Mark Diekhans

liftoff adds some attributes that look useful but are not documented - copy_num_ID - low_identity - partial_ORF - partial_mapping

add ability for toil-specific options to be prefixed with --toil-

9

It can be confusing which option in a program belongs to Toil and which to the application itself. If there was the option to add --toil- to the beginning of...

don't hang if exiftool unexpectedly exits

2

The select loop from exiftool does not check for EOF, causing some expect failure to cause pyexiftool to hang. This PR doesn't address the Window case, as I can't test...

------------------------------------- Translated Report (Full Report Below) ------------------------------------- Process: Persephone [27133] Path: /private/var/folders/*/Persephone.app/Contents/MacOS/Persephone Identifier: me.danbarber.Persephone Version: 0.18.1-alpha (425) Code Type: ARM-64 (Native) Parent Process: launchd [1] User ID: 501 Date/Time: 2024-09-14...

pybedtools does not install with python 3.13

2

This appears to be related to changes in the Python C API [pybedtools.log](https://github.com/user-attachments/files/18551966/pybedtools.log)

This makes it unfriendly to scripting and pipelines. ``` % paftools.js sam2paf >/dev/null [Exit 1] ``` vs ``` % paftools.js sam2paf 2>/dev/null Usage: paftools.js sam2paf [options] Options: -p convert primary...

close for Fasta object

2

There isn't a way to close a pyfastx.Fasta object, while would be consistent with python open, Have Fasta object as a context manager as well would be great. P.S. wow,...

https://luigi.readthedocs.io/en/stable/index.html has the sections luigi luigi.contrib luigi.tools luigi.local_target however , they are nearly empty

Toil-Internal Scheduler to run multiple Toil jobs per Batch System job, to make Toil jobs lightweight

2

General note: Toil is a pipeline manager that sits on top of cluster or cloud schedulers. This is the same niche as filled by Cromwell and Nextflow. It may be...

If the disk where a FileJobStore is stored fills up, Toil can get into a state where the root job does not exist, but neither does the ultimate source for its promised return value

3

inconsistent state after running out of disk space might be the cause of this: https://github.com/ComparativeGenomicsToolkit/cactus/issues/909 wastes a month of compute ┆Issue is synchronized with this [Jira Story](https://ucsc-cgl.atlassian.net/browse/TOIL-1270) ┆Issue Number: TOIL-1270