Apostrophes in nf-core create descriptions break things

[ewels]

Description of the bug

When using nf-core create with a description and a customised template, things break.

For example, Phil's test demo here is a problem, Phils test demo is not.

Command used and terminal output

$ nf-core create

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

    nf-core/tools version 2.7.dev0 - https://nf-co.re


? Workflow name demo
? Description Phil's test demo
? Author Phil
? Do you want to customize which parts of the template are used? Yes
? Pipeline prefix
ERROR    Pipeline prefix cannot start with digit or hyphen and cannot contain punctuation.    create.py:188
? Please provide a new pipeline prefix myprefix
? Skip template areas? [iGenomes config]
INFO     Creating new nf-core pipeline: 'myprefix/demo'                                       create.py:246
╭─────────────────────────────────── Traceback (most recent call last) ───────────────────────────────────╮
│ /Users/ewels/GitHub/nf-core/tools/nf_core/utils.py:293 in nextflow_cmd                                  │
│                                                                                                         │
│    292 │   try:                                                                                         │
│ ❱  293 │   │   nf_proc = subprocess.run(shlex.split(cmd), stdout=subprocess.PIPE,                       │
│        stderr=subprocess.PIPE, check=True)                                                              │
│    294 │   │   return nf_proc.stdout                                                                    │
│                                                                                                         │
│ /Users/ewels/.miniconda3/miniconda3/envs/py3.10/lib/python3.10/subprocess.py:524 in run                 │
│                                                                                                         │
│    523 │   │   if check and retcode:                                                                    │
│ ❱  524 │   │   │   raise CalledProcessError(retcode, process.args,                                      │
│    525 │   │   │   │   │   │   │   │   │    output=stdout, stderr=stderr)                               │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────╯
CalledProcessError: Command '['nextflow', 'config', '-flat', '/Users/ewels/demo/myprefix-demo']' returned
non-zero exit status 1.

During handling of the above exception, another exception occurred:

╭─────────────────────────────────── Traceback (most recent call last) ───────────────────────────────────╮
│ /Users/ewels/.miniconda3/miniconda3/envs/py3.10/bin/nf-core:8 in <module>                               │
│                                                                                                         │
│   7 │   sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])                                │
│ ❱ 8 │   sys.exit(run_nf_core())                                                                         │
│   9                                                                                                     │
│                                                                                                         │
│ /Users/ewels/GitHub/nf-core/tools/nf_core/__main__.py:104 in run_nf_core                                │
│                                                                                                         │
│    103 │   # Launch the click cli                                                                       │
│ ❱  104 │   nf_core_cli(auto_envvar_prefix="NFCORE")                                                     │
│    105                                                                                                  │
│                                                                                                         │
│ /Users/ewels/.miniconda3/miniconda3/envs/py3.10/lib/python3.10/site-packages/click/core.py:1130 in      │
│ __call__                                                                                                │
│                                                                                                         │
│   1129 │   │   """Alias for :meth:`main`."""                                                            │
│ ❱ 1130 │   │   return self.main(*args, **kwargs)                                                        │
│   1131                                                                                                  │
│                                                                                                         │
│ /Users/ewels/.miniconda3/miniconda3/envs/py3.10/lib/python3.10/site-packages/rich_click/rich_group.py:2 │
│ 1 in main                                                                                               │
│                                                                                                         │
│   20 │   │   try:                                                                                       │
│ ❱ 21 │   │   │   rv = super().main(*args, standalone_mode=False, **kwargs)                              │
│   22 │   │   │   if not standalone_mode:                                                                │
│                                                                                                         │
│ /Users/ewels/.miniconda3/miniconda3/envs/py3.10/lib/python3.10/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:                                                      │
│                                                                                                         │
│ /Users/ewels/.miniconda3/miniconda3/envs/py3.10/lib/python3.10/site-packages/click/core.py:1657 in      │
│ invoke                                                                                                  │
│                                                                                                         │
│   1656 │   │   │   │   with sub_ctx:                                                                    │
│ ❱ 1657 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))                      │
│   1658                                                                                                  │
│                                                                                                         │
│ /Users/ewels/.miniconda3/miniconda3/envs/py3.10/lib/python3.10/site-packages/click/core.py:1404 in      │
│ invoke                                                                                                  │
│                                                                                                         │
│   1403 │   │   if self.callback is not None:                                                            │
│ ❱ 1404 │   │   │   return ctx.invoke(self.callback, **ctx.params)                                       │
│   1405                                                                                                  │
│                                                                                                         │
│ /Users/ewels/.miniconda3/miniconda3/envs/py3.10/lib/python3.10/site-packages/click/core.py:760 in       │
│ invoke                                                                                                  │
│                                                                                                         │
│    759 │   │   │   with ctx:                                                                            │
│ ❱  760 │   │   │   │   return __callback(*args, **kwargs)                                               │
│    761                                                                                                  │
│                                                                                                         │
│ /Users/ewels/GitHub/nf-core/tools/nf_core/__main__.py:299 in create                                     │
│                                                                                                         │
│    298 │   │   )                                                                                        │
│ ❱  299 │   │   create_obj.init_pipeline()                                                               │
│    300 │   except UserWarning as e:                                                                     │
│                                                                                                         │
│ /Users/ewels/GitHub/nf-core/tools/nf_core/create.py:230 in init_pipeline                                │
│                                                                                                         │
│   229 │   │   # Make the new pipeline                                                                   │
│ ❱ 230 │   │   self.render_template()                                                                    │
│   231                                                                                                   │
│                                                                                                         │
│ /Users/ewels/GitHub/nf-core/tools/nf_core/create.py:330 in render_template                              │
│                                                                                                         │
│   329 │   │   if not self.template_params["igenomes"] or not                                            │
│       self.template_params["nf_core_configs"]:                                                          │
│ ❱ 330 │   │   │   self.update_nextflow_schema()                                                         │
│   331                                                                                                   │
│                                                                                                         │
│ /Users/ewels/GitHub/nf-core/tools/nf_core/create.py:354 in update_nextflow_schema                       │
│                                                                                                         │
│   353 │   │   schema.load_schema()                                                                      │
│ ❱ 354 │   │   schema.get_wf_params()                                                                    │
│   355 │   │   schema.remove_schema_notfound_configs()                                                   │
│                                                                                                         │
│ /Users/ewels/GitHub/nf-core/tools/nf_core/schema.py:631 in get_wf_params                                │
│                                                                                                         │
│   630 │   │   log.debug("Collecting pipeline parameter defaults\n")                                     │
│ ❱ 631 │   │   config = nf_core.utils.fetch_wf_config(os.path.dirname(self.schema_filename))             │
│   632 │   │   skipped_params = []                                                                       │
│                                                                                                         │
│ /Users/ewels/GitHub/nf-core/tools/nf_core/utils.py:256 in fetch_wf_config                               │
│                                                                                                         │
│    255 │   # Call `nextflow config`                                                                     │
│ ❱  256 │   nfconfig_raw = nextflow_cmd(f"nextflow config -flat {wf_path}")                              │
│    257 │   for l in nfconfig_raw.splitlines():                                                          │
│                                                                                                         │
│ /Users/ewels/GitHub/nf-core/tools/nf_core/utils.py:299 in nextflow_cmd                                  │
│                                                                                                         │
│    298 │   except subprocess.CalledProcessError as e:                                                   │
│ ❱  299 │   │   raise AssertionError(                                                                    │
│    300 │   │   │   f"Command '{cmd}' returned non-zero error code '{e.returncode}':\n[red]>             │
│        {e.stderr.decode()}{e.stdout.decode()}"                                                          │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────╯
AssertionError: Command 'nextflow config -flat /Users/ewels/demo/myprefix-demo' returned non-zero error
code '1':
[red]> Unable to parse config file: '/Users/ewels/demo/myprefix-demo/nextflow.config'

  Compile failed for sources
FixedSetSources[name='/groovy/script/Script004AAD2CD5730977755502F494F3DF30/_nf_config_da03c119']. Cause:
org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
  /groovy/script/Script004AAD2CD5730977755502F494F3DF30/_nf_config_da03c119: 180: Unexpected character:
'\'' @ line 180, column 40.
         description     = 'Phil's test demo'
                                            ^

  1 error

System information

No response

[mirpedrol]

Fixed in #2066