Environment Setup¶
Pipeline data¶
All the files needed for the hands-on activity are stored in the directory shown below:
$HOME/environment/hands-on
├── bin
│ └── gghist.R
├── data
│ ├── blacklist.bed
│ ├── genome.fa
│ ├── known_variants.vcf.gz
│ └── reads
│ ├── ENCSR000COQ1_1.fastq.gz
│ ├── ENCSR000COQ1_2.fastq.gz
│ ├── ENCSR000COQ2_1.fastq.gz
│ ├── ENCSR000COQ2_2.fastq.gz
│ ├── ENCSR000COR1_1.fastq.gz
│ ├── ENCSR000COR1_2.fastq.gz
│ ├── ENCSR000COR2_1.fastq.gz
│ ├── ENCSR000COR2_2.fastq.gz
│ ├── ENCSR000CPO1_1.fastq.gz
│ ├── ENCSR000CPO1_2.fastq.gz
│ ├── ENCSR000CPO2_1.fastq.gz
│ └── ENCSR000CPO2_2.fastq.gz
├── nextflow.config
└── README.md
3 directories, 19 files
Pulling the Docker image¶
Nextflow can pull Docker images at runtime, but let’s just download it manually to see how Docker works:
You should see the progress of the download:
sha256:93910bf77bc197cb790eca776e42950bc8eff117bdc6e67157295e09c98fc381: Pulling from cbcrg/callings-with-gatk
915665fee719: Downloading [=============================================> ] 47.08 MB/51.36 MB
f332de2321e6: Downloading [===========> ] 41.96 MB/187.8 MB
1577a6dd9e43: Downloading [===============================> ] 46.72 MB/73.45 MB
7059d9bb5245: Waiting
71863f70269f: Waiting
ce2a2879246d: Waiting
e38ba5d5f9fb: Waiting
90158da87bb2: Waiting
and the following message when the pull is completed:
Digest: sha256:93910bf77bc197cb790eca776e42950bc8eff117bdc6e67157295e09c98fc381
Status: Downloaded newer image for cbcrg/callings-with-gatk:latest
Script permission¶
Make sure the following R script has execute permissions: