At TowerArchiver resolve envar paths relative to baseDir #3438
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Signed-off-by: Jordi Deu-Pons <[email protected]>
pditommaso
reviewed
Nov 28, 2022
plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerArchiver.groovy
Outdated
Show resolved
Hide resolved
|
I've realized that previous solution was wrong because I was assuming that |
pditommaso
pushed a commit
that referenced
this pull request
Nov 29, 2022
… skip] Signed-off-by: Jordi Deu-Pons <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description
When archiving files defined in an environment variable, we should assume that they are relative paths to
baseDirno to the current working directory.Example
Given
NXF_ARCHIVE_DIR="/scratch,s3://fusionfs/archived"when running a normal pipeline with Tower we have for example this variableNXF_OUT_FILE=nf-3rvDYTUlUhJ1Ge.txtthat here it ends resolved to this absolute path/3rvDYTUlUhJ1Ge.txtbecause the launcher is running at/folder. But then here it is discarded becausebaseDiris/scratch(extracted fromNXF_ARCHIVE_DIR). Notice that both files (/3rvDYTUlUhJ1Ge.txtand/scratch/3rvDYTUlUhJ1Ge.txt) exists because the saveCacheFiles has copied them.