merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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Sra workflow update #2108

Closed FlorianTrigodet closed 1 year ago

FlorianTrigodet commented 1 year ago

I updated the workflow to be able to handle two issues:

The workflow was expected specific output, like and SRRXXXXX_1.sra SRRXXXXX_1.fastq.gz + SRRXXXXX_2.fastq.gz. I mostly just changed the input and output to .done files. Now if an SRA is only available in SRAlite format, it will still be processed. And if the SRA is single reads, this format can be handled too.

I have also added a final rule which creates either a samples.txt and/or samples_single_reads.txt (only has the column sample and r1).

And I updated the test to include a SRA accession for a single-reads sample.

meren commented 1 year ago

Thank you for making these changes, @FlorianTrigodet. They look good to me, but I will let @mschecht to merge it.

mschecht commented 1 year ago

Thanks a lot, @FlorianTrigodet! Great idea adding the samples.txt output.

I did a little polishing and we are ready to merge.