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nf-core / pathogensurveillance

Surveillance of pathogens using population genomics and sequencing
https://nf-co.re/pathogensurveillance
MIT License
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Sample sheet does not appear to contain a header #47

Closed bark9299 closed 5 months ago

bark9299 commented 8 months ago

Description of the bug

The error is saying I don't have a header in my csv file but I have the exact header as the tutorial.

sample,fastq_1,fastq_2 6_13_22,/hdd/2/elyse/microbiome/Sweden_MSU_metagenomics_shotgun/20240209_DNASeq_PE150/6_13_22_S36_L003_R1_001.fastq.gz,/hdd/2/elyse/microbiome/Sweden_MSU_metagenomics_shotgun/20240209_DNASeq_PE150/6_13_22_S36_L003_R2_001.fastq.gz 6_14_22,/hdd/2/elyse/microbiome/Sweden_MSU_metagenomics_shotgun/20240209_DNASeq_PE150/6_14_22_S37_L003_R1_001.fastq.gz,/hdd/2/elyse/microbiome/Sweden_MSU_metagenomics_shotgun/20240209_DNASeq_PE150/6_14_22_S37_L003_R2_001.fastq.gz

Command used and terminal output

nextflow run nf-core/pathogensurveillance -r dev -profile singularity --input pathogen_manifest.csv --outdir pathogen_results

Terminal Output:
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/plantpathsurveil] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_PATHOGENSURVEILLANCE:PATHOGENSURVEILLANCE:INPUT_CHECK:SAMPLESHEET_CHECK (pathogen_manifest.csv)'

Caused by:
  Process `NFCORE_PATHOGENSURVEILLANCE:PATHOGENSURVEILLANCE:INPUT_CHECK:SAMPLESHEET_CHECK (pathogen_manifest.csv)` terminated with an error exit status (1)

Command executed:

  check_samplesheet.py \
      pathogen_manifest.csv \
      samplesheet.valid.csv

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_PATHOGENSURVEILLANCE:PATHOGENSURVEILLANCE:INPUT_CHECK:SAMPLESHEET_CHECK":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Converting SIF file to temporary sandbox...
  WARNING: Skipping mount /home/elysebarker/miniconda3/envs/nextflow/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  [CRITICAL] The given sample sheet does not appear to contain a header.
  INFO:    Cleaning up image...

Work dir:
  /hdd/2/elyse/microbiome/Sweden_MSU_metagenomics_shotgun/20240209_DNASeq_PE150/work/d6/a0cdf03190be8bfe860c27bc6d4ebb

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

Relevant files

No response

System information

I am using nextflow version 23.10.1 on linux. nf-core/plantpathsurveil v1.0dev

zachary-foster commented 8 months ago

Thanks for the report!

This pipeline has not yet had a stable release, but the development version can be found here:

https://github.com/grunwaldlab/pathogensurveillance

This changes often and may not work correctly, but it is much more developed than the version here. If you would like to try out the pipeline I highly recommend using this fork for the near future. Once we have a first release, development will transition to the main nf-core repository (this repository).

For now, where you see nf-core in the instructions, substitute grunwaldlab. Also check the README there for information on the input format. If you still get errors, feel free to let us know here.