Closed adamkoletis closed 2 years ago
Morning!
Does this work? nextflow run epi2me-labs/wf-artic -r v0.3.9
If I do this I get:
nextflow run epi2me-labs/wf-artic -r v0.3.9
N E X T F L O W ~ version 21.10.4
Launching `epi2me-labs/wf-artic` [disturbed_leakey] - revision: 8d13aab29f [v0.3.9]
Thanks
Matt
Hi, I have tried how you have suggest me but after the info I am getting again v0.3.10. My point is that I do not want to have v.03.10. I have installed previously the latest version. After manually I deleted from /usr/local/bin folder and then I tried to download your previous version and to install in the same folder....the issue is that what ever I am trying I am still at the info getting v.0.3.10 Is possible that deleting the folder that contains wf-artic 0.3.10 it was not enough?
I understand that you want to run v0.3.9
and the command I posted should do that. Where is it reporting that it is running v0.3.10
?
Nextflow caches workflows in ~/.nextflow/assets/epi2me-labs/wf-artic
which you could remove and try the command above again.
We also have some more instructions here: https://labs.epi2me.io/managing-epi2me-labs-workflows-with-the-nextflow-command-line-interface/
Initially I have deleted ~/.nextflow/assets/epi2me-labs/wf-artic Then I have followed the commands and then when I have runned the info I had again v 0.3.10
Yes, it shows v0.3.10
is available, but when you ran with -r v0.3.9
it is running with v0.3.9
- can you please run some data using that command and check the workflow report for the version?
Yes I will do right now and I will update you thank you.
Hi Adam, I'll close this issue if you're not having any more issues with running an older version?
Hi, still I have some issues. I will send you screenshots in some minutes. Thanks
Yesterday I have followed exactly your command lines and I was able to get results. Used -r v0.3.9 and under the flag samples I have added the sample sheets Then with out to add -r I have run all the command line and I show the change of version to the newer one. Ofc I have added sample_sheet instead of samples. Today that I have tried again the same commands of yesterday and switch between the 2 versions I am getting the follow error in screenshot Also with the new version we are receiving in the html file and the unclassified results
Looks like something to do with the fastq input and the samplesheet - can you check both to make sure:
../basecalling/pass
is barcodeXX
etcunclassified
folder does that work?Ok I will try and I will update you again
I'm going to close this now as your original issue is solved, if you have any further problems please don't hesitate to raise a new issue.
Hi Matt,
Following up from Adam. To answer your points above:
This is something that we did not have until now - so all previous versions of wf-artic were generating reports without the unclassified folder despite the folder being present. It only seems to be showing up in the latests updates - is this on purpose?
Thanks a lot for your help!
Liana
Liana
Thanks Liana,
It could be a bug - I was having problems with the unclassified folder which I thought were fixed. Let me look into it and get a fix in the next release if I find something that can be done in a better way.
Matt
awesome thanks Matt! and thanks for getting back to us so quickly!
Hi Matt, Please I need to have a clean install of 0.3.9. So when I run nextflow info epi2me-labs/wf-artic to have only version until 0.3.9 and not 0.3.10. I know that i can get the latest version and with the appropriate flag to run the previous version. But is something that I do not want at this moment. I have tried to delete wf-artic v0.3.10 for /usr/local/bin/ folder but when I am downloading the zip file wf-artic0.3.9 and I am transferring the wf-artic folder into /usr/local/bin/ then I run again the info and I am still getting the latest version. I appreciate any help