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
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]
[1mInput/output options[0m
[0;34minput : [0;32m/home/runner/work/nf-aggregate/nf-aggregate/workflows/nf_aggregate/assets/test_run_ids.csv[0m
[0;34moutdir : [0;32m/home/runner/work/nf-aggregate/nf-aggregate/.nf-test/tests/a3c9f4c329dd487f4bd46a409a27814a/output[0m
[1mPipeline-specific options[0m
[0;34mremove_failed_tasks: [0;32mtrue[0m
[1mGeneric options[0m
[0;34mtrace_report_suffix: [0;32m2025-02-27_12-23-56[0m
[1mCore Nextflow options[0m
[0;34mrunName : [0;32mfestering_ride[0m
[0;34mcontainerEngine : [0;32mdocker[0m
[0;34mlaunchDir : [0;32m/home/runner/work/nf-aggregate/nf-aggregate/.nf-test/tests/a3c9f4c329dd487f4bd46a409a27814a[0m
[0;34mworkDir : [0;32m/home/runner/work/nf-aggregate/nf-aggregate/.nf-test/tests/a3c9f4c329dd487f4bd46a409a27814a/work[0m
[0;34mprojectDir : [0;32m/home/runner/work/nf-aggregate/nf-aggregate[0m
[0;34muserName : [0;32mrunner[0m
[0;34mprofile : [0;32mtest,docker[0m
[0;34mconfigFiles : [0;32m/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[0m
!! Only displaying parameters that differ from the pipeline defaults !!
-[2m----------------------------------------------------[0m-
[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:
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