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Process tag can cause failures on some systems when containing white spaces #789

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d4straub opened this issue Oct 29, 2024 · 0 comments
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d4straub commented Oct 29, 2024

Description of the bug

This came up in slack on https://nfcore.slack.com/archives/CEA7TBJGJ/p1727470357963289

[35/fec013] NOTE: Error submitting process 'NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_SEQFILTERTABLE (rep-seqs.qza filter by filtered-table.qza)' for execution -- Execution is retried (1)
[50/f8638f] NOTE: Error submitting process 'NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_SEQFILTERTABLE (rep-seqs.qza filter by filtered-table.qza)' for execution -- Execution is retried (2)
ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_SEQFILTERTABLE (rep-seqs.qza filter by filtered-table.qza)'

Caused by:
  Failed to submit process to grid scheduler for execution

Command executed:

  sbatch .command.run

Command exit status:
  255

Command output:
  sbatch: error: Invalid directive found in batch script: filter

Command used and terminal output

nextflow run nf-core/ampliseq \
    -r 2.11.0 \
    -c <PATH_TO_CUSTOM_CONFIG> \
    --input "samplesheet.tsv" \
    --FW_primer GTGYCAGCMGCCGCGGTAA \
    --RV_primer GGACTACNVGGGTWTCTAAT \
    --outdir "./results"

Relevant files

The following seems to fix the problem:
Appending to the command -c tag.config where tag.config contains:

process {
    withName: QIIME2_SEQFILTERTABLE {
        tag = "tag_without_white_space"
    }
}

System information

No response

@d4straub d4straub added the bug Something isn't working label Oct 29, 2024
@d4straub d4straub self-assigned this Nov 12, 2024
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