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nf-core download: Container image for Bowtie2 align module does not resolve #2392
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With great relief, this error can be somewhat downgraded. A first exploration of the bug showed that it affects version 2.0, but not in 2.1.2. The presentation of the error message is misleading in this respect, since the error is printed above the Obviously, issues in older revisions are vexing, but not as critical as problems with up-to-date versions of pipelines. |
Sadly, this is a won't fix case:
The problem with this module is, that the same quote character is used for the wrapping quotes and (without being escaped) also for the inner quotes. I am surprised that Nextflow accepts this without hiccups, but I do not see a way to accommodate the regex to that. I had already worked with a simpler regex Therefore, we now use a regex that is "aware" of the outer quote type being used. The other quote character is ignored and so are escaped versions of the outer quote type:
Evidently, this regex depends on different quotes being used. I also can't match on the correct double quote being accompanied by a closing bracket, since other modules use arbitrary white spaces before/after at this position. So accommodating the regex for this module would break it for others. |
Description of the bug
While downloading the newest release '2.1.2' of atacseq, I noticed that nf-core download fails to extract the container image string from the most recent versions of the Bowtie2 align module. Since Bowtie2 is a very frequently used module, this will soon affect further pipelines with new releases, too.
I will have time for that earliest in two weeks, so if somebody wants to investigate, go for it!
Command used and terminal output
System information
No response
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