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nf-core / fetchngs

Pipeline to fetch metadata and raw FastQ files from public databases
https://nf-co.re/fetchngs
MIT License
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nf-validation-1.1.3: Operation not supported #272

Closed adomingues closed 7 months ago

adomingues commented 7 months ago

Description of the bug

(possibly related to #254 ?)

I ran into this error while testing the pipeline on a small server (VM):

N E X T F L O W  ~  version 23.10.1
Launching `https://github.com/nf-core/fetchngs` [hungry_ptolemy] DSL2 - revision: 04ee5031a4 [1.11.0]
ERROR ~ .nextflow/plr/080f1e1a-75c1-40ed-a3c4-8e3ffbef76da/nf-validation-1.1.3: Operation not supported

 -- Check '.nextflow.log' file for details

Log file below. I initially though this was an issue with my .nextflow/plugins being too old so I removed it, but the error remains.

Command used and terminal output

nextflow run nf-core/fetchngs -profile test,singularity -revision 1.11.0 --outdir ./test

Relevant files

nextflow.log

System information

nextflow version 23.10.1.5891

local computer (VM on a server): OS: Ubuntu 20.04.6 LTS x86_64 Host: KVM RHEL 7.0.0 PC (i440FX + PIIX, 1996) Kernel: 5.4.0-170-generic Shell: bash 5.0.17 CPU: Intel Xeon (Skylake, IBRS) (32) @ 2.294GHz GPU: 00:02.0 Red Hat, Inc. QXL paravirtual graphic card Memory: 663MiB / 64302MiB

adomingues commented 7 months ago

oddly enough testing on my laptop there is a different error:

nextflow run nf-core/fetchngs -profile test,singularity -revision 1.11.0  --outdir ./test
N E X T F L O W  ~  version 23.10.1
Launching `https://github.com/nf-core/fetchngs` [hopeful_perlman] DSL2 - revision: 04ee5031a4 [1.11.0]
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/fetchngs v1.11.0-g04ee503
------------------------------------------------------
Core Nextflow options
  revision                  : 1.11.0
  runName                   : hopeful_perlman
  containerEngine           : singularity
  launchDir                 : /home/adomingues/sandbox
  workDir                   : /home/adomingues/sandbox/work
  projectDir                : /home/adomingues/.nextflow/assets/nf-core/fetchngs
  userName                  : adomingues
  profile                   : test,singularity
  configFiles               : 

Input/output options
  input                     : ${projectDir}/tests/sra_ids_test.csv
  outdir                    : ./test

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Max job request options
  max_cpus                  : 2
  max_memory                : 6.GB
  max_time                  : 6.h

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/fetchngs for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.5070524

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/fetchngs/blob/master/CITATIONS.md
------------------------------------------------------
ERROR ~ ERROR: Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --input: the file or directory '${projectDir}/tests/sra_ids_test.csv' does not exist.

 -- Check script '/home/adomingues/.nextflow/assets/nf-core/fetchngs/./subworkflows/local/nf_core_fetchngs_utils/../../nf-core/nfvalidation_plugin_utils/main.nf' at line: 55 or see '.nextflow.log' file for more details

OS: Ubuntu 22.04.3 LTS x86_64 Host: 21CB009UGE ThinkPad X1 Carbon Gen 10 Kernel: 6.5.0-15-generic Shell: bash 5.1.16 CPU: 12th Gen Intel i7-1255U (12) @ 4.700GHz GPU: Intel Device 46a8 Memory: 9816MiB / 15681MiB

maxulysse commented 7 months ago

Can you try the dev branch?

adomingues commented 7 months ago

Sorry, I forgot to mention that I also tested it had the the error remains (this one the server which is ultimately where I want to test pipelines):

nextflow run nf-core/fetchngs -profile test,singularity -revision dev --outdir ./test
N E X T F L O W  ~  version 23.10.1
Launching `https://github.com/nf-core/fetchngs` [zen_borg] DSL2 - revision: 32952832ba [dev]
ERROR ~ .nextflow/plr/4bff1783-0896-407e-881e-7229e0d04070/nf-validation-1.1.3: Operation not supported

 -- Check '.nextflow.log' file for details

tail -20 .nextflow.log 
Feb-13 09:51:24.703 [main] ERROR nextflow.cli.Launcher - .nextflow/plr/4bff1783-0896-407e-881e-7229e0d04070/nf-validation-1.1.3: Operation not supported
java.nio.file.FileSystemException: .nextflow/plr/4bff1783-0896-407e-881e-7229e0d04070/nf-validation-1.1.3: Operation not supported
        at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
        at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
        at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116)
        at java.base/sun.nio.fs.UnixFileSystemProvider.createSymbolicLink(UnixFileSystemProvider.java:462)
        at java.base/java.nio.file.Files.createSymbolicLink(Files.java:1059)
        at nextflow.plugin.LocalPluginManager.createLink0(LocalPluginManager.groovy:117)
        at nextflow.plugin.LocalPluginManager.createLinkFromPath(LocalPluginManager.groovy:110)
        at nextflow.plugin.LocalPluginManager.loadPluginFromPath(LocalPluginManager.groovy:96)
        at nextflow.plugin.PluginUpdater.load0(PluginUpdater.groovy:335)
        at nextflow.plugin.PluginUpdater.installPlugin(PluginUpdater.groovy:197)
        at nextflow.plugin.PluginUpdater.prepareAndStart(PluginUpdater.groovy:144)
        at nextflow.plugin.PluginsFacade.start(PluginsFacade.groovy:328)
        at nextflow.plugin.PluginsFacade.start(PluginsFacade.groovy:333)
        at nextflow.plugin.PluginsFacade.load(PluginsFacade.groovy:232)
        at nextflow.plugin.Plugins.load(Plugins.groovy:56)
        at nextflow.cli.CmdRun.run(CmdRun.groovy:334)
        at nextflow.cli.Launcher.run(Launcher.groovy:500)
        at nextflow.cli.Launcher.main(Launcher.groovy:672)
adomingues commented 7 months ago

FYI I did another test, this time on an ec2 instance without any prior nextflow install - go / singlularity / nextflow were are all installed for the first time - and the error remains:

extflow run nf-core/fetchngs -profile test,singularity -revision 1.11.0 --input --outdir ./test
N E X T F L O W  ~  version 23.10.1
Pulling nf-core/fetchngs ...
 downloaded from https://github.com/nf-core/fetchngs.git
Launching `https://github.com/nf-core/fetchngs` [boring_lamport] DSL2 - revision: 04ee5031a4 [1.11.0]
Downloading plugin nf-validation@1.1.3
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/fetchngs v1.11.0-g04ee503
------------------------------------------------------
Core Nextflow options
  revision                  : 1.11.0
  runName                   : boring_lamport
  containerEngine           : singularity
  launchDir                 : /home/ubuntu
  workDir                   : /home/ubuntu/work
  projectDir                : /home/ubuntu/.nextflow/assets/nf-core/fetchngs
  userName                  : ubuntu
  profile                   : test,singularity
  configFiles               : 

Input/output options
  input                     : true
  outdir                    : ./test

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Max job request options
  max_cpus                  : 2
  max_memory                : 6.GB
  max_time                  : 6.h

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/fetchngs for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.5070524

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/fetchngs/blob/master/CITATIONS.md
------------------------------------------------------
ERROR ~ ERROR: Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --input: the file or directory 'true' does not exist.
* --input: expected type: String, found: Boolean (true)
maxulysse commented 7 months ago

--input takes a file into account, so this failure is expected.

adamrtalbot commented 7 months ago

This looks like a Java version error, which version of Java are you using?

java -version

Currently we require 11 - 21, we recommend using SDKMan: https://www.nextflow.io/docs/latest/getstarted.html#requirements

adomingues commented 7 months ago

--input takes a file into account, so this failure is expected.

My bad. Without --input:

nextflow run nf-core/fetchngs -profile test,singularity -revision 1.11.0 --outdir ./test
N E X T F L O W  ~  version 23.10.1
Launching `https://github.com/nf-core/fetchngs` [mighty_goldwasser] DSL2 - revision: 04ee5031a4 [1.11.0]
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/fetchngs v1.11.0-g04ee503
------------------------------------------------------
Core Nextflow options
  revision                  : 1.11.0
  runName                   : mighty_goldwasser
  containerEngine           : singularity
  launchDir                 : /home/ubuntu
  workDir                   : /home/ubuntu/work
  projectDir                : /home/ubuntu/.nextflow/assets/nf-core/fetchngs
  userName                  : ubuntu
  profile                   : test,singularity
  configFiles               : 

Input/output options
  input                     : ${projectDir}/tests/sra_ids_test.csv
  outdir                    : ./test

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Max job request options
  max_cpus                  : 2
  max_memory                : 6.GB
  max_time                  : 6.h

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/fetchngs for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.5070524

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/fetchngs/blob/master/CITATIONS.md
------------------------------------------------------
ERROR ~ ERROR: Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --input: the file or directory '${projectDir}/tests/sra_ids_test.csv' does not exist.

 -- Check script '.nextflow/assets/nf-core/fetchngs/./subworkflows/local/nf_core_fetchngs_utils/../../nf-core/nfvalidation_plugin_utils/main.nf' at line: 55 or see '.nextflow.log' file for more details

It can't find the input file so I will point directly to the file in the repo and this time the pipeline runs!

nextflow run nf-core/fetchngs -profile test,singularity -revision 1.11.0 --input https://raw.githubusercontent.com/nf-core/fetchngs/1.11.0/tests/sra_ids_test.csv --outdir ./test

-[nf-core/fetchngs] Pipeline completed successfully-
WARN: =============================================================================
  Please double-check the samplesheet that has been auto-created by the pipeline.

  Public databases don't reliably hold information such as strandedness
  information, controls etc

  All of the sample metadata obtained from the ENA has been appended
  as additional columns to help you manually curate the samplesheet before
  running nf-core/other pipelines.
===================================================================================

This tells me that the issue is not related to fetchngs but rather my nextflow install. I will close the issue but appreciate any pointers on purging an nextflow / nf-core installation in the hop that a fresh install will help me.

adomingues commented 7 months ago

This looks like a Java version error, which version of Java are you using?

java -version

Currently we require 11 - 21, we recommend using SDKMan: https://www.nextflow.io/docs/latest/getstarted.html#requirements

The version seems correct but openjdk:

java -version
openjdk version "11.0.21" 2023-10-17
OpenJDK Runtime Environment (build 11.0.21+9-post-Ubuntu-0ubuntu120.04)
OpenJDK 64-Bit Server VM (build 11.0.21+9-post-Ubuntu-0ubuntu120.04, mixed mode, sharing)

For reference, this is the version in the ec2 ubuntu instance in which the pipeline runs successfully:

java -version
openjdk version "11.0.21" 2023-10-17
OpenJDK Runtime Environment (build 11.0.21+9-post-Ubuntu-0ubuntu120.04)
OpenJDK 64-Bit Server VM (build 11.0.21+9-post-Ubuntu-0ubuntu120.04, mixed mode, sharing)
maxulysse commented 7 months ago

Can you try this one?

nextflow run nf-core/fetchngs -profile test,singularity -revision dev --outdir ./test

maxulysse commented 7 months ago

The '${projectDir}/tests/sra_ids_test.csv' does not exist is fixed now

adomingues commented 7 months ago

Can you try this one?

nextflow run nf-core/fetchngs -profile test,singularity -revision dev --outdir ./test

The nf-validation error is still there :(

nextflow run nf-core/fetchngs -profile test,singularity -revision dev --outdir ./test N E X T F L O W ~ version 23.10.1
Launching https://github.com/nf-core/fetchngs [voluminous_mandelbrot] DSL2 - revision: 32952832ba [dev] ERROR ~ .nextflow/plr/27bb8b0f-89d2-4c87-903a-726c7f161b3c/nf-validation-1.1.3: Operation not supported

cat .nextflow.log
Feb-13 12:05:25.266 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/fetchngs -profile test,singularity -revision dev --outdir ./test Feb-13 12:05:25.398 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.10.1
Feb-13 12:05:25.442 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/mnt/genomics/.nextflow/plugins; core-plugins: nf-amazon@2.1.4,nf-azure@1 .3.3,nf-cloudcache@0.3.0,nf-codecommit@0.1.5,nf-console@1.0.6,nf-ga4gh@1.1.0,nf-google@1.8.3,nf-tower@1.6.3,nf-wave@1.0.1
Feb-13 12:05:25.467 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Feb-13 12:05:25.469 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Feb-13 12:05:25.473 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Feb-13 12:05:25.490 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Feb-13 12:05:25.514 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /mnt/genomics/.nextflow/scm
Feb-13 12:05:26.809 [main] DEBUG nextflow.scm.AssetManager - Git config: /mnt/genomics/.nextflow/assets/nf-core/fetchngs/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/fetchng s.git
Feb-13 12:05:26.841 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Feb-13 12:05:26.858 [main] DEBUG nextflow.scm.AssetManager - Git config: /mnt/genomics/.nextflow/assets/nf-core/fetchngs/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/fetchng s.git
Feb-13 12:05:27.842 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /mnt/genomics/.nextflow/assets/nf-core/fetchngs/nextflow.config
Feb-13 12:05:27.846 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mnt/genomics/.nextflow/assets/nf-core/fetchngs/nextflow.config Feb-13 12:05:27.869 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: test,singularity
Feb-13 12:05:29.088 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, uzl_omics, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, ilifu, uge, rosalind_uge, lugh, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, pdc_kth, googlels, daisybio, eddie, medair, biowulf, apptainer, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, icr_davros, ceres, munin, arm, rosalind, hasta, cfc, uzh, ebi_codon_slurm, ebc, ku_sund_dangpu, ccga_dx, crick, marv in, biohpc_gen, shifter, mana, mamba, unc_lccc, wehi, awsbatch, wustl_htcf, imperial, maestro, software_license, genotoul, nci_gadi, abims, janelia, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester , vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, computerome, ucd_sonic, seg_globe, sanger, dkfz, pasteur, ethz_euler, test_full, imb, tuos_stanage, azurebatch, hki, crukmi, csiro_petrichor, docker, engaging, gis, hypatia, psmn, eva, nygc, fgcz, conda, crg, singularity, self_hosted_runner, uw_hyak_pedslabs, utd_sysbio, debug, genouest, cbe, phoenix, gitpod, seawul f, uod_hpc, fub_curta, uct_hpc, aws_tower, binac]
Feb-13 12:05:29.162 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Feb-13 12:05:29.163 [main] INFO nextflow.cli.CmdRun - Launching https://github.com/nf-core/fetchngs [voluminous_mandelbrot] DSL2 - revision: 32952832ba [dev]
Feb-13 12:05:29.164 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-validation@1.1.3]
Feb-13 12:05:29.164 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Feb-13 12:05:29.164 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-validation@1.1.3] Feb-13 12:05:29.164 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: 1.1.3
Feb-13 12:05:29.170 [main] ERROR nextflow.cli.Launcher - .nextflow/plr/27bb8b0f-89d2-4c87-903a-726c7f161b3c/nf-validation-1.1.3: Operation not supported
java.nio.file.FileSystemException: .nextflow/plr/27bb8b0f-89d2-4c87-903a-726c7f161b3c/nf-validation-1.1.3: Operation not supported
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111) at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116) at java.base/sun.nio.fs.UnixFileSystemProvider.createSymbolicLink(UnixFileSystemProvider.java:462)
at java.base/java.nio.file.Files.createSymbolicLink(Files.java:1059) at nextflow.plugin.LocalPluginManager.createLink0(LocalPluginManager.groovy:117) at nextflow.plugin.LocalPluginManager.createLinkFromPath(LocalPluginManager.groovy:110)
at nextflow.plugin.LocalPluginManager.loadPluginFromPath(LocalPluginManager.groovy:96)
at nextflow.plugin.PluginUpdater.load0(PluginUpdater.groovy:335)
at nextflow.plugin.PluginUpdater.installPlugin(PluginUpdater.groovy:197)
at nextflow.plugin.PluginUpdater.prepareAndStart(PluginUpdater.groovy:144)
at nextflow.plugin.PluginsFacade.start(PluginsFacade.groovy:328)
at nextflow.plugin.PluginsFacade.start(PluginsFacade.groovy:333)
at nextflow.plugin.PluginsFacade.load(PluginsFacade.groovy:232)
at nextflow.plugin.Plugins.load(Plugins.groovy:56)
at nextflow.cli.CmdRun.run(CmdRun.groovy:334)
at nextflow.cli.Launcher.run(Launcher.groovy:500)
at nextflow.cli.Launcher.main(Launcher.groovy:672)

adomingues commented 7 months ago

But I can confirm on the clean nextflow install that '${projectDir}/tests/sra_ids_test.csv' does not exist is fixed now

adamrtalbot commented 7 months ago

It looks like Nextflow is trying to make a symbolic link to or from the plugin directory but is failing. Here is the code that throws the error: https://github.com/nextflow-io/nextflow/blob/5e2ce9ed82ccbc70ec24a83e04f24b8d45855a78/modules/nf-commons/src/main/nextflow/plugin/LocalPluginManager.groovy#L115

Do you have permissions to write to $NXF_HOME? By default this is at $HOME/.nextflow. You could set NXF_HOME or NXF_PLUGINS_DIR to modify where the plugins are stored.

adomingues commented 7 months ago

Do you have permissions to write to $NXF_HOME? By default this is at $HOME/.nextflow.

In my system it's changed to a mount point, but I have write permissions (just tested with touch $NXF_HOME/test)

NXF_PLUGINS_DIR is in a subdir of NXF_HOME, for which I also have write permissions. I have set it to ~/.nf_plugins for testing, but the issue remains. 

nextflow run nf-core/fetchngs -profile test,singularity -revision dev --outdir ./test
N E X T F L O W  ~  version 23.10.1
Launching `https://github.com/nf-core/fetchngs` [backstabbing_visvesvaraya] DSL2 - revision: 32952832ba [dev]
ERROR ~ .nextflow/plr/d5f4a7bd-accd-4d3c-8033-0add9ef29a00/nf-validation-1.1.3: Operation not supported

 -- Check '.nextflow.log' file for details

P.S.: I did change many of the default NFX paths in this system due to limited space in /home, but until about a year ago I was running pipelines without issues. In the intervening year I have been using tower / aws so not much use until today.

adamrtalbot commented 7 months ago

Hmmm this is confusing!

adamrtalbot commented 7 months ago

OK consulted with Nextflow team, does your filesystem support symbolic links? Can you run the following to symlink the nf-validation directory to the working directory?

ln -s $NXF_HOME/plugins/nf-validation-1.1.3 .nextflow/plr/d5f4a7bd-accd-4d3c-8033-0add9ef29a00/nf-validation-1.1.3
adomingues commented 7 months ago

Here you go - it fails:

adomingues@vm-ad-genome:sandbox$ ls $NXF_HOME/plugins/nf-validation-1.1.3
classes  lib  META-INF
adomingues@vm-ad-genome:sandbox$ ls .nextflow/plr/d5f4a7bd-accd-4d3c-8033-0add9ef29a00/nf-validation-1.1.3
ls: cannot access '.nextflow/plr/d5f4a7bd-accd-4d3c-8033-0add9ef29a00/nf-validation-1.1.3': No such file or directory
adomingues@vm-ad-genome:sandbox$ ln -s $NXF_HOME/plugins/nf-validation-1.1.3 .nextflow/plr/d5f4a7bd-accd-4d3c-8033-0add9ef29a00/nf-validation-1.1.3
ln: failed to create symbolic link '.nextflow/plr/d5f4a7bd-accd-4d3c-8033-0add9ef29a00/nf-validation-1.1.3': No such file or directory
adomingues@vm-ad-genome:sandbox$ ll .nextflow/plr/
total 0
drwxr-xr-x 2 root root 0 Feb 13 15:38 ./
drwxr-xr-x 2 root root 0 Feb 13 15:38 ../
drwxr-xr-x 2 root root 0 Mai 16  2022 empty/
adamrtalbot commented 7 months ago

OK that seems to be the problem, your filesystem doesn't support symbolic links. What filesystem are you using?

adomingues commented 7 months ago

@adamrtalbot it's a cifs mount on linux. I am in touch our sys admin to get it sorted, cheers!

adomingues commented 7 months ago

@adamrtalbot I can confirm that after the changes to the file system everything is working as expected. Thanks!