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quiltdata / nf-quilt

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debug-validation #207

Closed drernie closed 2 months ago

drernie commented 2 months ago

Running with an S3 URI or nf-quilt@0.4.5 completes successfully.

Running with the latest nf-quilt plugin crashes during the input validation phase after this error:

ERROR ~ No such file or directory: /tmp/QuiltPackage5049614505086286284/QuiltPackage.bfx_input_index_fetchngs_cellarity_nfcore_fetchngs_tpdi_292/pipeline_info/params_2024-06-11_20-17-30.json

Such a hard error it does not generate a log! Implies we are not catching the error somewhere.

drernie commented 2 months ago

./launch.sh run 'https://github.com/nf-core/fetchngs' \ -name test_fetchngs \ -params-file ./fetchngs-params.json \ -with-tower \ -r 1.12.0 \ -profile docker \ -latest

N E X T F L O W ~ version 24.03.0-edge

Pulling nf-core/fetchngs ... downloaded from https://github.com/nf-core/fetchngs.git Launching https://github.com/nf-core/fetchngs [test_fetchngs] DSL2 - revision: 8ec2d934f9 [1.12.0]

ERROR ~ Cannot invoke "org.pf4j.Plugin.start()" because the return value of "org.pf4j.PluginWrapper.getPlugin()" is null

drernie commented 2 months ago

Huh

installing nf-quilt/sarek from quilt-example...
ERROR ~ failed to install nf-quilt/sarek

 -- Check '.nextflow.log' file for details
ERROR ~ Install is not supported on dev mode - Missing plugin nf-validation
drernie commented 2 months ago

Okay, I find this error with sarek also:

../nextflow/nextflow run nf-core/sarek -profile test,docker -plugins nf-quilt@0.7.12 --outdir "quilt+s3://quilt-example#package=nf-quilt/sarek"

 N E X T F L O W   ~  version 24.04.0-edge

Launching `https://github.com/nf-core/sarek` [crazy_newton] DSL2 - revision: b5b766d3b4 [master]

installing nf-quilt/sarek from quilt-example...
ERROR ~ failed to install nf-quilt/sarek

 -- Check '.nextflow.log' file for details
ERROR ~ No such file or directory: /var/folders/tz/8q322ht10qzf9pswh01zv6880000gp/T/QuiltPackage1814548995306102923/QuiltPackage.quilt_example_nf_quilt_sarek/pipeline_info/params_2024-06-13_12-12-27.json

 -- Check script '/Users/ernest/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/utils_nfcore_sarek_pipeline/../../nf-core/utils_nextflow_pipeline/main.nf' at line: 85 or see '.nextflow.log' file for more details
drernie commented 2 months ago

[Ah! When I use nf-quilt latest instead of 0.7.11, I get the error.] DUE TO TYPO

drernie commented 2 months ago

Hmm. Can't run nf-validation in dev mode, and get WARN: Path integrity check failed when I try to run production.

drernie commented 2 months ago

Doh. nf-quilt failed due to typo. Also, v12 wasn't in public repo.

Checking again to see if v9 or v12 actually makes the default nf-quilt job fail. Also trying fetchngs with v12.

drernie commented 2 months ago

Sigh. v0.7.12 has the same problem. AND testing nf-quilt default (0.7.9) doesn't give me a valid error :-(

Downloading plugin nf-quilt@0.7.12
installing nf-core/fetchngs from nf-core-gallery...
Children: [ccle_ids.csv]
Downloading plugin nf-validation@1.1.3
ERROR ~ No such file or directory: /tmp/QuiltPackage9630287772571825406/QuiltPackage.nf_core_gallery_nf_core_fetchngs/pipeline_info/params_2024-06-13_23-27-47.json
 -- Check script '.nextflow/assets/nf-core/fetchngs/./subworkflows/local/utils_nfcore_fetchngs_pipeline/../../nf-core/utils_nextflow_pipeline/main.nf' at line: 85 or see 'nf-3UrUPdcJgiOeqi.log' file for more details
drernie commented 2 months ago

Okay, can reproduce locally with make sarek NF_BIN=../nextflow/nextflow nextflow.log

drernie commented 2 months ago 
    at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:92)
    at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
    at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
    at java.base/sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:291)
    at java.base/sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:104)
    at java.base/java.nio.file.Files.delete(Files.java:1152)
    at nextflow.quilt.nio.QuiltPath.deinstall(QuiltPath.groovy:85)
    at nextflow.quilt.nio.QuiltFileSystemProvider.upload(QuiltFileSystemProvider.groovy:151)
    at nextflow.file.FileHelper.copyPath(FileHelper.groovy:959)