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.

Note

Follow this link if you have not yet setup your Gitpod environment.

Getting started

You will complete this module in the hello-nextflow/ folder.

cd /workspace/gitpod/hello-nextflow

In this folder you will all test data, code and accessory needed to work through this training module.

Exercise

View all the folder and files in the hello-nextflow directory.

tree .

You should see the following output:

Output

/workspace/gitpod/hello-nextflow
├── data
│   ├── bam
│   │   ├── reads_father.bam
│   │   ├── reads_mother.bam
│   │   └── reads_son.bam
│   ├── greetings.txt
│   ├── intervals.list
│   ├── ref.tar.gz
│   ├── sample_bams.txt
│   └── samplesheet.csv
├── hello-gatk.nf
├── hello-modules.nf
├── hello-nf-test.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

Each file will be used in this training module.

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.

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.

The file greetings.txt is a plain text file used to provide inputs in Part 1: Hello World.

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 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.