Updating workflows/amplicon/qiime2/qiime2-I-import from 0.2 to 0.3 #422

gxydevbot · 2024-05-27T13:06:55Z

Hello! This is an automated update of the following workflow: workflows/amplicon/qiime2/qiime2-I-import. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.2.1+dist.he188c3c2
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_single/qiime2__demux__emp_single/2023.5.0+q2galaxy.2023.5.0.2 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_single/qiime2__demux__emp_single/2024.2.0+q2galaxy.2024.2.1
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2023.5.0+q2galaxy.2023.5.0.2 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2024.2.0+q2galaxy.2024.2.1
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.2.1+dist.he188c3c2
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_paired/qiime2__demux__emp_paired/2023.5.0+q2galaxy.2023.5.0.2 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_paired/qiime2__demux__emp_paired/2024.2.0+q2galaxy.2024.2.1
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2023.5.0+q2galaxy.2023.5.0.2 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2024.2.0+q2galaxy.2024.2.1
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.2.1+dist.he188c3c2
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2023.5.0+q2galaxy.2023.5.0.2 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2024.2.0+q2galaxy.2024.2.1
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.2.1+dist.he188c3c2
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2023.5.0+q2galaxy.2023.5.0.2 should be updated to toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2024.2.0+q2galaxy.2024.2.1

The workflow release number has been updated from 0.2 to 0.3.

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ia-multiplexed-data-single-end.ga

workflows/amplicon/qiime2/qiime2-I-import/CHANGELOG.md

bernt-matthias · 2024-05-28T14:32:38Z

@mvdbeek could you point me to the logs where it shows the reason for not updating?

I tried locally: if I run the autoupdate 2x then c is updated...

lldelisle · 2024-05-28T15:33:45Z

I got the same bug with #429 all 3 workflows of the directory should have been updated...

github-actions · 2024-06-10T04:46:47Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	4
Passed	3
Error	1
Failure	0
Skipped	0

Errored Tests

❌ QIIME2-Id-demultiplexed-data-paired-end.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

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/tmpo3e9ek65/job_working_directory/000/30/configs/tmpx0_uzjy0' '/tmp/tmpo3e9ek65/job_working_directory/000/30/outputs/dataset_b19671e3-6c99-4267-8271-77f6da64b715.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"e55208ec26e311ef89a8e76d21b9ab60"`
chromInfo	`"/tmp/tmpo3e9ek65/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/tmpo3e9ek65/files/b/1/9/dataset_b19671e3-6c99-4267-8271-77f6da64b715.dat' --output '/tmp/tmpo3e9ek65/job_working_directory/000/31/outputs/dataset_e5679c72-6c64-4fcc-abc4-614ff014c049.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__	`"e55208ec26e311ef89a8e76d21b9ab60"`
checks	`[{"__index__": 0, "pattern": "_L[0-9][0-9][0-9]_", "replacement": "_"}]`
chromInfo	`"/tmp/tmpo3e9ek65/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__	`"e55208ec26e311ef89a8e76d21b9ab60"`
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 error

Command Line:

q2galaxy run tools import '/tmp/tmpo3e9ek65/job_working_directory/000/33/configs/tmpjjwykbnu'

Exit Code:

```
125
```

Standard Error:

Unable to find image 'quay.io/qiime2/core:2023.5' locally
2023.5: Pulling from qiime2/core
42c077c10790: Pulling fs layer
1a23c9d790a3: Pulling fs layer
22a6fc63b9b5: Pulling fs layer
dd499ae3733f: Pulling fs layer
012a2b6b385e: Pulling fs layer
dd499ae3733f: Waiting
012a2b6b385e: Waiting
0921518aca19: Pulling fs layer
1c0e12e18f94: Pulling fs layer
0921518aca19: Waiting
1413bc183df8: Pulling fs layer
1c0e12e18f94: Waiting
795207d4f19b: Pulling fs layer
96364662752a: Pulling fs layer
c3edffcb7ece: Pulling fs layer
1413bc183df8: Waiting
795207d4f19b: Waiting
96364662752a: Waiting
3f541efa0329: Pulling fs layer
8ebefce780ee: Pulling fs layer
ee2b99347e51: Pulling fs layer
c6e473dc65aa: Pulling fs layer
c3edffcb7ece: Waiting
3f541efa0329: Waiting
8ebefce780ee: Waiting
ee2b99347e51: Waiting
c6e473dc65aa: Waiting
42c077c10790: Verifying Checksum
42c077c10790: Download complete
dd499ae3733f: Verifying Checksum
dd499ae3733f: Download complete
1a23c9d790a3: Verifying Checksum
1a23c9d790a3: Download complete
22a6fc63b9b5: Verifying Checksum
22a6fc63b9b5: Download complete
0921518aca19: Verifying Checksum
0921518aca19: Download complete
1c0e12e18f94: Verifying Checksum
1c0e12e18f94: Download complete
1413bc183df8: Verifying Checksum
1413bc183df8: Download complete
96364662752a: Verifying Checksum
96364662752a: Download complete
c3edffcb7ece: Verifying Checksum
c3edffcb7ece: Download complete
3f541efa0329: Verifying Checksum
3f541efa0329: Download complete
8ebefce780ee: Verifying Checksum
8ebefce780ee: Download complete
012a2b6b385e: Verifying Checksum
012a2b6b385e: Download complete
ee2b99347e51: Verifying Checksum
ee2b99347e51: Download complete
c6e473dc65aa: Verifying Checksum
c6e473dc65aa: Download complete
42c077c10790: Pull complete
1a23c9d790a3: Pull complete
22a6fc63b9b5: Pull complete
dd499ae3733f: Pull complete
795207d4f19b: Verifying Checksum
795207d4f19b: Download complete
012a2b6b385e: Pull complete
0921518aca19: Pull complete
1c0e12e18f94: Pull complete
1413bc183df8: Pull complete
docker: failed to register layer: write /opt/conda/envs/qiime2-2023.5/libexec/gcc/x86_64-conda-linux-gnu/12.2.0/cc1: no space left on device.
See 'docker run --help'.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e55208ec26e311ef89a8e76d21b9ab60"`
chromInfo	`"/tmp/tmpo3e9ek65/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 paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__q2galaxy__GUI__section__extra_opts__	`{"n": "10000"}`
__workflow_invocation_uuid__	`"e55208ec26e311ef89a8e76d21b9ab60"`
chromInfo	`"/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 669901bb54198fac
- history_state
  - error
- invocation_id
  - 669901bb54198fac
- invocation_state
  - scheduled
- workflow_id
  - 669901bb54198fac

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/tmpo3e9ek65/job_working_directory/000/4/configs/tmpcumx63x1'

Exit Code:

```
0
```

Standard Output:

｢type: EMPSingleEndSequences｣
｢format: EMPSingleEndDirFmt｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"abf73f9226e111ef89a8e76d21b9ab60"`
chromInfo	`"/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 7, "__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/tmpo3e9ek65/job_working_directory/000/5/configs/tmppyvky0y8'

Exit Code:

```
0
```

Standard Output:

｢type: ImmutableMetadata｣
｢format: ImmutableMetadataFormat｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"abf73f9226e111ef89a8e76d21b9ab60"`
chromInfo	`"/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 48, "__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/tmpo3e9ek65/job_working_directory/000/6/configs/tmp53selfg8'

Exit Code:

```
0
```

Standard Output:

｢seqs: 27388997-cb18-47ef-92b9-ce152a4bac8a｣
｢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__	`"abf73f9226e111ef89a8e76d21b9ab60"`
barcodes	`{"__current_case__": 1, "column": "barcode-sequence", "source": {"values": [{"id": 5, "src": "hda"}]}, "type": "qza"}`
chromInfo	`"/tmp/tmpo3e9ek65/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/tmpo3e9ek65/job_working_directory/000/7/configs/tmp6km6zgdo'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/seaborn/_oldcore.py:1119: FutureWarning: use_inf_as_na option is deprecated and will be removed in a future version. Convert inf values to NaN before operating instead.
  with pd.option_context('mode.use_inf_as_na', True):
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_demux/_summarize/_visualizer.py:180: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation.
  context['result_data'] = pd.concat([context['result_data'], df])
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_demux/_summarize/_visualizer.py:74: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '['152 nts' '152 nts' '152 nts' '152 nts' '152 nts' '152 nts' '152 nts']' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  stats[stats.index != 'count'] = \

Standard Output:

｢data: 2b1b85ab-1e26-41bf-b378-2505bac0a6f6｣
｢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__	`"abf73f9226e111ef89a8e76d21b9ab60"`
chromInfo	`"/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Other invocation details
- history_id
  - 91ad1f11f95a32d4
- history_state
  - ok
- invocation_id
  - 91ad1f11f95a32d4
- invocation_state
  - scheduled
- workflow_id
  - 91ad1f11f95a32d4

✅ 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/tmpo3e9ek65/job_working_directory/000/12/configs/tmpmqg6ywd9'

Exit Code:

```
0
```

Standard Output:

｢type: EMPPairedEndSequences｣
｢format: EMPPairedEndDirFmt｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5908059026e211ef89a8e76d21b9ab60"`
chromInfo	`"/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 6, "__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/tmpo3e9ek65/job_working_directory/000/13/configs/tmpzduuxm2u'

Exit Code:

```
0
```

Standard Output:

｢type: ImmutableMetadata｣
｢format: ImmutableMetadataFormat｣

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5908059026e211ef89a8e76d21b9ab60"`
chromInfo	`"/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 48, "__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/tmpo3e9ek65/job_working_directory/000/14/configs/tmp3chv84xx'

Exit Code:

```
0
```

Standard Output:

｢seqs: 943a7465-e3c3-4ed3-8037-66b9b14e8d80｣
｢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__	`"5908059026e211ef89a8e76d21b9ab60"`
barcodes	`{"__current_case__": 1, "column": "barcode-sequence", "source": {"values": [{"id": 14, "src": "hda"}]}, "type": "qza"}`
chromInfo	`"/tmp/tmpo3e9ek65/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/tmpo3e9ek65/job_working_directory/000/15/configs/tmp7py2w_no'

Exit Code:

```
0
```

Standard Error:

/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/seaborn/_oldcore.py:1119: FutureWarning: use_inf_as_na option is deprecated and will be removed in a future version. Convert inf values to NaN before operating instead.
  with pd.option_context('mode.use_inf_as_na', True):
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_demux/_summarize/_visualizer.py:180: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation.
  context['result_data'] = pd.concat([context['result_data'], df])
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_demux/_summarize/_visualizer.py:74: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '['151 nts' '151 nts' '151 nts' '151 nts' '151 nts' '151 nts' '151 nts']' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  stats[stats.index != 'count'] = \
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/seaborn/_oldcore.py:1119: FutureWarning: use_inf_as_na option is deprecated and will be removed in a future version. Convert inf values to NaN before operating instead.
  with pd.option_context('mode.use_inf_as_na', True):
/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_demux/_summarize/_visualizer.py:74: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '['151 nts' '151 nts' '151 nts' '151 nts' '151 nts' '151 nts' '151 nts']' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  stats[stats.index != 'count'] = \

Standard Output:

｢data: 88538a00-7b71-4f0f-adc5-6af6dd082bba｣
｢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__	`"5908059026e211ef89a8e76d21b9ab60"`
chromInfo	`"/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Other invocation details
- history_id
  - ab92eaf80407a21f
- history_state
  - ok
- invocation_id
  - ab92eaf80407a21f
- invocation_state
  - scheduled
- workflow_id
  - ab92eaf80407a21f

✅ 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/tmpo3e9ek65/job_working_directory/000/19/configs/tmpzjygeyiv' '/tmp/tmpo3e9ek65/job_working_directory/000/19/outputs/dataset_6fb29116-748f-4c3d-af44-85f0f64ff7bc.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"066906bc26e311ef89a8e76d21b9ab60"`
chromInfo	`"/tmp/tmpo3e9ek65/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/tmpo3e9ek65/files/6/f/b/dataset_6fb29116-748f-4c3d-af44-85f0f64ff7bc.dat' --output '/tmp/tmpo3e9ek65/job_working_directory/000/20/outputs/dataset_4cfb1f30-6159-448d-9d86-8d27b4f35146.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__	`"066906bc26e311ef89a8e76d21b9ab60"`
checks	`[{"__index__": 0, "pattern": "_L[0-9][0-9][0-9]_", "replacement": "_"}]`
chromInfo	`"/tmp/tmpo3e9ek65/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__	`"066906bc26e311ef89a8e76d21b9ab60"`
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/tmpo3e9ek65/job_working_directory/000/22/configs/tmps0dm3bfi'

Exit Code:

```
0
```

Standard Output:

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

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"066906bc26e311ef89a8e76d21b9ab60"`
chromInfo	`"/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
import_root	`{"__current_case__": 63, "__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/tmpo3e9ek65/job_working_directory/000/23/configs/tmpo4mfv_o_'

Exit Code:

```
0
```

Standard Output:

｢data: 51d5a6e8-3c79-435e-a956-1657231daf4a｣
｢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__	`"066906bc26e311ef89a8e76d21b9ab60"`
chromInfo	`"/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Other invocation details
- history_id
  - df2c825db99b816d
- history_state
  - ok
- invocation_id
  - df2c825db99b816d
- invocation_state
  - scheduled
- workflow_id
  - df2c825db99b816d

mvdbeek · 2024-06-17T08:36:07Z

Is this stuck on anything ? Looks like the tests are all passing ?

lldelisle · 2024-06-17T10:13:44Z

Changelog should be reordered.
Workflow versions should match the changelog.

bernt-matthias · 2024-06-17T10:35:27Z

Only 3 of the 4 workflows have been updated (xref). Also wondering why the description field is changed.

gxydevbot · 2024-08-26T04:26:00Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-02T04:29:44Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-09T04:27:52Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-16T04:26:23Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-23T04:29:31Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-23T14:06:17Z

There are new updates, they have been integrated to the PR, check the file diff.

gxydevbot · 2024-09-24T13:46:50Z

There are new updates, they have been integrated to the PR, check the file diff.

gxydevbot · 2024-11-04T04:29:06Z

There are new updates, they have been integrated to the PR, check the file diff.

bernt-matthias · 2024-11-23T18:30:22Z

Workflow versions should match the changelog.

Is this now correct?

gxydevbot · 2024-11-25T04:59:12Z

There are new updates, if you want to integrate them, close the PR and delete branch.

mvdbeek

LGTM!

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Id-demultiplexed-data-paired-end.ga

lldelisle reviewed May 27, 2024

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workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ia-multiplexed-data-single-end.ga Outdated Show resolved Hide resolved

bernt-matthias reviewed May 28, 2024

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workflows/amplicon/qiime2/qiime2-I-import/CHANGELOG.md Outdated Show resolved Hide resolved

bernt-matthias mentioned this pull request Jun 2, 2024

Fix autoupdate for workflows with overlapping tool updates galaxyproject/planemo#1452

Merged

gxydevbot changed the title ~~Updating workflows/amplicon/qiime2/qiime2-I-import from 0.2 to 0.3~~ Updating workflows/amplicon/qiime2/qiime2-I-import from 0.2 to 0.3 Jun 3, 2024

gxydevbot force-pushed the workflows/amplicon/qiime2/qiime2-I-import branch from d6975e5 to 67dd615 Compare August 22, 2024 15:47

gxydevbot force-pushed the workflows/amplicon/qiime2/qiime2-I-import branch from 67dd615 to df144be Compare September 23, 2024 14:06

gxydevbot force-pushed the workflows/amplicon/qiime2/qiime2-I-import branch from df144be to b3b0eb2 Compare September 24, 2024 13:46

Updating workflows/amplicon/qiime2/qiime2-I-import from 0.2 to 0.3

d04acd9

gxydevbot force-pushed the workflows/amplicon/qiime2/qiime2-I-import branch from b3b0eb2 to d04acd9 Compare November 4, 2024 04:29

bernt-matthias added 2 commits November 23, 2024 19:24

Fix annotation/description

6027fef

Reorder CHANGELOG.md

b0464cd

mvdbeek approved these changes Nov 25, 2024

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mvdbeek reviewed Nov 25, 2024

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workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Id-demultiplexed-data-paired-end.ga Show resolved Hide resolved

mvdbeek merged commit 072161d into galaxyproject:main Nov 26, 2024
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Updating workflows/amplicon/qiime2/qiime2-I-import from 0.2 to 0.3 #422

Updating workflows/amplicon/qiime2/qiime2-I-import from 0.2 to 0.3 #422

gxydevbot commented May 27, 2024

bernt-matthias commented May 28, 2024

lldelisle commented May 28, 2024

github-actions bot commented Jun 10, 2024

Workflow invocation details

Workflow invocation details

Workflow invocation details

Workflow invocation details

mvdbeek commented Jun 17, 2024

lldelisle commented Jun 17, 2024

bernt-matthias commented Jun 17, 2024

gxydevbot commented Aug 26, 2024

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bernt-matthias commented Nov 23, 2024

gxydevbot commented Nov 25, 2024

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Updating workflows/amplicon/qiime2/qiime2-I-import from 0.2 to 0.3 #422

Updating workflows/amplicon/qiime2/qiime2-I-import from 0.2 to 0.3 #422

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gxydevbot commented May 27, 2024

bernt-matthias commented May 28, 2024

lldelisle commented May 28, 2024

github-actions bot commented Jun 10, 2024

Test Results (powered by Planemo)

Test Summary

Workflow invocation details

Workflow invocation details

Workflow invocation details

Workflow invocation details

mvdbeek commented Jun 17, 2024

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