Why these two files changed? Which one should I use?

[wuhuiyun07]

line 12 has changed:
from
host_filter.adapter_fasta: https://raw.githubusercontent.com/broadinstitute/viral-pipelines/master/test/input/clipDb.fasta
https://github.com/chanzuckerberg/czid-workflows/blob/main/workflows/short-read-mngs/test/local_test_viral.yml
to
host_filter.star_genome: s3://czid-public-references/host_filter/ercc/2018-02-15-utc-1518652800-unixtime__2018-02-15-utc-1518652800-unixtime/STAR_genome.tar
https://github.com/chanzuckerberg/czid-workflows/blob/648154487fea2c461fcecd24d5f55479a8bbf772/workflows/short-read-mngs/test/local_test_viral.yml

Here is my error message
"check JSON input; unknown input/output: host_filter.star_genome" when I follow the second link.

[rzlim08]

sorry that PR is really old, I just refreshed from main, can you try repulling from that branch and rerunning?

[wuhuiyun07]

how to download the latest version of the workflow? Can you provide me a link? I just did git clone again, and it looks the same...

The result of the postprocess.wdl still did not provide results in .csv file and it is not providing the results from line 307 "OutputResultsCSV", https://github.com/chanzuckerberg/czid-workflows/pull/200/files.

please advise, thank you!

[rzlim08]

If you're in the branch rlim/add-output-csv-short-read try running git pull. Let me know if that works or not!

[rzlim08]

Hi! As per our meeting today, to get the latest changes with the output csv run:

git clone --branch rlim/add-output-csv-short-read [email protected]:chanzuckerberg/czid-workflows.git

This should create a new folder czid-workflows. After this you can check if the OutputResultsCSV is in the workflows/short-read-mngs/postprocess.wdl file.

Thanks, and let me know how it goes!

[rzlim08]

Also coming out of our meeting, I believe there was some interest in getting some contig information. The combined_contig_summary.json should give you the taxid with the contigs that belong to each taxid and the number of reads in each contig.

There was also some interest in the N50. Unfortunately we don't have the N50 calculated but have a python function to calculate it here

If there was any more contig information you needed, let me know and I'll take a look at which files are needed.