Unhandled exception when parsing config

[ewels]

From Slack:

---

Hello! I am trying to install the ampliseq pipeline with nf-core download --singularity-cache-only , but I get the following error:

 /cluster/projects/nn9305k/src/miniconda/envs/nf-core/lib/python3.8/site-packages/rich_click/rich_group.py:21 in   │
│ main                                                                                                              │
│                                                                                                                   │
│   20 │   │   try:                                                                                                 │
│ ❱ 21 │   │   │   rv = super().main(*args, standalone_mode=False, **kwargs)                                        │
│   22 │   │   │   if not standalone_mode:                                                                          │
│                                                                                                                   │
│ /cluster/projects/nn9305k/src/miniconda/envs/nf-core/lib/python3.8/site-packages/click/core.py:1055 in main       │
│                                                                                                                   │
│   1054 │   │   │   │   with self.make_context(prog_name, args, **extra) as ctx:                                   │
│ ❱ 1055 │   │   │   │   │   rv = self.invoke(ctx)                                                                  │
│   1056 │   │   │   │   │   if not standalone_mode:                                                                │
│                                                                                                                   │
│ /cluster/projects/nn9305k/src/miniconda/envs/nf-core/lib/python3.8/site-packages/click/core.py:1657 in invoke     │
│                                                                                                                   │
│   1656 │   │   │   │   with sub_ctx:                                                                              │
│ ❱ 1657 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))                                │
│   1658                                                                                                            │
│                                                                                                                   │
│ /cluster/projects/nn9305k/src/miniconda/envs/nf-core/lib/python3.8/site-packages/click/core.py:1404 in invoke     │
│                                                                                                                   │
│   1403 │   │   if self.callback is not None:                                                                      │
│ ❱ 1404 │   │   │   return ctx.invoke(self.callback, **ctx.params)                                                 │
│   1405                                                                                                            │
│                                                                                                                   │
│ /cluster/projects/nn9305k/src/miniconda/envs/nf-core/lib/python3.8/site-packages/click/core.py:760 in invoke      │
│                                                                                                                   │
│    759 │   │   │   with ctx:                                                                                      │
│ ❱  760 │   │   │   │   return __callback(*args, **kwargs)                                                         │
│    761                                                                                                            │
│                                                                                                                   │
│ /cluster/projects/nn9305k/src/miniconda/envs/nf-core/lib/python3.8/site-packages/nf_core/__main__.py:244 in       │
│ download                                                                                                          │
│                                                                                                                   │
│    243 │   )                                                                                                      │
│ ❱  244 │   dl.download_workflow()                                                                                 │
│    245                                                                                                            │
│                                                                                                                   │
│ /cluster/projects/nn9305k/src/miniconda/envs/nf-core/lib/python3.8/site-packages/nf_core/download.py:176 in       │
│ download_workflow                                                                                                 │
│                                                                                                                   │
│   175 │   │   if self.container == "singularity":                                                                 │
│ ❱ 176 │   │   │   self.find_container_images()                                                                    │
│   177 │   │   │   try:                                                                                            │
│                                                                                                                   │
│ /cluster/projects/nn9305k/src/miniconda/envs/nf-core/lib/python3.8/site-packages/nf_core/download.py:445 in       │
│ find_container_images                                                                                             │
│                                                                                                                   │
│   444 │   │   # Use linting code to parse the pipeline nextflow config                                            │
│ ❱ 445 │   │   self.nf_config = nf_core.utils.fetch_wf_config(os.path.join(self.outdir,                            │
│       "workflow"))                                                                                                │
│   446                                                                                                             │
│                                                                                                                   │
│ /cluster/projects/nn9305k/src/miniconda/envs/nf-core/lib/python3.8/site-packages/nf_core/utils.py:251 in          │
│ fetch_wf_config                                                                                                   │
│                                                                                                                   │
│    250 │   │   │   with open(cache_path, "r") as fh:                                                              │
│ ❱  251 │   │   │   │   config = json.load(fh)                                                                     │
│    252 │   │   │   return config                                                                                  │
│                                                                                                                   │
│ /cluster/projects/nn9305k/src/miniconda/envs/nf-core/lib/python3.8/json/__init__.py:293 in load                   │
│                                                                                                                   │
│   292 │   """                                                                                                     │
│ ❱ 293 │   return loads(fp.read(),                                                                                 │
│   294 │   │   cls=cls, object_hook=object_hook,                                                                   │
│                                                                                                                   │
│ /cluster/projects/nn9305k/src/miniconda/envs/nf-core/lib/python3.8/json/__init__.py:357 in loads                  │
│                                                                                                                   │
│   356 │   │   │   parse_constant is None and object_pairs_hook is None and not kw):                               │
│ ❱ 357 │   │   return _default_decoder.decode(s)                                                                   │
│   358 │   if cls is None:                                                                                         │
│                                                                                                                   │
│ /cluster/projects/nn9305k/src/miniconda/envs/nf-core/lib/python3.8/json/decoder.py:337 in decode                  │
│                                                                                                                   │
│   336 │   │   """                                                                                                 │
│ ❱ 337 │   │   obj, end = self.raw_decode(s, idx=_w(s, 0).end())                                                   │
│   338 │   │   end = _w(s, end).end()                                                                              │
│                                                                                                                   │
│ /cluster/projects/nn9305k/src/miniconda/envs/nf-core/lib/python3.8/json/decoder.py:355 in raw_decode              │
│                                                                                                                   │
│   354 │   │   except StopIteration as err:                                                                        │
│ ❱ 355 │   │   │   raise JSONDecodeError("Expecting value", s, err.value) from None                                │
│   356 │   │   return obj, end                                                                                     │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
JSONDecodeError: Expecting value: line 1 column 1 (char 0)

I have installed the newest version of nf-core using conda, with python version 3.8.15. I am using Java version 17.0.2.
I have set the NXF_SINGULARITY_CACHE variable in my .bashrc file: export NXF_SINGULARITY_CACHEDIR=${USERWORK}/images
Anyone know why I get this error? Any help is appreciated! (edited)

[awgymer]

That looks like the it's saying the JSON is empty?
You can see what file it is using with verbose logging.

• Is it actually empty?
• How did we end up with an empty JSON? (not just {})