How to use

[fbenedett]

Hello,

I am stuck with the usage of this piece of code.

I have nextflow installed, I have a qptiff file, and I have created the CSV samplesheet.
I am trying the following:

./bin/nextflow run ncihtan/nf-vectra-to-htan --input info.csv

 N E X T F L O W   ~  version 24.04.4

Pulling ncihtan/nf-vectra-to-htan ...
 downloaded from https://github.com/ncihtan/nf-vectra-to-htan.git
Project `ncihtan/nf-vectra-to-htan` is currently stuck on revision: main -- you need to explicitly specify a revision with the option `-r` in order to use it

It works with the following:
./bin/nextflow run ncihtan/nf-vectra-to-htan -r main --input info.csv

But then I have problem with the "s3" part. I have no idea of what is it.
According to the output:

./bin/nextflow run ncihtan/nf-vectra-to-htan -r main --input info.csv

 N E X T F L O W   ~  version 24.04.4

Launching `https://github.com/ncihtan/nf-vectra-to-htan` [gigantic_lovelace] DSL2 - revision: 20ddd3654e [main]

executor >  local (1)
[13/a32bad] VECTRA2HTAN:CONVERT:QPTIFF2OMETIFF (1ZRL) [  0%] 0 of 1
[-        ] VECTRA2HTAN:DEID:clean_ome                -
executor >  local (1)
[13/a32bad] VECTRA2HTAN:CONVERT:QPTIFF2OMETIFF (1ZRL) [  0%] 0 of 1
[-        ] VECTRA2HTAN:DEID:clean_ome                -
[-        ] VECTRA2HTAN:DEID:clean_tiff               -
WARN: Unable to get file attributes file: s3://mybucket/myimage.qptiff -- Cause: com.amazonaws.services.s3.model.AmazonS3Exceptiexecutor >  local (1)
[-        ] VECTRA2HTAN:CONVERT:QPTIFF2OMETIFF (1ZRL) -
[-        ] VECTRA2HTAN:DEID:clean_ome                -
[-        ] VECTRA2HTAN:DEID:clean_tiff               -
WARN: Unable to get file attributes file: s3://mybucket/myimage.qptiff -- Cause: com.amazonaws.services.s3.model.AmazonS3Exception: Access Denied (Service: Amazon S3; Status Code: 403; Error Code: AccessDenied; Request ID: J17V7XGJ2HESVZ2D; S3 Extended Request ID: VhME8OV/fOtAJqLv6ULHM0YNJ5kFHynlzabYHYRgjYcVTO7ruYes/VIft1n3mry9VtvlG+nIlmP7O8+9xZBWag==; Proxy: null), S3 Extended Request ID: VhME8OV/fOtAJqLv6ULHM0YNJ5kFHynlzabYHYRgjYcVTO7ruYes/VIft1n3mry9VtvlG+nIlmP7O8+9xZBWag==
ERROR ~ Error executing process > 'VECTRA2HTAN:CONVERT:QPTIFF2OMETIFF (2)'

Caused by:
  Access Denied (Service: Amazon S3; Status Code: 403; Error Code: AccessDenied; Request ID: 43GWQJKS1DPNS240; S3 Extended Request ID: kvDIVtTkoGvBXgW2twiZqcaaOO84esOghnGWx/PtO5JH5sSXVyxxDIkWDFXcYFA+Fg+nTrJ0Y8calTccSaYobQ==; Proxy: null)



 -- Check '.nextflow.log' file for details

it is an Amazon service. Do I really need it to convert the qptiff to the format that works with nextflow?