ERROR ~ Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sequences_inputNB.csv)'

[Jordthomas93]

Description of the bug

Trying to run nanoseq with nf-core installed via conda and runnig with singularity:

{
    "input": "sequences_inputNB.csv",
    "protocol": "DNA",
    "outdir": "NanoSeq_Out",
    "multiqc_title": "RV_WGS",
    "skip_demultiplexing": true,
    "call_variants": true,
    "skip_quantification": true,
    "skip_differential_analysis": true,
    "skip_fusion_analysis": true,
    "skip_modification_analysis": true,
    "skip_xpore": true,
    "skip_m6anet": true
}

nextflow`` run nf-core/nanoseq -r 3.1.0 -name RV_WGS_Taf3 -profile singularity -params-file nf-params.json

But get this error:

WARN: Access to undefined parameter `enable_conda` -- Initialise it to a default value eg. `params.enable_conda = some_value`
executor >  local (1)
[f1/f80899] process > NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sequences_inputNB.csv)        [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT                             -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:FASTQC                               -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GET_CHROM_SIZES                               -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GTF2BED                                       -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:SAMTOOLS_FAIDX                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_INDEX                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_ALIGN                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_VIEW_BAM                    -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_SORT_INDEX                  -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS    -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_VARIANT                         -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_BGZIP_VCF                       -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_TABIX_VCF                       -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES                          -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_SORT_VCF                 -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_TABIX_VCF                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGWIG:BEDTOOLS_GENOMECOV                      -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGWIG:UCSC_BEDGRAPHTOBIGWIG                   -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGBED:BEDTOOLS_BAMBED                         -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGBED:UCSC_BED12TOBIGBED                      -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:CUSTOM_DUMPSOFTWAREVERSIONS                                  -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:MULTIQC                                                      -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/nanoseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sequences_inputNB.csv)

Caused by:
  Process `NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sequences_inputNB.csv)` terminated with an error exit status (1)


Command executed:

  check_samplesheet.py \
      sequences_inputNB.csv \
      not_changed \
      samplesheet.valid.csv

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

Command exit status:
  1

Command output:


Command error:
  ERROR: Unknown option: --no-home

If I follow the work directory and open .command.sh as requested:

#!/bin/bash -euo pipefail
check_samplesheet.py \
    sequences_inputNB.csv \
    not_changed \
    samplesheet.valid.csv

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

System information

nextflow version 24.04.3.5916
singularity version 2.3.1-development.gbbaf71c

[xz289]

Any update on this? I got the same problem, with test
ERROR ~ Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_nobc_dx.csv)'

Caused by:
Missing output file(s) *.csv expected by process NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_nobc_dx.csv) (note: input files are not included in the default matching set)