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Fix params-in functionality in nf-core launch #1986

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merged 3 commits into from
Nov 2, 2022
Merged

Fix params-in functionality in nf-core launch #1986

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fec4a2d
fix name collision if input name is provided, add default value to ru…
mashehu Oct 31, 2022
eff0721
update changelog
mashehu Oct 31, 2022
e0baf78
still ask before overwriting
mashehu Oct 31, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@
- Mock biocontainers and anaconda api calls in modules and subworkflows tests [#1967](https://github.com/nf-core/tools/pull/1967)
- Run tests with Python 3.11 ([#1970](https://github.com/nf-core/tools/pull/1970))
- Bump promoted Python version from 3.7 to 3.8 ([#1971](https://github.com/nf-core/tools/pull/1971))
- Fix incorrect file deletion in `nf-core launch` when `--params_in` has the same name as `--params_out`

### Modules

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17 changes: 12 additions & 5 deletions nf_core/launch.py
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Expand Up @@ -120,12 +120,19 @@ def launch_pipeline(self):

# Check if the output file exists already
if os.path.exists(self.params_out):
log.warning(f"Parameter output file already exists! {os.path.relpath(self.params_out)}")
# if params_in has the same name as params_out, don't ask to overwrite
if self.params_in and os.path.abspath(self.params_in) == os.path.abspath(self.params_out):
log.warning(
f"The parameter input file has the same name as the output file! {os.path.relpath(self.params_out)} will be overwritten."
)
else:
log.warning(f"Parameter output file already exists! {os.path.relpath(self.params_out)}")
if Confirm.ask("[yellow]Do you want to overwrite this file?"):
os.remove(self.params_out)
log.info(f"Deleted {self.params_out}\n")
if not (self.params_in and os.path.abspath(self.params_in) == os.path.abspath(self.params_out)):
os.remove(self.params_out)
log.info(f"Deleted {self.params_out}\n")
else:
log.info("Exiting. Use --params-out to specify a custom filename.")
log.info("Exiting. Use --params-out to specify a custom output filename.")
return False

log.info(
Expand Down Expand Up @@ -716,6 +723,6 @@ def launch_workflow(self):
"""Launch nextflow if required"""
log.info(f"[bold underline]Nextflow command:[/]\n[magenta]{self.nextflow_cmd}\n\n")

if Confirm.ask("Do you want to run this command now? "):
if Confirm.ask("Do you want to run this command now? ", default=True):
log.info("Launching workflow! :rocket:")
subprocess.call(self.nextflow_cmd, shell=True)