Looking for sample sheet metadata not in the provided path

[buchanri]

After running this command to run the pipeline:

nextflow run main.nf --sample_data /nfs7/BPP/Chang_Lab/paradarc/paper3_bra/data/metadata/ncbi_and_usda_3516_metadata.csv  --out_dir /nfs7/BPP/Chang_Lab/paradarc/paper3_bra/results/nxf_07_23_24_p3 --bakta_db /nfs7/BPP/Grunwald_Lab/home/paradarc/nxf_dev/db -profile mamba --max_memory 500.GB --max_time 240.h --email_on_fail [email protected] --max_cpus 24 -resume --temp_dir /nfs7/BPP/Chang_Lab/paradarc/paper3_bra/scripts/pathogensurveillance/tmp

I get an error that it can't find the sample sheet metadata but it seems like it gives an unrelated path that doesn't exist in the first place. I'm not even sure where it got this path because I didn't provide any path like it in my command. I also tried with and without the resume flag.

[07/dea46a] NOTE: Process `PATHOGENSURVEILLANCE:PREPARE_INPUT:SAMPLESHEET_CHECK (ncbi_and_usda_3516_metadata.csv)` terminated with an error exit status (1) -- Execution is retried (1)
ERROR ~ Error executing process > 'PATHOGENSURVEILLANCE:PREPARE_INPUT:SAMPLESHEET_CHECK (ncbi_and_usda_3516_metadata.csv)'

Caused by:
  Process `PATHOGENSURVEILLANCE:PREPARE_INPUT:SAMPLESHEET_CHECK (ncbi_and_usda_3516_metadata.csv)` terminated with an error exit status (1)


Command executed:

  check_samplesheet.R ncbi_and_usda_3516_metadata.csv 
  
  cat <<-END_VERSIONS > versions.yml
  "PATHOGENSURVEILLANCE:PREPARE_INPUT:SAMPLESHEET_CHECK":
      r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Error in file(file, "rt") : cannot open the connection
  Calls: read.csv -> read.table -> file
  In addition: Warning message:
  In file(file, "rt") :
    cannot open file '/home/bpp/buchanri/Downloads/ncbi_and_usda_3516_metadata.csv': No such file or directory
  Execution halted

Work dir:
  /nfs7/BPP/Chang_Lab/paradarc/paper3_bra/scripts/pathogensurveillance/work/76/e814533c3dcaa7d5c7714b032fb00e

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details
ERROR ~ Cannot invoke method getAt() on null object

 -- Check script './workflows/pathogensurveillance.nf' at line: 277 or see '.nextflow.log' file for more details

Also all of the paths before the pipeline starts are correct:

Core Nextflow options
runName: chaotic_leavitt
launchDir: /nfs7/BPP/Chang_Lab/paradarc/paper3_bra/scripts/pathogensurveillance
workDir: /nfs7/BPP/Chang_Lab/paradarc/paper3_bra/scripts/pathogensurveillance/work
projectDir : /nfs7/BPP/Chang_Lab/paradarc/paper3_bra/scripts/pathogensurveillance
userName: buchanri
profile: mamba
configFiles : /nfs7/BPP/Chang_Lab/paradarc/paper3_bra/scripts/pathogensurveillance/nextflow.config
Input/output options
sample_data: /nfs7/BPP/Chang_Lab/paradarc/paper3_bra/data/metadata/ncbi_and_usda_3516_metadata.csv
out_dir: /nfs7/BPP/Chang_Lab/paradarc/paper3_bra/results/nxf_07_23_24_p3
temp_dir : /nfs7/BPP/Chang_Lab/paradarc/paper3_bra/scripts/pathogensurveillance/tmp 
bakta_db: /nfs7/BPP/Grunwald_Lab/home/paradarc/nxf_dev/db
Max job request options
max_cpus: 24
max_memory : 500. GB
Generic options
email_on_fail: [email protected]
trace_dir: /nfs7/BPP/Chang_Lab/paradarc/paper3_bra/results/nxf_07_23_24_p3/pipeline_info
enable_conda : true

[zachary-foster]

I forgot to uncomment a line in the samplesheet check R script that used a path to local test data. I think it should be fixed now.