nih-nichd / elements-of-style-workflow-creation-maintenance Goto Github PK

In
https://github.com/NIH-NICHD/Elements-of-Style-Workflow-Creation-Maintenance/blob/main/classes/WorkingWithAppsOnCAVATICA/WorkingWithAppsOnCAVATICA.md

Right after the line “Data are required and the same files that were used in the Nextflow workflow example were copied up onto the CAVATICA workspace.”

Next screenshot shows that two fastq files are already connected to the app and present in cavatica files. But when following directions students do not have the fastq files.

Workaround for adding the fastq files via zenodo attached.
missing fastq files for fastqc run cavatica.docx

The notebook for demonstrating how to run a jupyterlab notebook within a terminal window on CAVATICA https://github.com/NIH-NICHD/Elements-of-Style-Workflow-Creation-Maintenance/blob/main/classes/1-using-the-command-line/2-reading-data-and-plotting-in-R.ipynb uses data from Zenodo -- change this to use INCLUDE data publicly available