Skip to content
nf-core linting

Merge pull request #144 from tillenglert/bump_nf-test_version #719

Sign in to view logs

Merge pull request #144 from tillenglert/bump_nf-test_version

Merge pull request #144 from tillenglert/bump_nf-test_version #719

GitHub Actions / JUnit Test Report failed Oct 18, 2024 in 0s

1 tests run, 0 passed, 0 skipped, 1 failed.

Annotations

Check failure on line 1 in nf

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

nf.test taxa input with assembly id 

Assertion failed: 

2 of 15 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/metapep/metapep/main.nf` [focused_heyrovsky] DSL2 - revision: 7fa7aa2a4e
Downloading plugin [email protected]
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/metapep v1.0.0
------------------------------------------------------
Core Nextflow options
  runName                   : focused_heyrovsky
  containerEngine           : docker
  launchDir                 : /home/runner/work/metapep/metapep/.nf-test/tests/9c3df90acc496fe3dde6d4fd843ef497
  workDir                   : /home/runner/work/metapep/metapep/.nf-test/tests/9c3df90acc496fe3dde6d4fd843ef497/work
  projectDir                : /home/runner/work/metapep/metapep
  userName                  : runner
  profile                   : test_taxa_specific_assembly,docker
  configFiles               : 

Input/output options
  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/metapep/samplesheets/v1.0/samplesheet.taxa_specific_assembly.csv
  outdir                    : /home/runner/work/metapep/metapep/.nf-test/tests/9c3df90acc496fe3dde6d4fd843ef497/output

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Max job request options
  max_cpus                  : 2
  max_memory                : 6 GB
  max_time                  : 2d

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

* The pipeline

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

* Software dependencies
  https:/nf-core/metapep/blob/master/CITATIONS.md
------------------------------------------------------
[6c/52fd83] Submitted process > NFCORE_METAPEP:METAPEP:PROCESS_INPUT:CHECK_SAMPLESHEET_CREATE_TABLES (samplesheet.taxa_specific_assembly.csv)
[59/89bc22] Submitted process > NFCORE_METAPEP:METAPEP:PROCESS_INPUT:UNIFY_MODEL_LENGTHS (samplesheet.valid.csv)
[56/36f56e] Submitted process > NFCORE_METAPEP:METAPEP:ASSIGN_NUCL_ENTITY_WEIGHTS ()
[51/e64115] Submitted process > NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0, 1])
[51/e64115] NOTE: Process `NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0, 1])` terminated with an error exit status (1) -- Execution is retried (1)
[05/3d8206] Re-submitted process > NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0, 1])
[96/330a5c] Submitted process > NFCORE_METAPEP:METAPEP:GENERATE_PROTEIN_AND_ENTITY_IDS (1)
[d3/e97726] Submitted process > NFCORE_METAPEP:METAPEP:FINALIZE_MICROBIOME_ENTITIES (1)
[0c/174dca] Submitted process > NFCORE_METAPEP:METAPEP:GENERATE_PEPTIDES (1)
[24/4427e3] Submitted process > NFCORE_METAPEP:METAPEP:SPLIT_PRED_TASKS (1)
[7e/c7e16d] Submitted process > NFCORE_METAPEP:METAPEP:PREDICT_EPITOPES (2)
[9f/dd2f7b] Submitted process > NFCORE_METAPEP:METAPEP:PREDICT_EPITOPES (1)
[33/e665ad] Submitted process > NFCORE_METAPEP:METAPEP:MERGE_PREDICTIONS
[3f/e3a76c] Submitted process > NFCORE_METAPEP:METAPEP:COLLECT_STATS (1)
[3d/5e6f64] Submitted process > NFCORE_METAPEP:METAPEP:PREPARE_SCORE_DISTRIBUTION (1)
[ae/cc93b3] Submitted process > NFCORE_METAPEP:METAPEP:PREPARE_ENTITY_BINDING_RATIOS (1)
[fd/ad7f57] Submitted process > NFCORE_METAPEP:METAPEP:PLOT_SCORE_DISTRIBUTION (prediction_scores.allele_1.tsv)
[29/03ec20] Submitted process > NFCORE_METAPEP:METAPEP:PLOT_SCORE_DISTRIBUTION (prediction_scores.allele_0.tsv)
[12/e61448] Submitted process > NFCORE_METAPEP:METAPEP:PLOT_ENTITY_BINDING_RATIOS (entity_binding_ratios.allele_0.tsv)
[7f/850dcb] Submitted process > NFCORE_METAPEP:METAPEP:PLOT_ENTITY_BINDING_RATIOS (entity_binding_ratios.allele_1.tsv)
[d2/79f240] Submitted process > NFCORE_METAPEP:METAPEP:MULTIQC
-[nf-core/metapep] Pipeline completed successfully-
Nextflow stderr:
View more details on GitHub Actions