Skip to content

pipeline level test with snapshots #327

pipeline level test with snapshots

pipeline level test with snapshots #327

GitHub Actions / JUnit Test Report failed Feb 27, 2025 in 0s

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

Annotations

Check failure on line 1 in Test pipeline

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline.-profile test

Assertion failed: 

2 of 2 assertions failed
Raw output
Nextflow stdout:

N E X T F L O W  ~  version 25.01.0-edge
Launching `/home/runner/work/nf-aggregate/nf-aggregate/tests/../main.nf` [festering_ride] DSL2 - revision: 67e5fb1ec9
Downloading plugin [email protected]
Downloading plugin [email protected]
Input/output options
  input              : /home/runner/work/nf-aggregate/nf-aggregate/workflows/nf_aggregate/assets/test_run_ids.csv
  outdir             : /home/runner/work/nf-aggregate/nf-aggregate/.nf-test/tests/a3c9f4c329dd487f4bd46a409a27814a/output

Pipeline-specific options
  remove_failed_tasks: true

Generic options
  trace_report_suffix: 2025-02-27_12-23-56

Core Nextflow options
  runName            : festering_ride
  containerEngine    : docker
  launchDir          : /home/runner/work/nf-aggregate/nf-aggregate/.nf-test/tests/a3c9f4c329dd487f4bd46a409a27814a
  workDir            : /home/runner/work/nf-aggregate/nf-aggregate/.nf-test/tests/a3c9f4c329dd487f4bd46a409a27814a/work
  projectDir         : /home/runner/work/nf-aggregate/nf-aggregate
  userName           : runner
  profile            : test,docker
  configFiles        : /home/runner/work/nf-aggregate/nf-aggregate/nextflow.config, /home/runner/work/nf-aggregate/nf-aggregate/nextflow.config, /home/runner/work/nf-aggregate/nf-aggregate/tests/nextflow.config

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
[f6/e455fb] Submitted process > NF_AGGREGATE:SEQERA_RUNS_DUMP (38QXz4OfQDpwOV)
[45/8d9386] Submitted process > NF_AGGREGATE:SEQERA_RUNS_DUMP (4Bi5xBK6E2Nbhj)
[a1/cdc3ed] Submitted process > NF_AGGREGATE:SEQERA_RUNS_DUMP (2lXd1j7OwZVfxh)
[d7/b840e8] Submitted process > NF_AGGREGATE:SEQERA_RUNS_DUMP (4LWT4uaXDaGcDY)
[2e/a33531] Submitted process > NF_AGGREGATE:SEQERA_RUNS_DUMP (3iFMo0NtH1Byvy)
[94/041b06] Submitted process > NF_AGGREGATE:PLOT_RUN_GANTT (38QXz4OfQDpwOV)
[69/590c72] Submitted process > NF_AGGREGATE:PLOT_RUN_GANTT (2lXd1j7OwZVfxh)
[e3/034993] Submitted process > NF_AGGREGATE:PLOT_RUN_GANTT (4Bi5xBK6E2Nbhj)
ERROR ~ Error executing process > 'NF_AGGREGATE:PLOT_RUN_GANTT (38QXz4OfQDpwOV)'

Caused by:
  Process `NF_AGGREGATE:PLOT_RUN_GANTT (38QXz4OfQDpwOV)` terminated with an error exit status (125)


Command executed:

  plot_run_gantt.py \
      --title "GANTT plot for run: 38QXz4OfQDpwOV" \
      --input-dir 38QXz4OfQDpwOV \
      --output-file ./38QXz4OfQDpwOV_gantt.html
  
  cat <<-END_VERSIONS > versions.yml
  "NF_AGGREGATE:PLOT_RUN_GANTT":
      python: $(python --version | sed 's/Python //g')
      pandas: $(python -c "import pandas; print(pandas.__version__)")
      plotly_express: $(python -c "import plotly_express; print(plotly_express.__version__)")
      click: $(python -c "import click; print(click.__version__)")
  END_VERSIONS

Command exit status:
  125

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/seqeralabs/nf-aggregate:click-8.0.1_pandas-1.1.5_plotly_express-0.4.1_typing-3.10.0.0--ccea219dc6c3d6a1' locally
  docker: Error response from daemon: Get "https://quay.io/v2/": net/http: request canceled while waiting for connection (Client.Timeout exceeded while awaiting headers).
  See 'docker run --help'.

Work dir:
  /home/runner/work/nf-aggregate/nf-aggregate/.nf-test/tests/a3c9f4c329dd487f4bd46a409a27814a/work/94/041b063149782ebc2128bfbdadb0aa

Container:
  quay.io/seqeralabs/nf-aggregate:click-8.0.1_pandas-1.1.5_plotly_express-0.4.1_typing-3.10.0.0--ccea219dc6c3d6a1

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '/home/runner/work/nf-aggregate/nf-aggregate/.nf-test/tests/a3c9f4c329dd487f4bd46a409a27814a/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr: