Apostrophes in nf-core create descriptions break things #1989
Description
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 errorSystem information
No response