Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix markdown template: add missing closing details tag #1440

Merged

Conversation

bernt-matthias
Copy link
Contributor

If I'm not wrong this is missing and leads to a display like here where

  • the first test is only shown if Passed is unfolded
  • the other three tests are shown also if passed is folded

Copy link
Member

@mvdbeek mvdbeek left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Feel free to merge it if you have tried it ?

@bernt-matthias
Copy link
Contributor Author

Will test it. But seems that the display of the nesting is still not correct.

@bernt-matthias
Copy link
Contributor Author

The following has been created with the last commit

@bernt-matthias
Copy link
Contributor Author

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 4
Passed 4
Error 0
Failure 0
Skipped 0
Passed Tests
  • ✅ QIIME2-Ia-multiplexed-data-single-end.ga_0

    Workflow invocation details

    • Invocation Messages

    • Steps
      • Step 1: Sequences:

        • step_state: scheduled
      • Step 2: Barcodes:

        • step_state: scheduled
      • Step 3: Metadata:

        • step_state: scheduled
      • Step 4: Metadata parameter:

        • step_state: scheduled
      • Step 5: Reverse complement barcodes:

        • step_state: scheduled
      • Step 6: Input files:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • q2galaxy run tools import '/tmp/tmpjl26zyu6/job_working_directory/000/4/configs/tmplbelsa3p'

            Exit Code:

            • 0

            Standard Output:

            • 「type: EMPSingleEndSequences」
              「format: EMPSingleEndDirFmt」
              

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "7834f75aeb5c11ee8272e5b5b5f371a2"
              chromInfo "/tmp/tmpjl26zyu6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              import_root {"__current_case__": 5, "__q2galaxy__GUI__cond__format__": {"__current_case__": 1, "format": "EMPSingleEndDirFmt", "import_barcodes": {"data": {"values": [{"id": 2, "src": "hda"}]}, "name": "barcodes.fastq.gz"}, "import_sequences": {"data": {"values": [{"id": 1, "src": "hda"}]}, "name": "sequences.fastq.gz"}}, "type": "EMPSingleEndSequences"}
      • Step 7: Metadata as artifact:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • q2galaxy run tools import '/tmp/tmpjl26zyu6/job_working_directory/000/5/configs/tmpk2f8jo9s'

            Exit Code:

            • 0

            Standard Output:

            • 「type: ImmutableMetadata」
              「format: ImmutableMetadataFormat」
              

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "7834f75aeb5c11ee8272e5b5b5f371a2"
              chromInfo "/tmp/tmpjl26zyu6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              import_root {"__current_case__": 29, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "ImmutableMetadataFormat", "import": {"data": {"values": [{"id": 3, "src": "hda"}]}, "name": "__q2galaxy__::literal::None"}}, "type": "ImmutableMetadata"}
      • Step 8: Demultiplex single-end data:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • q2galaxy run demux emp_single '/tmp/tmpjl26zyu6/job_working_directory/000/6/configs/tmp7bkdxmy4'

            Exit Code:

            • 0

            Standard Error:

            • /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_demux.py:253: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead.
                for sample_id, barcode in barcodes.to_series().iteritems():
              

            Standard Output:

            • 「seqs: 15825508-6a0f-4542-a81e-9679a9f98517」
              「barcodes: <CategoricalMetadataColumn name='barcode-sequence' id_count=34>」
              「golay_error_correction: True」
              「rev_comp_barcodes: False」
              「rev_comp_mapping_barcodes: False」
              「ignore_description_mismatch: False」
                                                                                                                                                                                                                                                                             
              Saved SampleData[SequencesWithQuality] to: per_sample_sequences.qza
              Saved ErrorCorrectionDetails to: error_correction_details.qza
              

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __q2galaxy__GUI__section__extra_opts__ {"golay_error_correction": true, "ignore_description_mismatch": false, "rev_comp_barcodes": false, "rev_comp_mapping_barcodes": false}
              __workflow_invocation_uuid__ "7834f75aeb5c11ee8272e5b5b5f371a2"
              barcodes {"__current_case__": 1, "column": "barcode-sequence", "source": {"values": [{"id": 5, "src": "hda"}]}, "type": "qza"}
              chromInfo "/tmp/tmpjl26zyu6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
      • Step 9: Summarize demultiplexed output:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • q2galaxy run demux summarize '/tmp/tmpjl26zyu6/job_working_directory/000/7/configs/tmplcjhwq8f'

            Exit Code:

            • 0

            Standard Error:

            • /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py:191: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
                context['result_data'] = context['result_data'].append(df)
              

            Standard Output:

            • 「data: be3c3fa8-51f0-4dce-b112-aa115fa317b1」
              「n: 10000」
                                                                                                                                                                                                                                                                             
              Saved Visualization to: visualization.qzv
              

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __q2galaxy__GUI__section__extra_opts__ {"n": "10000"}
              __workflow_invocation_uuid__ "7834f75aeb5c11ee8272e5b5b5f371a2"
              chromInfo "/tmp/tmpjl26zyu6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
    • Other invocation details
      • history_id

        • 910b34869dd1c5ba
      • history_state

        • ok
      • invocation_id

        • 910b34869dd1c5ba
      • invocation_state

        • scheduled
      • workflow_id

        • 910b34869dd1c5ba
  • ✅ QIIME2-Ib-multiplexed-data-paired-end.ga_0

    Workflow invocation details

    • Invocation Messages

    • Steps
      • Step 1: Forward sequences:

        • step_state: scheduled
      • Step 2: Reverse sequences:

        • step_state: scheduled
      • Step 3: Barcodes:

        • step_state: scheduled
      • Step 4: Metadata:

        • step_state: scheduled
      • Step 5: Metadata parameter:

        • step_state: scheduled
      • Step 6: Reverse complement of barcodes needed?:

        • step_state: scheduled
      • Step 7: Import data into the pipeline:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • q2galaxy run tools import '/tmp/tmpjl26zyu6/job_working_directory/000/12/configs/tmpyd6fnvk3'

            Exit Code:

            • 0

            Standard Output:

            • 「type: EMPPairedEndSequences」
              「format: EMPPairedEndDirFmt」
              

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "0b3038a8eb5d11ee8272e5b5b5f371a2"
              chromInfo "/tmp/tmpjl26zyu6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              import_root {"__current_case__": 4, "__q2galaxy__GUI__cond__format__": {"__current_case__": 1, "format": "EMPPairedEndDirFmt", "import_barcodes": {"data": {"values": [{"id": 11, "src": "hda"}]}, "name": "barcodes.fastq.gz"}, "import_forward": {"data": {"values": [{"id": 9, "src": "hda"}]}, "name": "forward.fastq.gz"}, "import_reverse": {"data": {"values": [{"id": 10, "src": "hda"}]}, "name": "reverse.fastq.gz"}}, "type": "EMPPairedEndSequences"}
      • Step 8: Metadata as artifact:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • q2galaxy run tools import '/tmp/tmpjl26zyu6/job_working_directory/000/13/configs/tmpbh03njl7'

            Exit Code:

            • 0

            Standard Output:

            • 「type: ImmutableMetadata」
              「format: ImmutableMetadataFormat」
              

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "0b3038a8eb5d11ee8272e5b5b5f371a2"
              chromInfo "/tmp/tmpjl26zyu6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              import_root {"__current_case__": 29, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "ImmutableMetadataFormat", "import": {"data": {"values": [{"id": 12, "src": "hda"}]}, "name": "__q2galaxy__::literal::None"}}, "type": "ImmutableMetadata"}
      • Step 9: Demultiplex paired-end sequences:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • q2galaxy run demux emp_paired '/tmp/tmpjl26zyu6/job_working_directory/000/14/configs/tmpf7_jtt7d'

            Exit Code:

            • 0

            Standard Error:

            • /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_demux.py:253: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead.
                for sample_id, barcode in barcodes.to_series().iteritems():
              

            Standard Output:

            • 「seqs: 6bd1217b-7e56-4dcc-855c-9391f3a67bf8」
              「barcodes: <CategoricalMetadataColumn name='barcode-sequence' id_count=75>」
              「golay_error_correction: True」
              「rev_comp_barcodes: False」
              「rev_comp_mapping_barcodes: True」
              「ignore_description_mismatch: False」
                                                                                                                                                                                                                                                                             
              Saved SampleData[PairedEndSequencesWithQuality] to: per_sample_sequences.qza
              Saved ErrorCorrectionDetails to: error_correction_details.qza
              

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __q2galaxy__GUI__section__extra_opts__ {"golay_error_correction": true, "ignore_description_mismatch": false, "rev_comp_barcodes": false, "rev_comp_mapping_barcodes": true}
              __workflow_invocation_uuid__ "0b3038a8eb5d11ee8272e5b5b5f371a2"
              barcodes {"__current_case__": 1, "column": "barcode-sequence", "source": {"values": [{"id": 14, "src": "hda"}]}, "type": "qza"}
              chromInfo "/tmp/tmpjl26zyu6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
      • Step 10: Summarising the demultiplexed output:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • q2galaxy run demux summarize '/tmp/tmpjl26zyu6/job_working_directory/000/15/configs/tmpj7drptj8'

            Exit Code:

            • 0

            Standard Error:

            • /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py:191: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
                context['result_data'] = context['result_data'].append(df)
              /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py:191: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
                context['result_data'] = context['result_data'].append(df)
              

            Standard Output:

            • 「data: 4d8430fb-be67-40ca-8622-592ad6a0c18e」
              「n: 10000」
                                                                                                                                                                                                                                                                             
              Saved Visualization to: visualization.qzv
              

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __q2galaxy__GUI__section__extra_opts__ {"n": "10000"}
              __workflow_invocation_uuid__ "0b3038a8eb5d11ee8272e5b5b5f371a2"
              chromInfo "/tmp/tmpjl26zyu6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
    • Other invocation details
      • history_id

        • 421f1ba3e1644824
      • history_state

        • ok
      • invocation_id

        • 421f1ba3e1644824
      • invocation_state

        • scheduled
      • workflow_id

        • 421f1ba3e1644824
  • ✅ QIIME2-Ic-demultiplexed-data-single-end.ga_0

    Workflow invocation details

    • Invocation Messages

    • Steps
      • Step 1: Sequence collection:

        • step_state: scheduled
      • Step 2: Extract element identifiers:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • mv '/tmp/tmpjl26zyu6/job_working_directory/000/19/configs/tmpscyaj0p3' '/tmp/tmpjl26zyu6/job_working_directory/000/19/outputs/dataset_8abd4267-ae4f-44fe-bfa2-e13f766c9488.dat'

            Exit Code:

            • 0

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "fastqsanger.gz"
              __workflow_invocation_uuid__ "a9bb0cdceb5d11ee8272e5b5b5f371a2"
              chromInfo "/tmp/tmpjl26zyu6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              input_collection {"values": [{"id": 1, "src": "hdca"}]}
      • Step 3: Screening laneless and single-lane:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/503bcd6ebe4b/regex_find_replace/regex.py' --input '/tmp/tmpjl26zyu6/files/8/a/b/dataset_8abd4267-ae4f-44fe-bfa2-e13f766c9488.dat' --output '/tmp/tmpjl26zyu6/job_working_directory/000/20/outputs/dataset_a3de58e4-37dc-4cf0-bc45-843c21874560.dat' --input_display_name 'Extract element identifiers on data 3, data 2, and data 1' --pattern='_L[0-9][0-9][0-9]_' --replacement='_'

            Exit Code:

            • 0

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "a9bb0cdceb5d11ee8272e5b5b5f371a2"
              checks [{"__index__": 0, "pattern": "_L[0-9][0-9][0-9]_", "replacement": "_"}]
              chromInfo "/tmp/tmpjl26zyu6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
      • Step 4: Relabel sequence files:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __workflow_invocation_uuid__ "a9bb0cdceb5d11ee8272e5b5b5f371a2"
              how {"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 22, "src": "hda"}]}, "strict": false}
              input {"values": [{"id": 1, "src": "hdca"}]}
      • Step 5: Import data into the pipeline:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • q2galaxy run tools import '/tmp/tmpjl26zyu6/job_working_directory/000/22/configs/tmpcdajhk4i'

            Exit Code:

            • 0

            Standard Output:

            • 「type: SampleData[SequencesWithQuality]」
              「format: CasavaOneEightLanelessPerSampleDirFmt」
              

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "a9bb0cdceb5d11ee8272e5b5b5f371a2"
              chromInfo "/tmp/tmpjl26zyu6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              import_root {"__current_case__": 49, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "CasavaOneEightLanelessPerSampleDirFmt", "import_sequences": {"__q2galaxy__GUI__cond__sequences__": {"__current_case__": 0, "__q2galaxy__GUI__cond__add_ext__": {"__current_case__": 1, "__q2galaxy__GUI__select__ext_pick__": "no"}, "__q2galaxy__GUI__select__picker__": "collection", "elements": {"values": [{"id": 2, "src": "hdca"}]}}}}, "type": "SampleData__ob__SequencesWithQuality__cb__"}
      • Step 6: Summarising the demultiplexed output:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • q2galaxy run demux summarize '/tmp/tmpjl26zyu6/job_working_directory/000/23/configs/tmp58icwoz1'

            Exit Code:

            • 0

            Standard Error:

            • /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py:191: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
                context['result_data'] = context['result_data'].append(df)
              

            Standard Output:

            • 「data: ca3dc4a5-2033-42bc-b762-9bfd495b3921」
              「n: 10000」
                                                                                                                                                                                                                                                                             
              Saved Visualization to: visualization.qzv
              

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __q2galaxy__GUI__section__extra_opts__ {"n": "10000"}
              __workflow_invocation_uuid__ "a9bb0cdceb5d11ee8272e5b5b5f371a2"
              chromInfo "/tmp/tmpjl26zyu6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
    • Other invocation details
      • history_id

        • 986e9c56085356d2
      • history_state

        • ok
      • invocation_id

        • 986e9c56085356d2
      • invocation_state

        • scheduled
      • workflow_id

        • 986e9c56085356d2
  • ✅ QIIME2-Id-demultiplexed-data-paired-end.ga_0

    Workflow invocation details

    • Invocation Messages

    • Steps
      • Step 1: Sequence collection:

        • step_state: scheduled
      • Step 2: Extract element identifiers:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • mv '/tmp/tmpjl26zyu6/job_working_directory/000/30/configs/tmp4vwz35cs' '/tmp/tmpjl26zyu6/job_working_directory/000/30/outputs/dataset_ecc63933-d559-4468-b63a-f4bd5dddc6cc.dat'

            Exit Code:

            • 0

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "fastqsanger.gz"
              __workflow_invocation_uuid__ "14cab6bceb5e11ee8272e5b5b5f371a2"
              chromInfo "/tmp/tmpjl26zyu6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              input_collection {"values": [{"id": 3, "src": "hdca"}]}
      • Step 3: Screening laneless and single-lane:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/503bcd6ebe4b/regex_find_replace/regex.py' --input '/tmp/tmpjl26zyu6/files/e/c/c/dataset_ecc63933-d559-4468-b63a-f4bd5dddc6cc.dat' --output '/tmp/tmpjl26zyu6/job_working_directory/000/31/outputs/dataset_0b620853-0247-49b4-91dc-2608f2878996.dat' --input_display_name 'Extract element identifiers on data 6, data 5, and others' --pattern='_L[0-9][0-9][0-9]_' --replacement='_'

            Exit Code:

            • 0

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "14cab6bceb5e11ee8272e5b5b5f371a2"
              checks [{"__index__": 0, "pattern": "_L[0-9][0-9][0-9]_", "replacement": "_"}]
              chromInfo "/tmp/tmpjl26zyu6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
      • Step 4: Relabel sequence files:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __workflow_invocation_uuid__ "14cab6bceb5e11ee8272e5b5b5f371a2"
              how {"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 35, "src": "hda"}]}, "strict": false}
              input {"values": [{"id": 3, "src": "hdca"}]}
      • Step 5: Import data into the pipeline:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • q2galaxy run tools import '/tmp/tmpjl26zyu6/job_working_directory/000/33/configs/tmpgmqx83bu'

            Exit Code:

            • 0

            Standard Output:

            • 「type: SampleData[PairedEndSequencesWithQuality]」
              「format: CasavaOneEightLanelessPerSampleDirFmt」
              

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "14cab6bceb5e11ee8272e5b5b5f371a2"
              chromInfo "/tmp/tmpjl26zyu6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              import_root {"__current_case__": 46, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "CasavaOneEightLanelessPerSampleDirFmt", "import_sequences": {"__q2galaxy__GUI__cond__sequences__": {"__current_case__": 0, "__q2galaxy__GUI__cond__add_ext__": {"__current_case__": 1, "__q2galaxy__GUI__select__ext_pick__": "no"}, "__q2galaxy__GUI__select__picker__": "collection", "elements": {"values": [{"id": 4, "src": "hdca"}]}}}}, "type": "SampleData__ob__PairedEndSequencesWithQuality__cb__"}
      • Step 6: Summarising the demultiplexed output:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • q2galaxy run demux summarize '/tmp/tmpjl26zyu6/job_working_directory/000/34/configs/tmpuhjz61jy'

            Exit Code:

            • 0

            Standard Error:

            • /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py:191: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
                context['result_data'] = context['result_data'].append(df)
              /opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py:191: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
                context['result_data'] = context['result_data'].append(df)
              

            Standard Output:

            • 「data: 21410f01-e912-44a8-85e9-78c66f5ba73a」
              「n: 10000」
                                                                                                                                                                                                                                                                             
              Saved Visualization to: visualization.qzv
              

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __q2galaxy__GUI__section__extra_opts__ {"n": "10000"}
              __workflow_invocation_uuid__ "14cab6bceb5e11ee8272e5b5b5f371a2"
              chromInfo "/tmp/tmpjl26zyu6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
    • Other invocation details
      • history_id

        • aa2cfe91c7e18557
      • history_state

        • ok
      • invocation_id

        • aa2cfe91c7e18557
      • invocation_state

        • scheduled
      • workflow_id

        • aa2cfe91c7e18557

Because `Test galaxyproject#1` is rendered as `Test LINK_TO_ISSUE_1`
if posted in a comment (which we do not do yet).
@mvdbeek mvdbeek merged commit 995f5c1 into galaxyproject:master Mar 28, 2024
14 checks passed
@mvdbeek
Copy link
Member

mvdbeek commented Mar 28, 2024

Thank you!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants