Sample sheet error

[buchanri]

Hello, after following the new outline for the sample sheet and ref sheet, I attempted the pipeline. However, there is a prescient error I encounter with the sample sheet. This is the command I used:

nextflow run main.nf --sample_data /nfs7/BPP/Chang_Lab/paradarc/paper1_bra/data/metadata/sample_data_N273_14ncbigenomes.csv --reference_data /nfs7/BPP/Chang_Lab/paradarc/paper1_bra/data/metadata/ref_data.csv --out_dir /nfs7/BPP/Chang_Lab/paradarc/paper1_bra/results/nxf_062524 --bakta_db /nfs7/BPP/Grunwald_Lab/home/paradarc/nxf_dev/db -profile mamba --max_memory 200.GB --max_time 240.h --email_on_fail [email protected] --max_cpus 32 -resume --temp_dir /nfs7/BPP/Grunwald_Lab/home/paradarc/nxf_dev/pathogensurveillance/tmp --n_ref_closest 1

and this is the error I got:

ERROR ~ Error executing process > 'PATHOGENSURVEILLANCE:PREPARE_INPUT:SAMPLESHEET_CHECK (sample_data_N273_14ncbigenomes.csv)'

Caused by:
  Process `PATHOGENSURVEILLANCE:PREPARE_INPUT:SAMPLESHEET_CHECK (sample_data_N273_14ncbigenomes.csv)` terminated with an error exit status (1)


Command executed:

  check_samplesheet.R sample_data_N273_14ncbigenomes.csv ref_data.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 ans[[1]] : subscript out of bounds
  Calls: lapply ... parse_esearch.XMLInternalDocument -> xmlValue -> [[ -> [[.XMLInternalDocument
  Execution halted

Work dir:
  /nfs7/BPP/Chang_Lab/paradarc/paper1_bra/scripts/pathogensurveillance/work/0d/282e1ecc1ce88431555abf0f01fc87

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- 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
-[nf-core/plantpathsurveil] Sent summary e-mail to [email protected] (sendmail)-
WARN: Access to undefined parameter `outdir` -- Initialise it to a default value eg. `params.outdir = some_value`
-[nf-core/plantpathsurveil] Pipeline completed with errors

 To clean the cache, run the command:
 nextflow clean voluminous_jang -f

I checked the .nextflow.log but I didnt say anything in addition to the outputted error. Here's the sample sheet and ref sheet for troubleshooting.
sample_data_N273_14ncbigenomes.csv
ref_data.csv
Any advice would be appreciated!

[zachary-foster]

I think I fixed it. Git it a try now