|
1 | 1 | # Orientation |
2 | 2 |
|
3 | | -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. |
| 3 | +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. |
| 4 | +However, you do need a (free) account to log in, and you should take a few minutes to familiarize yourself with the interface. |
4 | 5 |
|
5 | | -!!! note |
| 6 | +If you have not yet done so, please follow [this link](../../envsetup/) before going any further. |
6 | 7 |
|
7 | | - Follow [this link](../../envsetup/) if you have not yet setup your Gitpod environment. |
| 8 | +## Materials provided |
8 | 9 |
|
9 | | -## Getting started |
| 10 | +Throughout this training course, we'll be working in the `hello-nextflow/` directory, which loads by default when you open the Gitpod workspace. |
| 11 | +This directory contains all the code files, test data and accessory files you will need. |
10 | 12 |
|
11 | | -You will complete this module in the `hello-nextflow/` folder. |
| 13 | +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. |
| 14 | +Alternatively, you can use the `tree` command. |
| 15 | +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. |
| 16 | + |
| 17 | +Here we generate a table of contents to the second level down: |
12 | 18 |
|
13 | 19 | ```bash |
14 | | -cd /workspace/gitpod/hello-nextflow |
| 20 | +tree . -L 2 |
15 | 21 | ``` |
16 | 22 |
|
17 | | -In this folder you will all test data, code and accessory needed to work through this training module. |
18 | | - |
19 | | -!!! question "Exercise" |
| 23 | +If you run this inside `hello-nextflow`, you should see the following output: |
20 | 24 |
|
21 | | - View all the folder and files in the `hello-nextflow` directory. |
22 | | - |
23 | | - ```console |
24 | | - tree . |
25 | | - ``` |
26 | | - |
27 | | -You should see the following output: |
28 | | - |
29 | | -```console title="Output" |
30 | | -/workspace/gitpod/hello-nextflow |
| 25 | +```console title="Directory contents" |
| 26 | +. |
| 27 | +├── containers |
| 28 | +│ ├── build |
| 29 | +│ ├── data |
| 30 | +│ ├── results |
| 31 | +│ └── scripts |
31 | 32 | ├── data |
32 | 33 | │ ├── bam |
33 | | -│ │ ├── reads_father.bam |
34 | | -│ │ ├── reads_mother.bam |
35 | | -│ │ └── reads_son.bam |
36 | | -│ ├── greetings.txt |
37 | | -│ ├── intervals.list |
38 | | -│ ├── ref.tar.gz |
| 34 | +│ ├── greetings.csv |
| 35 | +│ ├── ref |
39 | 36 | │ ├── sample_bams.txt |
40 | 37 | │ └── samplesheet.csv |
41 | | -├── hello-gatk.nf |
42 | | -├── hello-modules.nf |
43 | | -├── hello-nf-test.nf |
| 38 | +├── hello-config |
| 39 | +│ ├── demo-params.json |
| 40 | +│ ├── main.nf |
| 41 | +│ └── nextflow.config |
| 42 | +├── hello-containers.nf |
| 43 | +├── hello-genomics.nf |
| 44 | +├── hello-modules |
| 45 | +│ ├── demo-params.json |
| 46 | +│ ├── main.nf |
| 47 | +│ └── nextflow.config |
| 48 | +├── hello-nf-test |
| 49 | +│ ├── demo-params.json |
| 50 | +│ ├── main.nf |
| 51 | +│ └── nextflow.config |
| 52 | +├── hello-operators.nf |
44 | 53 | ├── hello-world.nf |
45 | 54 | ├── nextflow.config |
46 | | -└── scripts |
47 | | - ├── hello-gatk-1.nf |
48 | | - ├── hello-gatk-2.nf |
49 | | - ├── hello-gatk-3.nf |
50 | | - ├── hello-gatk-4.nf |
51 | | - ├── hello-gatk-5.nf |
52 | | - ├── hello-gatk-6.nf |
53 | | - ├── hello-modules-1.nf |
54 | | - ├── hello-modules-2.nf |
55 | | - ├── hello-modules-3.nf |
56 | | - ├── hello-world-10.nf |
57 | | - ├── hello-world-1.nf |
58 | | - ├── hello-world-2.nf |
59 | | - ├── hello-world-3.nf |
60 | | - ├── hello-world-4.nf |
61 | | - ├── hello-world-5.nf |
62 | | - ├── hello-world-6.nf |
63 | | - ├── hello-world-7.nf |
64 | | - ├── hello-world-8.nf |
65 | | - ├── hello-world-9.nf |
66 | | - ├── modules |
67 | | - │ └── local |
68 | | - │ ├── gatk |
69 | | - │ │ ├── haplotypecaller |
70 | | - │ │ │ └── main.nf |
71 | | - │ │ └── jointgenotyping |
72 | | - │ │ ├── main.nf |
73 | | - │ │ └── tests |
74 | | - │ │ └── inputs |
75 | | - │ │ ├── family_trio_map.tsv |
76 | | - │ │ ├── reads_father.bam.g.vcf |
77 | | - │ │ ├── reads_father.bam.g.vcf.idx |
78 | | - │ │ ├── reads_mother.bam.g.vcf |
79 | | - │ │ ├── reads_mother.bam.g.vcf.idx |
80 | | - │ │ ├── reads_son.bam.g.vcf |
81 | | - │ │ └── reads_son.bam.g.vcf.idx |
82 | | - │ └── samtools |
83 | | - │ └── index |
84 | | - │ └── main.nf |
85 | | - └── nextflow.config |
86 | | - |
87 | | -12 directories, 43 files |
88 | | - |
| 55 | +└── solutions |
| 56 | + ├── hello-config |
| 57 | + ├── hello-genomics |
| 58 | + ├── hello-modules |
| 59 | + ├── hello-nf-test |
| 60 | + ├── hello-operators |
| 61 | + └── hello-world |
| 62 | + |
| 63 | +18 directories, 17 files |
89 | 64 | ``` |
90 | 65 |
|
91 | | -Each file will be used in this training module. |
| 66 | +!!!note |
92 | 67 |
|
93 | | -**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. |
| 68 | + Don't worry if this seems like a lot; we'll go through the relevant pieces at each step of the course. |
| 69 | + This is just meant to give you an overview. |
94 | 70 |
|
95 | | -**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. |
| 71 | +**Here's a summary of what you should know to get started:** |
96 | 72 |
|
97 | | -**The file `greetings.txt`** is a plain text file used to provide inputs in Part 1: Hello World. |
| 73 | +- **The `.nf` files** are workflow scripts that are named based on what part of the course they're used in. |
98 | 74 |
|
99 | | -**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. |
| 75 | +- **The `hello-*` directories** are directories used in the later Parts of the course where we are working with more than just one workflow file. |
100 | 76 |
|
101 | | -**The file `hello-world.nf`** is a simple but fully functional workflow script that serves as a starting point to Part 1: Hello World. |
| 77 | +- **The file `nextflow.config`** is a configuration file that sets minimal environment properties. |
| 78 | + You can ignore it for now. |
| 79 | + |
| 80 | +- **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. |
| 81 | + |
| 82 | +- **The `solutions` directory** contains the completed workflow scripts that result from each step of the course. |
| 83 | + They are intended to be used as a reference to check your work and troubleshoot any issues. |
| 84 | + The name and number in the filename correspond to the step of the relevant part of the course. |
| 85 | + For example, the file `hello-world-4.nf` is the expected result of completing steps 1 through 4 of Part 1: Hello World. |
| 86 | + |
| 87 | +!!!tip |
| 88 | + |
| 89 | + If for whatever reason you move out of this directory, you can always run this command to return to it: |
| 90 | + |
| 91 | + ```bash |
| 92 | + cd /workspace/gitpod/hello-nextflow |
| 93 | + ``` |
102 | 94 |
|
103 | | -**The file `nextflow.config`** is a configuration file that sets minimal environment properties. |
| 95 | +Now, to begin the course, click on the arrow in the bottom right corner of this page. |
0 commit comments