From fec4a2df5db072b33fb473e49561dde012b7cd29 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 31 Oct 2022 11:48:53 +0100
Subject: [PATCH 1/3] fix name collision if input name is provided, add default
value to run command at the end of launch
---
nf_core/launch.py | 20 +++++++++++++-------
1 file changed, 13 insertions(+), 7 deletions(-)
diff --git a/nf_core/launch.py b/nf_core/launch.py
index d57d9f112f..2287ae76f1 100644
--- a/nf_core/launch.py
+++ b/nf_core/launch.py
@@ -120,13 +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 Confirm.ask("[yellow]Do you want to overwrite this file?"):
- os.remove(self.params_out)
- log.info(f"Deleted {self.params_out}\n")
+ # 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.info("Exiting. Use --params-out to specify a custom filename.")
- return False
+ 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")
+ else:
+ log.info("Exiting. Use --params-out to specify a custom filename.")
+ return False
log.info(
"NOTE: This tool ignores any pipeline parameter defaults overwritten by Nextflow config files or profiles\n"
@@ -716,6 +722,6 @@ 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)
From eff0721fd5535ee666214e31d36e8dd71f68cf10 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 31 Oct 2022 11:50:57 +0100
Subject: [PATCH 2/3] update changelog
---
CHANGELOG.md | 1 +
1 file changed, 1 insertion(+)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index e51660e52c..61ca21ffed 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -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
From e0baf780a077f1b7e3567d7bd9cf0ac3decdb510 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 31 Oct 2022 11:57:19 +0100
Subject: [PATCH 3/3] still ask before overwriting
---
nf_core/launch.py | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/nf_core/launch.py b/nf_core/launch.py
index 2287ae76f1..53fce1f43f 100644
--- a/nf_core/launch.py
+++ b/nf_core/launch.py
@@ -127,12 +127,13 @@ def launch_pipeline(self):
)
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?"):
+ if Confirm.ask("[yellow]Do you want to overwrite this file?"):
+ 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.")
- return False
+ else:
+ log.info("Exiting. Use --params-out to specify a custom output filename.")
+ return False
log.info(
"NOTE: This tool ignores any pipeline parameter defaults overwritten by Nextflow config files or profiles\n"