Request: Harden qiime2_core__tools__import_fastq

[jennaj]

https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import_fastq/qiime2_core__tools__import_fastq/2026.1.0+dist.h02a552c2

The new specialized version for fastq data is amazing!

The only wrinkle is that the tool complains if the reads are in an uncompressed fastq format. This is confusing for Galaxy users. While they can convert the format themselves, it would be very very nice to smooth this out for them. Any read based collection -> a one step process into a qza artifact.

Could the tool could trigger an implicit conversion in Galaxy to the appropriate compression expected. I see that datatypes are already being discussed but perhaps just the fastq format variations could be captured for this one?

Accepted

fastq.gz
fastqsanger.gz
(all the other compressed..)

Not accepted (trigger the implicit compression)

fastq
fastqsanger
(all the other uncompressed..)

[bgruening]

Thanks Jen for reporting. We do see those errors on the European Galaxy instance as well. Btw. on EU we have more than 40.000 tool runs (excluding the import_fastq tool) :)

[gregcaporaso]

@jennaj, thanks for bringing this up. We agree this makes a lot of sense to support and @Oddant1 is going to work on this.

Also, glad to hear that folks are using this and that you like it! Is that 40.000 tool runs for QIIME 2 as a whole? How does that compare to other tools?