test pulling latest data and adding it Oscar

[aguang]

August will test Paul's data pipeline to pull in the latest data and add it to Oscar

[aguang]

@paulcao-brown I was wondering if there is documentation for pulling the latest data somewhere? I figured I'd just try to run the nextflow pipeline and see what happens and this is what I got:

(nextflow_env_aguang) [aguang@login007 workflows]$ nextflow run covid19.nf 
N E X T F L O W  ~  version 23.04.3
Launching `covid19.nf` [elegant_kimura] DSL2 - revision: 4c890d8c9d
[-        ] process > downloadGISAID -
Pulling Singularity image docker://cowmoo/covid_pipeline:latest [cache /oscar/data/ris3/covid19_analysis/workflows/work/singularity/cowmoo-covid_pipeline-latesexecutor >  slurm (1)
[b8/c75ed0] process > downloadGISAID [  0%] 0 of 1
ERROR ~ Error executing process > 'downloadGISAID'

Caused by:
  Process `downloadGISAID` terminated with an error exit status (1)

Command executed:

  export GISAIDR_USERNAME='null'
  export GISAIDR_PASSWORD='null'
  Rscript /data/gisaid_download.R
executor >  slurm (1)
[b8/c75ed0] process > downloadGISAID [100%] 1 of 1, failed: 1 ✘
ERROR ~ Error executing process > 'downloadGISAID'

Caused by:
  Process `downloadGISAID` terminated with an error exit status (1)

Command executed:

  export GISAIDR_USERNAME='null'
  export GISAIDR_PASSWORD='null'
  Rscript /data/gisaid_download.R

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred

  Attaching package: ‘GISAIDR’

  The following object is masked from ‘package:utils’:

      timestamp

  Attaching package: ‘dplyr’

  The following objects are masked from ‘package:stats’:

      filter, lag

  The following objects are masked from ‘package:base’:

      intersect, setdiff, setequal, union

  Loading required package: proto
  Warning message:
  no DISPLAY variable so Tk is not available 

  Attaching package: ‘seqinr’

  The following object is masked from ‘package:dplyr’:

      count

  The following object is masked from ‘package:GISAIDR’:

      query

  Attaching package: ‘collections’

  The following object is masked from ‘package:utils’:

      stack

  Error in parseResponse(response) : Username or password wrong!
  Calls: login -> parseResponse
  Execution halted

Work dir:
  /oscar/data/ris3/covid19_analysis/workflows/work/b8/c75ed0f15e46030c5f3384bca86fea

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

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

[paulcao-brown]

Hi August, the issue is I need to add documentation on running of the pipeline, specifically how to add the GISAID login authentication. I'll do this and update the documentation; and follow up on this thread. Thanks for running the test!