Update SlimNT and create thorough documentation for how to update

GW-HIVE / slimNT

MIT License

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Update SlimNT and create thorough documentation for how to update #7

Open penningtonea opened 2 weeks ago

penningtonea commented 2 weeks ago

The slimNT database must be updated every 6 months and indexed on HIVE 1. The procedure to update the database is by running the entire nextflow pipeline on pegasus.

Create thorough documentation on executing the workflow, moving the db to hive, and indexing.

penningtonea commented 2 weeks ago

BLOCKER:

Seem to have an issue with Pegasus disconnecting and stopping the job. Email Adam Wong to coordinate slurm controller exiting before the job is finished.

penningtonea commented 1 week ago

slimNT can't move past the second step (getGenomes). I used the same script that Joe submitted with his final documentation and was not able to fix the error.

penningtonea commented 1 week ago

Using the HighMem node and allotting 72 hours allowed the script to complete 4/5 steps. The last step failed with the following error message:

I changed to the work directory as stated but could not find a script called .command.sh and need to troubleshoot further.

penningtonea commented 1 week ago

the testing directory for slimNT includes a line of code in process concatZip that does not exist in the prod folder.

commented out publishDir "$params.outdir/genomes/", mode: 'copy', overwrite: true