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dsarov / ARDaP

Comprehensive resistance detection from WGS data
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Drop _sequence input glob #6

Closed esteinig closed 5 years ago

esteinig commented 5 years ago

Can we drop the _sequence_ substring requirement from the default configuration for the Fastq input in the Nextflow implementation? I think the most common ones are simple .fq.gz and .fastq.gz. It'd be more of a hurdle for users to rename their files or to specify a different glob pattern on the command line.

dsarov commented 5 years ago

Will do. It's just how the raw data is setup on my drives (and a hangover from SPANDx)

esteinig commented 5 years ago

Hey Derek, thanks for this - you can always specify the sequence pattern on the command line with --fastq '*_{1,2}_sequence.fq.gz' so you don't have to adjust your old collections. Just thought this would be more convenient for other users :)

Removed _sequence from config in commit 1951a74ee38b73cecd98820eeba4e1e7d59c02e7.