Harshil Patel comments

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                                            Harshil Patel

Make the presence of a GTF file optional

Hi @Temperche ! Apologies for the delay in responding! We are about to release a much updated version of the pipeline that has been completely refactored to be written in...

treatment vs control

Hi @elffairy90 ! Thanks for reporting and apologies for the delay in responding! We have decided to strip out the differential analysis that has been in this pipeline until v1.2.2....

Wrong parameterization causing error

Hi @taylordm ! Thanks for reporting! We are about to release a much updated version of the pipeline that has been completely refactored to be written in Nextflow DSL2. When...

Test run for fetchngs failed

Assuming the fix above resolved the issue. In the future it may be easier to join the #fetchngs channel on nf-core Slack to get real-time help. You can join via...

some samples fail with --force_sratools_download due to changes in prefetch results

This issue should mostly be solved I think after the API was fixed. Feel free to re-open if the problem persists.

Add support for prefetch argument `--max-size`

Looks like this is resolved so closing.

Choice between fastq and fasterq-dump when using --force_sratools_download

Hi @dmalzl ! Any updates on this issue?

Choice between fastq and fasterq-dump when using --force_sratools_download

Thanks for the update! Ok, will close this for now but feel free to re-open if the issue persists and if you have any suggestions for how this can be...

Wrong use of --progress in prefetch command leads to failure of pipeline

Looks like this has been resolved. Will close for now but feel free to re-open if the problem persists.

Parameter for using the --save_reference 'genome' directory

Hi @kaboroevich ! This is a good suggestion and something I have been thinking about to make it easier to re-use the references saved when using `--save_reference`. The idea with...