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kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
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relative fastq path in amalgkit integrate #71

Closed kfuku52 closed 2 years ago

kfuku52 commented 2 years ago

integrate records only a relative PATH of local fastq. This will cause an error if the current directory is different when getfastq is executed. @Hego-CCTB Could you fix it?

Hego-CCTB commented 2 years ago

If you provide the absolute path for the fastq file directory, it should record the absolute path for the individual reads.

That is not ideal, though. I'll fix this.

Hego-CCTB commented 2 years ago

Should be fixed in https://github.com/kfuku52/amalgkit/commit/6d74e9dfad32ebd034bcfee8e7f19c1a01202e6e Tested with both relative and absolute paths for --fastq_dir, as well as single and paired samples