Remove old references to CUSTOMDUMPSOFTWAREVERSIONS #2897
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@mirpedrol @mashehu help! |
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haha, you ran into the same nf-core tools trap as @Joon-Klaps did 🙂 |
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but I can have a look after I found a fix for #2890 |
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nf_core/lint/configs.py
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| # Return a failed status if we can't find the file | ||
| if not fn.is_file(): | ||
| return {"failed": [f"`${file_path}` not found"]} |
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Would it be better to make this a warning? Some pipelines (like sarek) don't use these config files.
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better to have them ignore it, imo
nf_core/lint/configs.py
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| f"`{file_path}` contains `withName:{section}`, but the corresponding process is not present in any of the following workflow files: `{nf_files}`." | ||
| ) | ||
| else: | ||
| passed.append(f"both `{file_path}` and `{[str(f) for f in nf_files]} contain `{section}`.") |
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Not sure if the list of .nf files will be too long. Maybe a general message is enough
| passed.append(f"both `{file_path}` and `{[str(f) for f in nf_files]} contain `{section}`.") | |
| passed.append(f"`{section}` found in `{file_path}` and Nextflow scripts.") |
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okay, but I'll add a debuggin log, so it is a bit easier to debug
…-core/tools into remove-old-customdumpsoftwareversions
Removes left over CUSTOMDUMPSOFTWAREVERSIONS references from template that has been since replaced with a dedicated special function
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CHANGELOG.mdis updateddocsis updated