0.1.0
docker tag example:v0.1.0 skchronicles/example # latest

# Check out new tag(s)
docker image ls

# Push new tagged image to DockerHub
docker push skchronicles/example:v0.1.0
docker push skchronicles/example:latest
```

### Other Recommended Steps

Scan your image for known vulnerabilities:

```bash
docker scan example:v0.1.0
```

> **Please Note**: Any references to `skchronicles` should be replaced your username if you would also like to push the image to a non-org account.
Loading

0 comments on commit 7ca73c5

Please sign in to comment.