Skip to content

Instantly share code, notes, and snippets.

@natefoo

natefoo/wf-test-results.md

Last active May 23, 2023 20:38
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save natefoo/2c02814fffc7384e833c5df0e8f28b00 to your computer and use it in GitHub Desktop.
Save natefoo/2c02814fffc7384e833c5df0e8f28b00 to your computer and use it in GitHub Desktop.
Download ZIP
Raw
wf-test-results.md

Still working on it

Retest in progress

None

Fixing tool data then retest

None

Fixing tool resources then retest

None

Passing

  • ./topics/assembly/tutorials/debruijn-graph-assembly/workflows/debruijn-graph.ga
  • ./topics/assembly/tutorials/general-introduction/workflows/assembly-general-introduction.ga
  • ./topics/assembly/tutorials/unicycler-assembly/workflows/unicycler.ga
  • ./topics/computational-chemistry/tutorials/analysis-md-simulations/workflows/main_workflow.ga
  • ./topics/computational-chemistry/tutorials/md-simulation-gromacs/workflows/main_workflow.ga
  • ./topics/ecology/tutorials/obisindicators/workflows/Obis-indicators.ga
  • ./topics/epigenetics/tutorials/tal1-binding-site-identification/workflows/tal1-binding-site-identification-workflow.ga
  • ./topics/fair/tutorials/ro-crate-submitting-life-monitor/sort-and-change-case-workflow/sort-and-change-case.ga
  • ./topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga
  • ./topics/genome-annotation/tutorials/repeatmasker/workflows/RepeatMasker.ga
  • ./topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow.ga
  • ./topics/introduction/tutorials/galaxy-intro-101-everyone/workflows/main_workflow.ga
  • ./topics/introduction/tutorials/galaxy-intro-peaks2genes/workflows/Galaxy-Introduction-Peaks2Genes-Part-1-Workflow.ga
  • ./topics/introduction/tutorials/galaxy-intro-short/workflows/Galaxy-Workflow-galaxy-intro-short.ga
  • ./topics/sequence-analysis/tutorials/quality-control/workflows/quality_control.ga
  • ./topics/metagenomics/tutorials/beer-data-analysis/workflows/main_workflow.ga
  • ./topics/metagenomics/tutorials/general-tutorial/workflows/amplicon.ga
  • ./topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/Nanopore_Datasets_Pathogen_Tracking_among_all_samples.ga
  • ./topics/single-cell/tutorials/scatac-preprocessing-tenx/workflows/scATAC-seq-Count-Matrix-Filtering.ga
  • ./topics/single-cell/tutorials/scatac-preprocessing-tenx/workflows/scATAC-seq-FASTQ-to-Count-Matrix.ga
  • ./topics/single-cell/tutorials/scrna-case_alevin/workflows/Generating-a-single-cell-matrix-using-Alevin-1.9.ga
  • ./topics/single-cell/tutorials/scrna-case_monocle3-trajectories/workflows/Trajectory-analysis-using-Monocle3---full-tutorial-workflow.ga
  • ./topics/statistics/tutorials/machinelearning/workflows/machine_learning.ga
  • ./topics/transcriptomics/tutorials/rna-interactome/workflows/rna-rna-interactome-data-analysis-chira.ga
  • ./topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/workflows/rna-seq-viz-with-heatmap2.ga
  • ./topics/transcriptomics/tutorials/small_ncrna_clustering/workflows/blockclust_clustering.ga
  • ./topics/variant-analysis/tutorials/non-dip/workflows/Calling_variants_in_non-diploid_systems.ga
  • ./topics/variant-analysis/tutorials/somatic-variants/workflows/somatic_variants_tutorial_workflow.ga
  • ./topics/variant-analysis/tutorials/tb-variant-analysis/workflows/tb-variant-analysis.ga

"Failed" but actually passed

  • ./topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/workflows/rna-seq-viz-with-volcanoplot.ga

    this seems fine actually, pdf diff but it renders and looks like something

  • ./topics/computational-chemistry/tutorials/analysis-md-simulations/workflows/advanced_workflow.ga

    Tools run fine but output check fails with:

      File "/home/nate/.virtualenvs/planemo/lib/python3.9/site-packages/planemo/test/_check_output.py", line 24, in check_output
    return checker(runnable, output_properties, test_properties, **kwds)
  File "/home/nate/.virtualenvs/planemo/lib/python3.9/site-packages/planemo/test/_check_output.py", line 88, in _check_output_file
    _verify_output_file(runnable, output_properties, test_properties, **kwds)
  File "/home/nate/.virtualenvs/planemo/lib/python3.9/site-packages/planemo/test/_check_output.py", line 73, in _verify_output_file
    test_properties["assert_list"] = __to_test_assert_list(test_properties["asserts"])
  File "/home/nate/.virtualenvs/planemo/lib/python3.9/site-packages/galaxy/tool_util/parser/yaml.py", line 269, in __to_test_assert_list
    for assertion in assertions:
  File "/home/nate/.virtualenvs/planemo/lib/python3.9/site-packages/galaxy/tool_util/parser/yaml.py", line 261, in expand_dict_form
    new_value = value.copy()
AttributeError: 'int' object has no attribute 'copy'

  • ./topics/proteomics/tutorials/DIA_Analysis_MSstats/workflows/Galaxy-Workflow-DIA_MSstats_Training_export_tabular.ga

    Passes if you use the latest version (1.0.4) of Grep1 rather than the workflow version (1.0.1), this is just a dep issue with training mode.

  • ./topics/proteomics/tutorials/DIA_Analysis_MSstats/workflows/Galaxy-Workflow-DIA_MSstats_Training_msstats_input_tabular.ga

    As with above, passes if you use Grep1 1.0.4.

  • ./topics/variant-analysis/tutorials/microbial-variants/workflows/microbial_variant_calling.ga

    Fails with the ancient Snippy 3.2 in the workflow but works fine with latest (4.6.0+galaxy0)

Failing

Container errors

None

Missing tools at specified versions

None

Missing inputs

  • ./topics/epigenetics/tutorials/formation_of_super-structures_on_xi/workflows/formation_of_super_structures_on_xi.ga

  • ./topics/metabolomics/tutorials/gc_ms_with_xcms/workflows/main_workflow.ga

  • ./topics/metagenomics/tutorials/metatranscriptomics/workflows/main_workflow.ga

  • ./topics/metagenomics/tutorials/metatranscriptomics-short/workflows/workflow1_preprocessing.ga

  • ./topics/metagenomics/tutorials/metatranscriptomics-short/workflows/workflow2_community_profile.ga

  • ./topics/metagenomics/tutorials/metatranscriptomics-short/workflows/workflow3_functional_information.ga

  • ./topics/metagenomics/tutorials/metatranscriptomics-short/workflows/workflow3_functional_information_quick.ga

    this one is also missing tools but probably inputs as well I didn't check just assuming based on the others

  • ./topics/metagenomics/tutorials/taxonomic-profiling/workflows/main-workflow.ga

  • ./topics/proteomics/tutorials/maxquant-label-free/workflows/maxquant_label_free.ga

  • ./topics/proteomics/tutorials/metaquantome-data-creation/workflows/main_workflow.ga

  • ./topics/proteomics/tutorials/protein-quant-sil/workflows/workflow.ga

  • ./topics/transcriptomics/tutorials/ref-based/workflows/deg-analysis.ga

  • ./topics/transcriptomics/tutorials/ref-based/workflows/qc-mapping-counting-paired-and-single.ga

  • ./topics/transcriptomics/tutorials/ref-based/workflows/qc-mapping-counting.ga

  • ./topics/variant-analysis/tutorials/pox-tiled-amplicon/workflows/pox-virus-tiled-amplicon-ref-masking.ga

Missing data

Workflow run errors

Tool errors

  • ./topics/ecology/tutorials/remote-sensing/workflows/Sentinel-2-example.ga

    Most tools fixed but error with toolshed.g2.bx.psu.edu/repos/ecology/srs_diversity_maps/srs_diversity_maps/0.0.1:

    Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/usr/local/lib/R/library/terra/libs/terra.so':
  libproj.so.15: cannot open shared object file: No such file or directory
Calls: loadNamespace ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted

    Needs a lot of memory too, plus some tools don't work on Pulsar due to nested tool files?

  • ./topics/epigenetics/tutorials/methylation-seq/workflows/methylation-seq.ga

    MethylDackl (pileometh) segfaults regardless of resources

  • ./topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/Nanopore_Datasets_Gene_based_pathogenic_Identification.ga

    error is with flye, reported to GTN channel because I am not sure

  • ./topics/sequence-analysis/tutorials/mapping/workflows/mapping.ga

    parameter 'ref_file': an invalid option ('mm10full') was selected (valid options: mm10)

  • ./topics/statistics/tutorials/classification_regression/workflows/classification_LSVC.ga

    output diff but i think it's ok maybe?

  • ./topics/statistics/tutorials/classification_regression/workflows/regression_GradientBoosting.ga

    output diff but i think it's ok maybe?

  • ./topics/statistics/tutorials/clustering_machinelearning/workflows/clustering.ga

    missing libxrender (libSM.so.6)

  • ./topics/variant-analysis/tutorials/trio-analysis/workflows/main_workflow.ga

    Workflow fails because EGA Download produces empty outputs (semi-intentionally) so I started runinng it with the Zenodo inputs, only to discover at the first step that the Column Regex Find and Replace outputs have the invalid datatype input, which is a pretty serious bug if it is recurring:

    https://usegalaxy.org/u/nate-test/h/gtn-wf-testvariant-analysistrio-analysismainworkflowga

  • ./topics/genome-annotation/tutorials/tnseq/workflows/essential-genes-detection-transposon-insertion-sequencing-workflow.ga

    Bowtie (1) fails after a long while claiming the input is not FASTQ even though it is:

    Error aligning sequence. Error: reads file does not look like a FASTQ file
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment