Clean instal of wf-artic 0.3.9

[adamkoletis]

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

[mattdmem]

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

[adamkoletis]

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?

[mattdmem]

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/

[adamkoletis]

[adamkoletis]

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

[mattdmem]

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?

[adamkoletis]

Yes I will do right now and I will update you thank you.

[mattdmem]

Hi Adam, I'll close this issue if you're not having any more issues with running an older version?

[adamkoletis]

Hi, still I have some issues. I will send you screenshots in some minutes. Thanks

[adamkoletis]

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

[mattdmem]

Looks like something to do with the fastq input and the samplesheet - can you check both to make sure:

1. The structure under ../basecalling/pass is barcodeXX etc
2. The samplesheet barcode matches the barcodes present in the fastq dir
3. If you move/delete the unclassified folder does that work?

[adamkoletis]

Ok I will try and I will update you again

[mattdmem]

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.

[LianaKafetzopoulou]

Hi Matt,

Following up from Adam. To answer your points above:

• We have checked our folder structure and looks good - as you mention under ../basecalling/pass is barcodeXX etc and also an unclassified folder
• Our sample_sheet - no unclassified included in there
• If we remove the unclassified folder then this results in a report without the unclassified included

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

[mattdmem]

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

[LianaKafetzopoulou]

awesome thanks Matt! and thanks for getting back to us so quickly!