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CHANGELOG.md

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CHANGELOG

This document tracks changes to the master branch of the profile.

Unreleased

Added

  • jobscript_timeout cookiecutter variable that sets the number of seconds to wait for the jobscript to exist before submiting the job

0.3.0 - 13/07/2022

Added

  • Exposed max_status_check and wait_between_tries for status checker [#48]

Changed

  • Cluster cancel is now a script instead of the bkill command in order to handle the log file paths that come with the job ID [#55]

0.2.0 - 28/05/2022

Added

  • Default project in cookiecutter
  • Cluster cancel (--cluster-cancel) command (bkill)

Removed

  • Default threads in cookiecutter

Changed

  • Default project and queue will be removed from the submission command if they are present in the lsf.yaml

Fixed

  • Support quoted jobid from snakemake>=v7.1.1 [#45]

0.1.2 - 01/04/2021

Added

  • Support for runtime resources [#38]

0.1.1 - 16/03/2021

Added

  • Support for complex quote-expansion via shlex [#39]]
  • Function docstrings in lsf_config.py for documentation

0.1.0 - 18/01/2021

Added

  • Version tagging to allow for user notification of changes to functionality

Changed

  • Parameters given in the config file are now deduplicated. For instance, if a default for -q is given, and a rule specifies -q also, the rule's value for -q is chosen. Previously, parameters were just concatenated [#36]

23/10/2020

Changed

  • When log file is not found, we now return failed instead of running. Returning running was effectively causing an infinite loop.
  • Unknown line status now also returns failed instead of raising an error. Raising errors without returning a status causes problems with the snakemake master process.

09/04/2020

Added:

  • Look at the log file if bsub returns an empty job status. See #5 for more information.
  • Allow specifying per-rule cluster resource settings (similar to deprecated cluster config). See #15 and #7 for more information.
  • Added a CONTRIBUTING.md document #15
  • TESTS!! A big thanks to @leoisl for getting this off the ground. See #12 for a request to add him to the repository as a contributor.
  • Add CHANGELOG to track major changes.

Changed:

  • The naming of log files. See #14 and #15 for more information.
  • Robust memory handling #18 and #20
  • README is now much more thorough #15