I had some issues running the newly released

1.12.0

in the

fasterq-dump

step. I am wondering whether anyone has similar issues. Here is the command I used

nextflow run nf-core/fetchngs -r 1.12.0 --input samplesheet.csv --outdir fetchngsout -profile tufts --download_method sratools

. My

samplesheet.csv

only has one identifier

GSE80182

. Below is the error message

ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX1693957_SRR3362667)'

Caused by:
  Process `NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX1693957_SRR3362667)` terminated with an error exit status (3)

Command executed:

  export NCBI_SETTINGS="$PWD/user-settings.mkfg"
  
  fasterq-dump \
      --split-files --include-technical \
      --threads 6 \
      --outfile SRX1693957_SRR3362667 \
       \
      SRR3362667
  
  pigz \
       \
      --no-name \
      --processes 6 \
      *.fastq
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP":
      sratools: $(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
      pigz: $( pigz --version 2>&1 | sed 's/pigz //g' )
  END_VERSIONS

Command exit status:
  3

Command output:
  (empty)

Command error:
  2024-03-01T14:11:02 fasterq-dump.2.11.0 err: invalid accession 'SRR3362667'
  fasterq-dump quit with error code 3

Work dir:
  /cluster/home/tutln02/nf-core_workshp/1.12.0/work/db/35ade848d7ce0b53d4db4b492c8bc3

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