| tags |
|---|
ggg, ggg2021, ggg298 |
Due by 7pm, Monday March 15th
Please note that you may freely work together with others, but you must hand it in separately.
Remember to execute all of the below in an srun session!
Starting in your first HW repository, add the following samples to your variant calling workflow:
SRR2584857_1.fastq.gz - https://osf.io/aksmc/download
SRR2584405_1.fastq.gz - https://osf.io/7qek6/download
SRR2584404_1.fastq.gz - https://osf.io/s24ky/download
SRR2584403_1.fastq.gz - https://osf.io/6jx7z/download
Your snakemake workflow should download these files if they don't exist, and produce separate .vcf files for each one.
There are multiple ways to do this --
You can do this using trick #1 in my blog post if you like.
Simpler and easier-to-debug alternatives:
- create four rules that each provide an
output:of a different one of the raw data files, and provide a wget or curl command in the associatedshell:block that produces each file. - create a single rule that provides a single
output:block that contains all four of the raw data file names, and write four separate commands (one on each line) in theshell:block that download the four files.
Side note: you can now run with -j 4 to run it ~four times faster.
You should end up with four (different) VCF files.
- Make sure that
snakemake --delete-all-outputremoves all of the generated files. - Make sure that you can rerun the pipeline from scratch without any errors.
Run git commit -am and git push to submit. Make sure that your latest changes are reflected on your github site.
After accepting the HW #2 assignment URL (see Canvas or Slack), please clone the new github repository for assembly into your farm account.
Adjust the Snakefile to generate assemblies and quast evaluations for three different subsets (I suggest you keep them between 0 and 2000000 in size).
After sucessfully generating three different assemblies and quast evaluations, fill out this form with your resulting numbers.
Also please commit and push your Snakefile.