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Fix double slash in directory urls #332

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jhanifen opened this issue Aug 24, 2023 · 2 comments
Closed

Fix double slash in directory urls #332

jhanifen opened this issue Aug 24, 2023 · 2 comments
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@jhanifen
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Description of the bug

When using newer versions of Nextflow, the follow error may occur when moving files.

java.lang.IllegalArgumentException: I/O not allowed on dot-dirs or extra slashes when !permitEmptyPathComponents:

This is due to the path to the files having a double slash //

Example:
macs2//narrow

Command used and terminal output

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Relevant files

conf/modules.config

System information

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@jhanifen jhanifen added the bug Something isn't working label Aug 24, 2023
@jhanifen
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0001-fix-double-slash-logic.patch

patch for a fix

bjlang pushed a commit to bjlang/nf-core-atacseq that referenced this issue Mar 20, 2024
Fix double slash in directory urls nf-core#332
3687239
@bjlang
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bjlang commented Mar 20, 2024

#355 implements your patch. Thank you for that.

@bjlang bjlang closed this as completed Mar 20, 2024
@bjlang bjlang mentioned this issue Jul 9, 2024
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@jhanifen @bjlang