Fix markdown template: add missing closing details tag

[bernt-matthias]

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

[bernt-matthias]

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

[bernt-matthias]

The following has been created with the last commit

[bernt-matthias]

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:** * ```console q2galaxy run tools import '/tmp/tmpjl26zyu6/job_working_directory/000/4/configs/tmplbelsa3p' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢type: EMPSingleEndSequences｣ ｢format: EMPSingleEndDirFmt｣ ``` **Traceback:** * ```console ``` **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

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           q2galaxy run tools import '/tmp/tmpjl26zyu6/job_working_directory/000/5/configs/tmpk2f8jo9s'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Standard Output:**

         * ```console
           ｢type: ImmutableMetadata｣
           ｢format: ImmutableMetadataFormat｣

           ```
        **Traceback:**

         * ```console

           ```
        **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"} ` |

      </details>

 - **Step 8: Demultiplex single-end data**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           q2galaxy run demux emp_single '/tmp/tmpjl26zyu6/job_working_directory/000/6/configs/tmp7bkdxmy4'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Standard Error:**

         * ```console
           /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:**

         * ```console
           ｢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:**

         * ```console

           ```
        **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 | ` "?" ` |

      </details>

 - **Step 9: Summarize demultiplexed output**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           q2galaxy run demux summarize '/tmp/tmpjl26zyu6/job_working_directory/000/7/configs/tmplcjhwq8f'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Standard Error:**

         * ```console
           /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:**

         * ```console
           ｢data: be3c3fa8-51f0-4dce-b112-aa115fa317b1｣
           ｢n: 10000｣

           Saved Visualization to: visualization.qzv

           ```
        **Traceback:**

         * ```console

           ```
        **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 | ` "?" ` |

      </details>
  </details>

• 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:** * ```console q2galaxy run tools import '/tmp/tmpjl26zyu6/job_working_directory/000/12/configs/tmpyd6fnvk3' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢type: EMPPairedEndSequences｣ ｢format: EMPPairedEndDirFmt｣ ``` **Traceback:** * ```console ``` **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:** * ```console q2galaxy run tools import '/tmp/tmpjl26zyu6/job_working_directory/000/13/configs/tmpbh03njl7' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢type: ImmutableMetadata｣ ｢format: ImmutableMetadataFormat｣ ``` **Traceback:** * ```console ``` **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:** * ```console q2galaxy run demux emp_paired '/tmp/tmpjl26zyu6/job_working_directory/000/14/configs/tmpf7_jtt7d' ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console /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:** * ```console ｢seqs: 6bd1217b-7e56-4dcc-855c-9391f3a67bf8｣ ｢barcodes: ｣ ｢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:** * ```console ``` **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:** * ```console q2galaxy run demux summarize '/tmp/tmpjl26zyu6/job_working_directory/000/15/configs/tmpj7drptj8' ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console /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:** * ```console ｢data: 4d8430fb-be67-40ca-8622-592ad6a0c18e｣ ｢n: 10000｣ Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **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

[mvdbeek]

Thank you!