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Feature/publishing updates #289
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- Options are now 'copy', 'link', 'symlink', etc. and are set in params.utils.publish.mode - Default value is 'link' - Fixes #265
- Avoid duplicating the input file, this is replaced with a hard link - Input/output file collisions are avoided by renaming the input file before creating the link - SC__PUBLISH_PROXY is removed from the workflow. The PUBLISH workflow now only needs a single process (instead of two) to publish a file
- Uses single_sample + two clustering parameters
dweemx
approved these changes
Jan 20, 2021
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Updates to the publishing system:
copy). Default value is to use hardlinks. ([BUG] Failed to publish file across filesystems #265)publishworkflow:SC__PUBLISHprocess to use hard links instead of copying internally. This partially addresses [BUG] Publish processes are not cached when resuming #258 (by avoiding making additional copies of the published file in the work directory upon each resume), but the process still does not cache.SC__PUBLISH_PROXYstep is no longer needed and is removed. No longer need two processes to publish one file.