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Hello Nextflow refresh including new modules on containers, config, nf-core, and seqera
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| # Orientation | ||
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| 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. | ||
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| !!! note | ||
| If you have not yet done so, please follow [this link](../../envsetup/) before going any further. | ||
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| Follow [this link](../../envsetup/) if you have not yet setup your Gitpod environment. | ||
| ## Materials provided | ||
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| ## 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. | ||
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| 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. | ||
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| Here we generate a table of contents to the second level down: | ||
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| ```bash | ||
| cd /workspace/gitpod/hello-nextflow | ||
| tree . -L 2 | ||
| ``` | ||
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| In this folder you will all test data, code and accessory needed to work through this training module. | ||
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| !!! question "Exercise" | ||
| If you run this inside `hello-nextflow`, you should see the following output: | ||
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| View all the folder and files in the `hello-nextflow` directory. | ||
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| ```console | ||
| tree . | ||
| ``` | ||
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| You should see the following output: | ||
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| ```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 | ||
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| 12 directories, 43 files | ||
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| └── solutions | ||
| ├── hello-config | ||
| ├── hello-genomics | ||
| ├── hello-modules | ||
| ├── hello-nf-test | ||
| ├── hello-operators | ||
| └── hello-world | ||
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| 18 directories, 17 files | ||
| ``` | ||
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| Each file will be used in this training module. | ||
| !!!note | ||
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| **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. | ||
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| **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:** | ||
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| **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. | ||
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| **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. | ||
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| **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. | ||
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| - **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. | ||
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| - **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. | ||
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| !!!tip | ||
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| If for whatever reason you move out of this directory, you can always run this command to return to it: | ||
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| ```bash | ||
| cd /workspace/gitpod/hello-nextflow | ||
| ``` | ||
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| **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. |
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