Not submitting processes

[MetteBoge]

Description of the bug

I run mhcquant v.2.6.0, but the pipeline only submit OPENMS_DECOYDATABASE and MULTIQC processes. All the rest are not submitted. I get no error, but also no results.

Best regards.

Command used and terminal output

nextflow run nf-core/mhcquant -r 2.6.0 -profile singularity -c results/CT26_tumour_mhcquant.config --outdir results/test_out --peptide_min_length 8 --peptide_max_length 12 --fdr_threshold 0.01 --precursor_mass_tolerance 20 --fragment_mass_tolerance 0.01 --activation_method CID

Nextflow 24.10.4 is available - Please consider updating your version to it

 N E X T F L O W   ~  version 24.10.2

Launching `https://github.com/nf-core/mhcquant` [big_brattain] DSL2 - revision: 1b3069246d [2.6.0]

WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`


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                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/mhcquant v2.6.0-g1b30692
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Core Nextflow options
  revision                 : 2.6.0
  runName                  : big_brattain
  containerEngine          : singularity
  launchDir                : /home/mbp/immunopeptidomics
  workDir                  : /home/mbp/immunopeptidomics/work
  projectDir               : /home/mbp/.nextflow/assets/nf-core/mhcquant
  userName                 : mbp
  profile                  : singularity
  configFiles              :

Input/output options
  input                    : /home/mbp/immunopeptidomics/results/CT26_tumour_inputfile.tsv
  outdir                   : results/test_out

Database Options
  fasta                    : /work/mbp/massspec_tumorantigens/references/human_proteome_uniprot9606.fasta

Database Search Settings
  activation_method        : CID
  digest_mass_range        : 800:2500
  prec_charge              : 2:3
  precursor_mass_tolerance : 20
  fixed_mods               :
  default_params_file_comet:

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/mhcquant for your analysis please cite:

* The pipeline
  https://doi.org/10.1021/acs.jproteome.9b00313

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/mhcquant/blob/master/CITATIONS.md
------------------------------------------------------
executor >  local (2)
[-        ] NFCORE_MHCQUANT:MHCQUANT:PREPARE_SPECTRA:THERMORAWFILEPARSER               -
[-        ] NFCORE_MHCQUANT:MHCQUANT:PREPARE_SPECTRA:UNTAR                             -
[-        ] NFCORE_MHCQUANT:MHCQUANT:PREPARE_SPECTRA:UNZIP                             -
[-        ] NFCORE_MHCQUANT:MHCQUANT:PREPARE_SPECTRA:TDF2MZML                          -
[-        ] NFCORE_MHCQUANT:MHCQUANT:PREPARE_SPECTRA:GUNZIP                            -
[c8/60cea3] NFCORE_MHCQUANT:MHCQUANT:OPENMS_DECOYDATABASE (human_proteome_uniprot9606) [100%] 1 of 1 ✔
[-        ] NFCORE_MHCQUANT:MHCQUANT:OPENMS_COMETADAPTER                               -
[-        ] NFCORE_MHCQUANT:MHCQUANT:OPENMS_PEPTIDEINDEXER                             -
[-        ] NFCORE_MHCQUANT:MHCQUANT:OPENMS_IDMERGER                                   -
[-        ] NFCORE_MHCQUANT:MHCQUANT:MS2RESCORE                                        -
[-        ] NFCORE_MHCQUANT:MHCQUANT:OPENMS_PSMFEATUREEXTRACTOR                        -
[-        ] NFCORE_MHCQUANT:MHCQUANT:OPENMS_PERCOLATORADAPTER                          -
[-        ] NFCORE_MHCQUANT:MHCQUANT:OPENMS_IDFILTER_Q_VALUE                           -
[-        ] NFCORE_MHCQUANT:MHCQUANT:OPENMS_TEXTEXPORTER                               -
[-        ] NFCORE_MHCQUANT:MHCQUANT:OPENMS_MZTABEXPORTER                              -
[1e/20552a] NFCORE_MHCQUANT:MHCQUANT:MULTIQC                                           [100%] 1 of 1 ✔
-[nf-core/mhcquant] Pipeline completed successfully-

Relevant files

nextflow.log
CT26_tumour_inputfile.txt

*NB! I changed the extension .tsv to .txt of the input file to be able to load it into github. But the file I use as input in the config is with .tsv extension.

results/CT26_tumour_mhcquant.config :

params {
    // Input data
    fasta = '/work/mbp/massspec_tumorantigens/references/human_proteome_uniprot9606.fasta'
    input = '/home/mbp/immunopeptidomics/results/CT26_tumour_inputfile.tsv'
}

process {
    errorStrategy = { (task.attempt <= process.maxRetries) ? 'retry' : 'ignore' }
    maxRetries = 2
    maxErrors = '-1'
}

System information

No response

[jonasscheid]

Thanks for reporting this! Based on the samplesheet you provided in Slack

ID Sample Condition ReplicateFileName
1 CT26 ACKP-Tumour /home/mbp/data/immunopeptidomics_data/CT26_tumour_DDA_2021April/11-26-2020_ACKP-Tumour_CT26_EXP0288_id_5_8_14_24_108_P1_07-21-09_Slot1-46_795_5.3.236_rep1.mzML
2 CT26 ACKP-Tumour /home/mbp/data/immunopeptidomics_data/CT26_tumour_DDA_2021April/11-26-2020_ACKP-Tumour_CT26_EXP0288_id_5_8_14_24_108_P2_10-05-39_Slot1-47_796_5.3.236_rep1.mzML
..

I suspect that . in the filenames results in mhcquant not properly parsing the extension here.

Can you throw out the dots or replace them and verify?

[MetteBoge]

Hi, I just changed file names, and now it seems like it submits the processes as intended.
Thanks a lot !!

[jonasscheid]

Perfect! We still should investigate if there is a more robust solution to parsing the extension