I managed to run the

fetchngs

pipeline successfully on my computer but I've had no success with running it on the institute server that I have access to with the following command

nextflow run nf-core/fetchngs -profile docker --input ids.csv --outdir test

The output is as follows:

N E X T F L O W  ~  version 21.10.6
Project `nf-core/fetchngs` currently is sticked on revision: 1.7 -- you need to specify explicitly a revision with the option `-r` to use it`

When I add the

-r

tag:

nextflow run nf-core/fetchngs -r v1.7 -profile docker --input ids.csv --outdir test

This is the output: N E X T F L O W ~ version 21.10.6

Cannot find revision `v1.7` -- Make sure that it exists in the remote repository `<https://github.com/nf-core/fetchngs>`

I do I go about sorting this issue?

You can just throw away your directory where its kept, likely

~/. nextflow/assets

but for nextflow 21.10 is very old and I'm doubtful what maintained pipelines you can run with that, so you should update that.

Also there is no

v1.7

, it's

1.7

Try again with

nextflow run nf-core/fetchngs -r v1.7 -profile docker --input ids.csv --outdir test

if it's this versions you wished to try

So I removed the directory as @pontus suggested and re-ran the command:

nextflow run nf-core/fetchngs -r 1.7 -profile docker --input ids.csv --outdir test
N E X T F L O W  ~  version 21.10.6
Pulling nf-core/fetchngs ...
 downloaded from <https://github.com/nf-core/fetchngs.git>
Launching `nf-core/fetchngs` [special_ardinghelli] - revision: b79cde2fb5 [1.7]

ERROR: Validation of pipeline parameters failed!


* --input: string [ids.csv] does not match pattern ^\S+\.txt$ (ids.csv)

Unfortunately that's the only version of Nextflow I can find on the institute server.

Can you rename

ids.csv

to

ids.txt

That is the pipeline at least attempting to start but telling you that you aren't passing what it expects (particularly as Maxime implies, it wants something ending with

.txt

). And unless all Java versions you have access to are ancient, nextflow installation is really simple and can be done as a user (it's just a short launch script). https://www.nextflow.io/docs/latest/install.html#install-nextflow

I changed the file extension but still no luck. Even

nextflow run nf-core/fetchngs -r 1.7 -profile test,docker --outdir test

fails with exit status 126.

a different error is a sign of progress

You will likely need to iterate and fix errors as you see them.

I forgot to mention here that this issue was solved by using singularity for profile instead of docker on the server.

I see