Harshil Patel
Harshil Patel
Yup, how can we go about troubleshooting this @pditommaso ? It seems to be an issue on the DNAnexus side because the pipeline is happily chugging away on other platforms...
The command below should reproduce the first error where we had weird permissions issue using `untar` (fixed in 0b4b140): ``` nextflow run nf-core/rnaseq -r profile test,docker ``` The second error...
Hmmm...ok. Is there somewhere else we can push this issue or get the DNAnexus folks involved to help?
Yes, I moved it to s3 in the latest release because downloading over `https` was causing too many incomplete downloads. Latest version of the test samplesheet is [here](https://github.com/nf-core/test-datasets/blob/rnaseq/samplesheet/v3.4/samplesheet_test.csv)
Nope, it is a public bucket. I am using it for Github Actions CI without any issues. Although the region may be a problem 🤔 because it is hosted in...
Man, you are too quick! What was the problem?
@GHAStVHenry I have now closed the other issues running this pipeline on DNAnexus! Getting things together for a release at the moment so would be great if we can identify...
Been a while since this issue has been updated. Please feel free to re-open if the issue persists. Thanks!
Agree, it would be nice to output CRAM by default 👍🏽 Definitely not impossible but definitely not trivial either 😅 If we want to do it properly, we would have...
Hi @schaffman5 ! Thanks for reporting and apologies for the delay in responding. Yep, this is a tricky one because as you mentioned, the STAR parameters used by RSEM are...