error downloading singularity image from nf-core #16
Description
Description of the bug
I tried to pre-download the singularity image as suggested but hit an error. Any suggestions? Thanks in advance.
Command used and terminal output
? Choose compression type: none
INFO Saving 'systemsgenetics/entapnf'
Pipeline revision: '0.1.0'
Use containers: 'singularity'
Container library: 'quay.io'
Using $NXF_SINGULARITY_CACHEDIR': /home/jmy/bin/entapnf'
Output directory: 'systemsgenetics-entapnf_0.1.0'
Include default institutional configuration: 'True'
INFO Downloading centralised configs from GitHub
INFO Downloading workflow files from GitHub
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /home/jmy/miniconda3/bin/nf-core:10 in <module> │
│ │
│ 7 │
│ 8 if __name__ == '__main__': │
│ 9 │ sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0]) │
│ ❱ 10 │ sys.exit(run_nf_core()) │
│ 11 │
│ │
│ /home/jmy/miniconda3/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() │
│ │
│ /home/jmy/miniconda3/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): │
│ │
│ /home/jmy/miniconda3/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): │
│ │
│ /home/jmy/miniconda3/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! │
│ │
│ /home/jmy/miniconda3/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 │
│ │
│ /home/jmy/miniconda3/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 │
│ │
│ /home/jmy/miniconda3/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 │
│ │
│ /home/jmy/miniconda3/lib/python3.12/site-packages/nf_core/__main__.py:471 in download │
│ │
│ 468 │ │ container_cache_index, │
│ 469 │ │ parallel_downloads, │
│ 470 │ ) │
│ ❱ 471 │ dl.download_workflow() │
│ 472 │
│ 473 │
│ 474 # nf-core licences │
│ │
│ /home/jmy/miniconda3/lib/python3.12/site-packages/nf_core/download.py:257 in download_workflow │
│ │
│ 254 │ │ if self.platform: │
│ 255 │ │ │ self.download_workflow_platform() │
│ 256 │ │ else: │
│ ❱ 257 │ │ │ self.download_workflow_static() │
│ 258 │ │
│ 259 │ def download_workflow_static(self): │
│ 260 │ │ """Downloads a nf-core workflow from GitHub to the local file system in a self-c │
│ │
│ /home/jmy/miniconda3/lib/python3.12/site-packages/nf_core/download.py:271 in │
│ download_workflow_static │
│ │
│ 268 │ │ log.info("Downloading workflow files from GitHub") │
│ 269 │ │ │
│ 270 │ │ for item in zip(self.revision, self.wf_sha.values(), self.wf_download_url.values │
│ ❱ 271 │ │ │ revision_dirname = self.download_wf_files(revision=item[0], wf_sha=item[1], │
│ 272 │ │ │ │
│ 273 │ │ │ if self.include_configs: │
│ 274 │ │ │ │ try: │
│ │
│ /home/jmy/miniconda3/lib/python3.12/site-packages/nf_core/download.py:638 in download_wf_files │
│ │
│ 635 │ │ │
│ 636 │ │ # Rename the internal directory name to be more friendly │
│ 637 │ │ gh_name = f"{self.pipeline}-{wf_sha if bool(wf_sha) else ''}".split("/")[-1] │
│ ❱ 638 │ │ os.rename( │
│ 639 │ │ │ os.path.join(self.outdir, gh_name), │
│ 640 │ │ │ os.path.join(self.outdir, revision_dirname), │
│ 641 │ │ ) │Relevant files
No response
System information
No response