-
Notifications
You must be signed in to change notification settings - Fork 115
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #412 from nextflow-io/dev
Hello Nextflow refresh including new modules on containers, config, nf-core, and seqera
- Loading branch information
Showing
151 changed files
with
11,949 additions
and
2,500 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,103 +1,95 @@ | ||
# Orientation | ||
|
||
The Gitpod environment contains some test data that will be used in this workshop. All software required are already installed and configured in it too. | ||
The Gitpod environment contains all the software, code and data necessary to work through this training course, so you don't need to install anything yourself. | ||
However, you do need a (free) account to log in, and you should take a few minutes to familiarize yourself with the interface. | ||
|
||
!!! note | ||
If you have not yet done so, please follow [this link](../../envsetup/) before going any further. | ||
|
||
Follow [this link](../../envsetup/) if you have not yet setup your Gitpod environment. | ||
## Materials provided | ||
|
||
## Getting started | ||
Throughout this training course, we'll be working in the `hello-nextflow/` directory, which loads by default when you open the Gitpod workspace. | ||
This directory contains all the code files, test data and accessory files you will need. | ||
|
||
You will complete this module in the `hello-nextflow/` folder. | ||
Feel free to explore the contents of this directory; the easiest way to do so is to use the file explorer on the left hand side of the Gitpod workspace. | ||
Alternatively, you can use the `tree` command. | ||
Throughout the course, we use the output of `tree` to represent directory structure and contents in a readable form, sometimes with minor modifications for clarity. | ||
|
||
Here we generate a table of contents to the second level down: | ||
|
||
```bash | ||
cd /workspace/gitpod/hello-nextflow | ||
tree . -L 2 | ||
``` | ||
|
||
In this folder you will all test data, code and accessory needed to work through this training module. | ||
|
||
!!! question "Exercise" | ||
If you run this inside `hello-nextflow`, you should see the following output: | ||
|
||
View all the folder and files in the `hello-nextflow` directory. | ||
|
||
```console | ||
tree . | ||
``` | ||
|
||
You should see the following output: | ||
|
||
```console title="Output" | ||
/workspace/gitpod/hello-nextflow | ||
```console title="Directory contents" | ||
. | ||
├── containers | ||
│ ├── build | ||
│ ├── data | ||
│ ├── results | ||
│ └── scripts | ||
├── data | ||
│ ├── bam | ||
│ │ ├── reads_father.bam | ||
│ │ ├── reads_mother.bam | ||
│ │ └── reads_son.bam | ||
│ ├── greetings.txt | ||
│ ├── intervals.list | ||
│ ├── ref.tar.gz | ||
│ ├── greetings.csv | ||
│ ├── ref | ||
│ ├── sample_bams.txt | ||
│ └── samplesheet.csv | ||
├── hello-gatk.nf | ||
├── hello-modules.nf | ||
├── hello-nf-test.nf | ||
├── hello-config | ||
│ ├── demo-params.json | ||
│ ├── main.nf | ||
│ └── nextflow.config | ||
├── hello-containers.nf | ||
├── hello-genomics.nf | ||
├── hello-modules | ||
│ ├── demo-params.json | ||
│ ├── main.nf | ||
│ └── nextflow.config | ||
├── hello-nf-test | ||
│ ├── demo-params.json | ||
│ ├── main.nf | ||
│ └── nextflow.config | ||
├── hello-operators.nf | ||
├── hello-world.nf | ||
├── nextflow.config | ||
└── scripts | ||
├── hello-gatk-1.nf | ||
├── hello-gatk-2.nf | ||
├── hello-gatk-3.nf | ||
├── hello-gatk-4.nf | ||
├── hello-gatk-5.nf | ||
├── hello-gatk-6.nf | ||
├── hello-modules-1.nf | ||
├── hello-modules-2.nf | ||
├── hello-modules-3.nf | ||
├── hello-world-10.nf | ||
├── hello-world-1.nf | ||
├── hello-world-2.nf | ||
├── hello-world-3.nf | ||
├── hello-world-4.nf | ||
├── hello-world-5.nf | ||
├── hello-world-6.nf | ||
├── hello-world-7.nf | ||
├── hello-world-8.nf | ||
├── hello-world-9.nf | ||
├── modules | ||
│ └── local | ||
│ ├── gatk | ||
│ │ ├── haplotypecaller | ||
│ │ │ └── main.nf | ||
│ │ └── jointgenotyping | ||
│ │ ├── main.nf | ||
│ │ └── tests | ||
│ │ └── inputs | ||
│ │ ├── family_trio_map.tsv | ||
│ │ ├── reads_father.bam.g.vcf | ||
│ │ ├── reads_father.bam.g.vcf.idx | ||
│ │ ├── reads_mother.bam.g.vcf | ||
│ │ ├── reads_mother.bam.g.vcf.idx | ||
│ │ ├── reads_son.bam.g.vcf | ||
│ │ └── reads_son.bam.g.vcf.idx | ||
│ └── samtools | ||
│ └── index | ||
│ └── main.nf | ||
└── nextflow.config | ||
|
||
12 directories, 43 files | ||
|
||
└── solutions | ||
├── hello-config | ||
├── hello-genomics | ||
├── hello-modules | ||
├── hello-nf-test | ||
├── hello-operators | ||
└── hello-world | ||
|
||
18 directories, 17 files | ||
``` | ||
|
||
Each file will be used in this training module. | ||
!!!note | ||
|
||
**The `data` directory** contains the input data we'll use in Part 2: Hello GATK, which uses an example from genomics to demonstrate how to build a simple analysis pipeline. The data is described in detail in that section of the training. | ||
Don't worry if this seems like a lot; we'll go through the relevant pieces at each step of the course. | ||
This is just meant to give you an overview. | ||
|
||
**The `scripts` directory** contains the completed workflow scripts that result from each step of the tutorial and are intended to be used as a reference to check your work. The name and number in the filename correspond to the step of the relevant tutorial. For example, the file `hello-world-4.nf` is the expected result of completing steps 1 through 4 of Part 1: Hello World. | ||
**Here's a summary of what you should know to get started:** | ||
|
||
**The file `greetings.txt`** is a plain text file used to provide inputs in Part 1: Hello World. | ||
- **The `.nf` files** are workflow scripts that are named based on what part of the course they're used in. | ||
|
||
**The file `hello-gatk.nf`** is a stub that serves as a starting point to Part 2: Hello GATK. In its initial state, it is NOT a functional workflow script. | ||
- **The `hello-*` directories** are directories used in the later Parts of the course where we are working with more than just one workflow file. | ||
|
||
**The file `hello-world.nf`** is a simple but fully functional workflow script that serves as a starting point to Part 1: Hello World. | ||
- **The file `nextflow.config`** is a configuration file that sets minimal environment properties. | ||
You can ignore it for now. | ||
|
||
- **The `data` directory** contains the input data we'll use in most of the course. The dataset is described in detail in Part 3, when we introduce it for the first time. | ||
|
||
- **The `solutions` directory** contains the completed workflow scripts that result from each step of the course. | ||
They are intended to be used as a reference to check your work and troubleshoot any issues. | ||
The name and number in the filename correspond to the step of the relevant part of the course. | ||
For example, the file `hello-world-4.nf` is the expected result of completing steps 1 through 4 of Part 1: Hello World. | ||
|
||
!!!tip | ||
|
||
If for whatever reason you move out of this directory, you can always run this command to return to it: | ||
|
||
```bash | ||
cd /workspace/gitpod/hello-nextflow | ||
``` | ||
|
||
**The file `nextflow.config`** is a configuration file that sets minimal environment properties. | ||
Now, to begin the course, click on the arrow in the bottom right corner of this page. |
Oops, something went wrong.