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Update support for local TES executor with GA4GH TES Plugin #4608

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merged 3 commits into from
Feb 12, 2024
Merged

Update support for local TES executor with GA4GH TES Plugin #4608

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dc8997d
Update behavior to only pass bin files as inputs to the TES task
lbeckman314 Feb 2, 2024
e0f3eeb
Add null check for remoteBinDir as TES Input
lbeckman314 Feb 2, 2024
4c8c21b
Revert unneeded import in TesTaskHandler.groovy
lbeckman314 Feb 2, 2024
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1 change: 1 addition & 0 deletions plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/executor/TesFileCopyStrategy.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -113,6 +113,7 @@ class TesFileCopyStrategy implements ScriptFileCopyStrategy {
copy.remove('PATH')
// when a remote bin directory is provide managed it properly
if( remoteBinDir ) {
result << "mkdir \$PWD/nextflow-bin/\n"
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This line resolves an error we were encountering when attempting to run the .command.run file within the container:

root@<container id>:/work $ ./.command.run
cp: cannot create regular file '/work/nextflow-bin/': Not a directory

result << "cp -r ${remoteBinDir}/* \$PWD/nextflow-bin/\n"
result << "chmod +x \$PWD/nextflow-bin/* || true\n"
result << "export PATH=\$PWD/nextflow-bin:\$PATH\n"
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8 changes: 7 additions & 1 deletion plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/executor/TesTaskHandler.groovy
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Expand Up @@ -190,6 +190,11 @@ class TesTaskHandler extends TaskHandler {
body.addInputsItem(inItem(scriptFile))
body.addInputsItem(inItem(wrapperFile))

Path remoteBinDir = executor.getRemoteBinDir()
if (remoteBinDir) {
body.addInputsItem(inItem(remoteBinDir, null, true))
}
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This is where each file in bin is added as a TES input.


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@lbeckman314 lbeckman314 Feb 2, 2024 •
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Updated here to only pass the bin directory as a TES Input (passes the directory itself as opposed to individual files, need to confirm that this is compatible with the TES Schema).

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@lbeckman314 lbeckman314 Feb 2, 2024 •
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Confirmed with @kellrott that passing a directory as a TES input is compatible with the schema (as long as all items in that directory are recursively added as TES inputs by the executor).

// add task input files
if(inputFile.exists()) body.addInputsItem(inItem(inputFile))

Expand Down Expand Up @@ -234,11 +239,12 @@ class TesTaskHandler extends TaskHandler {
return size != null ? ((double)size.bytes)/1073741824 : null
}

private TesInput inItem( Path realPath, String fileName = null) {
private TesInput inItem( Path realPath, String fileName = null, boolean isBin = false) {
def result = new TesInput()
result.url = realPath.toUriString()
result.path = fileName ? "$WORK_DIR/$fileName" : "$WORK_DIR/${realPath.getName()}"
log.trace "[TES] Adding INPUT file: $result"
result.path = isBin ? realPath : result.path
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@lbeckman314 lbeckman314 Feb 2, 2024 •
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This will result in the bin directory being mounted in the container at the same path as Nextflow's main working directory.

All other "non-bin" TES inputs will be mounted at /work by default in the container.

return result
}

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