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nf-core / tools

Python package with helper tools for the nf-core community.
https://nf-co.re
MIT License
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can't create nf-core.yml file #3002

Closed paulsenlab closed 3 months ago

paulsenlab commented 4 months ago

Have you checked the docs?

Description of the bug

when I run "nf-core modules install deeptmhmm", the error "WARNING 'repository_type' not defined in .nf-core.yml " occurs.

Prompts to create this and add configuration then lead to an error output. The issue seems to that ".nf-core.yml" is being writen to the root directory ie "/.nf-core.yml. Is there an environmental variable or path that can be set to avoid this behaviour?

Command used and terminal output

(virtualnextflow) liamelbourne [virtualnextflow] $ nf-core modules install deeptmhmm

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.14.1 - https://nf-co.re

WARNING  'repository_type' not defined in .nf-core.yml                                                                                                                                                                                                                                                
? Is this repository an nf-core pipeline or a fork of nf-core/modules? nf-core/modules
INFO     To avoid this prompt in the future, add the 'repository_type' key to your .nf-core.yml file.                                                                                                                                                                                                 
? Would you like me to add this config now? [y/n] (y): 
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /Users/liamelbourne/virtualnextflow/bin/nf-core:8 in <module>                                    │
│                                                                                                  │
│   5 from nf_core.__main__ import run_nf_core                                                     │
│   6 if __name__ == '__main__':                                                                   │
│   7 │   sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])                         │
│ ❱ 8 │   sys.exit(run_nf_core())                                                                  │
│   9                                                                                              │
│                                                                                                  │
│ /Users/liamelbourne/virtualnextflow/lib/python3.12/site-packages/nf_core/__main__.py:150 in      │
│ run_nf_core                                                                                      │
│                                                                                                  │
│    147 │   │   │   log.debug(f"Could not check latest version: {e}")                             │
│    148 │   │   stderr.print("\n")                                                                │
│    149 │   # Launch the click cli                                                                │
│ ❱  150 │   nf_core_cli(auto_envvar_prefix="NFCORE")                                              │
│    151                                                                                           │
│    152                                                                                           │
│    153 @tui()                                                                                    │
│                                                                                                  │
│ /Users/liamelbourne/virtualnextflow/lib/python3.12/site-packages/rich_click/rich_command.py:367  │
│ in __call__                                                                                      │
│                                                                                                  │
│   364 │   │   # Include this here because I run into a false warning                             │
│   365 │   │   # in the PyCharm IDE otherwise; for some reason PyCharm doesn't                    │
│   366 │   │   # seem to think RichGroups are callable. (No issues with Mypy, though.)            │
│ ❱ 367 │   │   return super().__call__(*args, **kwargs)                                           │
│   368                                                                                            │
│   369                                                                                            │
│   370 class RichCommandCollection(CommandCollection, RichGroup):                                 │
│                                                                                                  │
│ /Users/liamelbourne/virtualnextflow/lib/python3.12/site-packages/click/core.py:1157 in __call__  │
│                                                                                                  │
│   1154 │                                                                                         │
│   1155 │   def __call__(self, *args: t.Any, **kwargs: t.Any) -> t.Any:                           │
│   1156 │   │   """Alias for :meth:`main`."""                                                     │
│ ❱ 1157 │   │   return self.main(*args, **kwargs)                                                 │
│   1158                                                                                           │
│   1159                                                                                           │
│   1160 class Command(BaseCommand):                                                               │
│                                                                                                  │
│ /Users/liamelbourne/virtualnextflow/lib/python3.12/site-packages/rich_click/rich_command.py:152  │
│ in main                                                                                          │
│                                                                                                  │
│   149 │   │   try:                                                                               │
│   150 │   │   │   try:                                                                           │
│   151 │   │   │   │   with self.make_context(prog_name, args, **extra) as ctx:                   │
│ ❱ 152 │   │   │   │   │   rv = self.invoke(ctx)                                                  │
│   153 │   │   │   │   │   if not standalone_mode:                                                │
│   154 │   │   │   │   │   │   return rv                                                          │
│   155 │   │   │   │   │   # it's not safe to `ctx.exit(rv)` here!                                │
│                                                                                                  │
│ /Users/liamelbourne/virtualnextflow/lib/python3.12/site-packages/click/core.py:1688 in invoke    │
│                                                                                                  │
│   1685 │   │   │   │   super().invoke(ctx)                                                       │
│   1686 │   │   │   │   sub_ctx = cmd.make_context(cmd_name, args, parent=ctx)                    │
│   1687 │   │   │   │   with sub_ctx:                                                             │
│ ❱ 1688 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))               │
│   1689 │   │                                                                                     │
│   1690 │   │   # In chain mode we create the contexts step by step, but after the                │
│   1691 │   │   # base command has been invoked.  Because at that point we do not                 │
│                                                                                                  │
│ /Users/liamelbourne/virtualnextflow/lib/python3.12/site-packages/click/core.py:1688 in invoke    │
│                                                                                                  │
│   1685 │   │   │   │   super().invoke(ctx)                                                       │
│   1686 │   │   │   │   sub_ctx = cmd.make_context(cmd_name, args, parent=ctx)                    │
│   1687 │   │   │   │   with sub_ctx:                                                             │
│ ❱ 1688 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))               │
│   1689 │   │                                                                                     │
│   1690 │   │   # In chain mode we create the contexts step by step, but after the                │
│   1691 │   │   # base command has been invoked.  Because at that point we do not                 │
│                                                                                                  │
│ /Users/liamelbourne/virtualnextflow/lib/python3.12/site-packages/click/core.py:1434 in invoke    │
│                                                                                                  │
│   1431 │   │   │   echo(style(message, fg="red"), err=True)                                      │
│   1432 │   │                                                                                     │
│   1433 │   │   if self.callback is not None:                                                     │
│ ❱ 1434 │   │   │   return ctx.invoke(self.callback, **ctx.params)                                │
│   1435 │                                                                                         │
│   1436 │   def shell_complete(self, ctx: Context, incomplete: str) -> t.List["CompletionItem"]:  │
│   1437 │   │   """Return a list of completions for the incomplete value. Looks                   │
│                                                                                                  │
│ /Users/liamelbourne/virtualnextflow/lib/python3.12/site-packages/click/core.py:783 in invoke     │
│                                                                                                  │
│    780 │   │                                                                                     │
│    781 │   │   with augment_usage_errors(__self):                                                │
│    782 │   │   │   with ctx:                                                                     │
│ ❱  783 │   │   │   │   return __callback(*args, **kwargs)                                        │
│    784 │                                                                                         │
│    785 │   def forward(                                                                          │
│    786 │   │   __self, __cmd: "Command", *args: t.Any, **kwargs: t.Any  # noqa: B902             │
│                                                                                                  │
│ /Users/liamelbourne/virtualnextflow/lib/python3.12/site-packages/click/decorators.py:33 in       │
│ new_func                                                                                         │
│                                                                                                  │
│    30 │   """                                                                                    │
│    31 │                                                                                          │
│    32 │   def new_func(*args: "P.args", **kwargs: "P.kwargs") -> "R":                            │
│ ❱  33 │   │   return f(get_current_context(), *args, **kwargs)                                   │
│    34 │                                                                                          │
│    35 │   return update_wrapper(new_func, f)                                                     │
│    36                                                                                            │
│                                                                                                  │
│ /Users/liamelbourne/virtualnextflow/lib/python3.12/site-packages/nf_core/__main__.py:839 in      │
│ modules_install                                                                                  │
│                                                                                                  │
│    836 │   from nf_core.modules import ModuleInstall                                             │
│    837 │                                                                                         │
│    838 │   try:                                                                                  │
│ ❱  839 │   │   module_install = ModuleInstall(                                                   │
│    840 │   │   │   dir,                                                                          │
│    841 │   │   │   force,                                                                        │
│    842 │   │   │   prompt,                                                                       │
│                                                                                                  │
│ /Users/liamelbourne/virtualnextflow/lib/python3.12/site-packages/nf_core/modules/install.py:16   │
│ in __init__                                                                                      │
│                                                                                                  │
│   13 │   │   no_pull=False,                                                                      │
│   14 │   │   installed_by=False,                                                                 │
│   15 │   ):                                                                                      │
│ ❱ 16 │   │   super().__init__(                                                                   │
│   17 │   │   │   pipeline_dir,                                                                   │
│   18 │   │   │   "modules",                                                                      │
│   19 │   │   │   force=force,                                                                    │
│                                                                                                  │
│ /Users/liamelbourne/virtualnextflow/lib/python3.12/site-packages/nf_core/components/install.py:3 │
│ 5 in __init__                                                                                    │
│                                                                                                  │
│    32 │   │   no_pull=False,                                                                     │
│    33 │   │   installed_by=False,                                                                │
│    34 │   ):                                                                                     │
│ ❱  35 │   │   super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)        │
│    36 │   │   self.force = force                                                                 │
│    37 │   │   self.prompt = prompt                                                               │
│    38 │   │   self.sha = sha                                                                     │
│                                                                                                  │
│ /Users/liamelbourne/virtualnextflow/lib/python3.12/site-packages/nf_core/components/components_c │
│ ommand.py:40 in __init__                                                                         │
│                                                                                                  │
│    37 │   │   self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress)        │
│    38 │   │   self.hide_progress = hide_progress                                                 │
│    39 │   │   self.no_prompts = no_prompts                                                       │
│ ❱  40 │   │   self._configure_repo_and_paths()                                                   │
│    41 │                                                                                          │
│    42 │   def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None:                  │
│    43 │   │   """                                                                                │
│                                                                                                  │
│ /Users/liamelbourne/virtualnextflow/lib/python3.12/site-packages/nf_core/components/components_c │
│ ommand.py:53 in _configure_repo_and_paths                                                        │
│                                                                                                  │
│    50 │   │                                                                                      │
│    51 │   │   try:                                                                               │
│    52 │   │   │   if self.dir:                                                                   │
│ ❱  53 │   │   │   │   self.dir, self.repo_type, self.org = get_repo_info(self.dir, use_prompt=   │
│    54 │   │   │   else:                                                                          │
│    55 │   │   │   │   self.repo_type = None                                                      │
│    56 │   │   │   │   self.org = ""                                                              │
│                                                                                                  │
│ /Users/liamelbourne/virtualnextflow/lib/python3.12/site-packages/nf_core/components/components_u │
│ tils.py:47 in get_repo_info                                                                      │
│                                                                                                  │
│    44 │   │   # Save the choice in the config file                                               │
│    45 │   │   log.info(f"To avoid this prompt in the future, add the 'repository_type' key to    │
│    46 │   │   if rich.prompt.Confirm.ask("[bold][blue]?[/] Would you like me to add this confi   │
│ ❱  47 │   │   │   with open(config_fn, "a+") as fh:                                              │
│    48 │   │   │   │   fh.write(f"repository_type: {repo_type}\n")                                │
│    49 │   │   │   │   log.info(f"Config added to '{config_fn.name}'")                            │
│    50                                                                                            │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
OSError: [Errno 30] Read-only file system: '/.nf-core.yml'
(virtualnextflow) liamelbourne [virtualnextflow] $

Relevant files

(virtualnextflow) liamelbourne [virtualnextflow] $ cat .nextflow.log May-27 15:46:45.501 [main] DEBUG nextflow.cli.Launcher - $> nextflow run hello May-27 15:46:45.541 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.04.1 May-27 15:46:45.564 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/liamelbourne/.nextflow/plugins; core-plugins: nf-amazon@2.5.2,nf-azure@1.6.0,nf-cloudcache@0.4.1,nf-codecommit@0.2.0,nf-console@1.1.3,nf-ga4gh@1.3.0,nf-google@1.13.2,nf-tower@1.9.1,nf-wave@1.4.2 May-27 15:46:45.570 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] May-27 15:46:45.571 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] May-27 15:46:45.572 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode May-27 15:46:45.583 [main] INFO org.pf4j.AbstractPluginManager - No plugins May-27 15:46:45.589 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /Users/liamelbourne/.nextflow/scm May-27 15:46:45.593 [main] DEBUG nextflow.scm.AssetManager - Listing projects in folder: /Users/liamelbourne/.nextflow/assets May-27 15:46:45.608 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] May-27 15:46:45.614 [main] INFO nextflow.cli.CmdRun - Pulling nextflow-io/hello ... May-27 15:46:45.616 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nextflow-io/hello/contents/nextflow.config May-27 15:46:46.353 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nextflow-io/hello/contents/main.nf May-27 15:46:46.702 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nextflow-io/hello May-27 15:46:47.084 [main] DEBUG nextflow.scm.AssetManager - Pulling nextflow-io/hello -- Using remote clone url: https://github.com/nextflow-io/hello.git May-27 15:46:51.354 [main] INFO nextflow.cli.CmdRun - downloaded from https://github.com/nextflow-io/hello.git May-27 15:46:51.369 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /Users/liamelbourne/.nextflow/assets/nextflow-io/hello/nextflow.config May-27 15:46:51.369 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/liamelbourne/.nextflow/assets/nextflow-io/hello/nextflow.config May-27 15:46:51.375 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /Users/liamelbourne/.nextflow/secrets/store.json May-27 15:46:51.376 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@7015ebef] - activable => nextflow.secret.LocalSecretsProvider@7015ebef May-27 15:46:51.379 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard May-27 15:46:51.399 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default May-27 15:46:51.399 [main] DEBUG nextflow.cli.CmdRun - Launching https://github.com/nextflow-io/hello [elated_saha] DSL2 - revision: 7588c46ffe [master] May-27 15:46:51.400 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] May-27 15:46:51.400 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] May-27 15:46:51.423 [main] DEBUG nextflow.Session - Session UUID: c1ce7fae-c30b-419e-aaf5-22b4dda385ea May-27 15:46:51.424 [main] DEBUG nextflow.Session - Run name: elated_saha May-27 15:46:51.424 [main] DEBUG nextflow.Session - Executor pool size: 16 May-27 15:46:51.427 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null May-27 15:46:51.448 [main] DEBUG nextflow.cli.CmdRun - Version: 24.04.1 build 5913 Created: 20-05-2024 09:48 UTC (19:48 AEDT) System: Mac OS X 14.5 Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 21.0.3 Encoding: UTF-8 (UTF-8) Process: 10476@LiamMacBookPro [10.69.40.106] CPUs: 16 - Mem: 128 GB (56.4 GB) - Swap: 0 (0) - Virtual threads ON May-27 15:46:51.458 [main] DEBUG nextflow.Session - Work-dir: /Users/liamelbourne/virtualnextflow/work [Mac OS X] May-27 15:46:51.459 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /Users/liamelbourne/.nextflow/assets/nextflow-io/hello/bin May-27 15:46:51.465 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] May-27 15:46:51.469 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory May-27 15:46:51.484 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory May-27 15:46:51.488 [main] DEBUG nextflow.util.CustomPoolFactory - Creating virtual thread pool May-27 15:46:51.519 [main] DEBUG nextflow.Session - Session start May-27 15:46:51.620 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution May-27 15:46:51.665 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-27 15:46:51.665 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-27 15:46:51.668 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local May-27 15:46:51.671 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=16; memory=128 GB; capacity=16; pollInterval=100ms; dumpInterval=5m May-27 15:46:51.672 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) May-27 15:46:51.707 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: sayHello May-27 15:46:51.707 [main] DEBUG nextflow.Session - Igniting dataflow network (2) May-27 15:46:51.708 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > sayHello May-27 15:46:51.708 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_45e06ae60646ee81: /Users/liamelbourne/.nextflow/assets/nextflow-io/hello/main.nf May-27 15:46:51.708 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination May-27 15:46:51.708 [main] DEBUG nextflow.Session - Session await May-27 15:46:51.782 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-27 15:46:51.782 [Task submitter] INFO nextflow.Session - [be/4567f2] Submitted process > sayHello (4) May-27 15:46:51.786 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-27 15:46:51.786 [Task submitter] INFO nextflow.Session - [41/c5653b] Submitted process > sayHello (1) May-27 15:46:51.789 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-27 15:46:51.789 [Task submitter] INFO nextflow.Session - [e4/04eae7] Submitted process > sayHello (2) May-27 15:46:51.802 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: sayHello (4); status: COMPLETED; exit: 0; error: -; workDir: /Users/liamelbourne/virtualnextflow/work/be/4567f2fa4f8f4d523fa83905ba6a46] May-27 15:46:51.803 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-27 15:46:51.804 [Task submitter] INFO nextflow.Session - [42/4d0b10] Submitted process > sayHello (3) May-27 15:46:51.805 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: sayHello (1); status: COMPLETED; exit: 0; error: -; workDir: /Users/liamelbourne/virtualnextflow/work/41/c5653bada60d540ecf4139b1c6af44] May-27 15:46:51.807 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: sayHello (2); status: COMPLETED; exit: 0; error: -; workDir: /Users/liamelbourne/virtualnextflow/work/e4/04eae733d10f4e4d33adf9005db3ee] May-27 15:46:51.811 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: sayHello (3); status: COMPLETED; exit: 0; error: -; workDir: /Users/liamelbourne/virtualnextflow/work/42/4d0b10fbbd51348463f1b40233156a] May-27 15:46:51.813 [main] DEBUG nextflow.Session - Session await > all processes finished May-27 15:46:51.914 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop May-27 15:46:51.914 [main] DEBUG nextflow.Session - Session await > all barriers passed May-27 15:46:51.915 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false) May-27 15:46:51.917 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=4; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=3ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=4; peakCpus=4; peakMemory=0; ] May-27 15:46:51.956 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done May-27 15:46:51.962 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) May-27 15:46:51.962 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye (virtualnextflow) liamelbourne [virtualnextflow] $

System information

nextflow version 24.04.1.5913 Docker version 26.1.3, build b72abbb6f0 Apple MacBook Pro M3

local

macOS 14.5

mirpedrol commented 4 months ago

Hi @paulsenlab, thanks for pointing this error out. This PR will fix the bug, once it's merged you can try running the same command with the dev version of nf-core tools. Otherwise you can manually recreate the .nf-core.yml file containing repository_type: pipeline

paulsenlab commented 3 months ago

Hi,

Apologies, is there any other workaround you can suggest? Creating a file in a read-only filesystem is not a great solution, I’d have to disable SIP to do that, and would rather not. Surely I can specifiy a directory or path for the file to reside in, without actually changing the code?

Regards, Liam.

On 27 May 2024, at 9:10 PM, Júlia Mir Pedrol @.***> wrote:

Hi @paulsenlabhttps://github.com/paulsenlab, thanks for pointing this error out. Thishttps://github.com/nf-core/tools/pull/3003 PR will fix the bug, once it's merged you can try running the same command with the dev version of nf-core toolshttps://github.com/nf-core/tools?tab=readme-ov-file#development-version. Otherwise you can manually recreate the .nf-core.yml file containing repository_type: pipeline

— Reply to this email directly, view it on GitHubhttps://github.com/nf-core/tools/issues/3002#issuecomment-2133246139, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABVLJN62ZKINWYKZLPHRPRLZEMICFAVCNFSM6AAAAABIK6IGCKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZTGI2DMMJTHE. You are receiving this because you were mentioned.Message ID: @.***>

mirpedrol commented 3 months ago

@paulsenlab sorry I didn't explain properly, the file must be created in the root directory of your pipeline

mirpedrol commented 3 months ago

I will close this issue now, it's solved on the dev version. Please don't hesitate to re-open it if the error continues.