Nextflow for bigdata course

Contains RMD file to generate course website page using knitr package.

Creates manual for bigdata course

Required files for the course

MZML data: Present in the private git
Solutions: Present in the private git

For docker manual go to docker folder (working with minor issues)

For singularity manual go to singularity folder (not working in uppmax)

For the MZML folder, remember to keep the permission as "-rwxr-xr-x". Remove group and other write permission

chmod -R g-w foldername

Path changes

Edit the RMD file with uppmax path every year and reupload the website. Example: /crex/proj/uppmax2025-2-288/nobackup/$USER/nextflow_lab1
Edit path in the file main.nf under xcms_pipeline

Future edits

• Change instructions on what to submit (remove config submission for part2)
• Make them to use consistent name for all parameter and mzml channels in part 2 (makes it easy for evaluation)
• Make a python script to check for names, and other checks while they submit (maybe give it to the students, so they can check and submit the pipleline after that)
• Reduce the number of submission attempt to 2 or 3(max)
• Mark in the assignment how echo command would help to see how the bash command look like