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

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merged 3 commits into from
Nov 26, 2024
Merged

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

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d04acd9
Updating workflows/amplicon/qiime2/qiime2-I-import from 0.2 to 0.3
Nov 4, 2024
6027fef
Fix annotation/description
bernt-matthias Nov 23, 2024
b0464cd
Reorder CHANGELOG.md
bernt-matthias Nov 23, 2024
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13 changes: 11 additions & 2 deletions workflows/amplicon/qiime2/qiime2-I-import/CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,6 +1,15 @@
# Changelog

## [0.3] 2024-11-04

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.10.0+dist.h3d8a7e27`
- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_single/qiime2__demux__emp_single/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_single/qiime2__demux__emp_single/2024.10.0+q2galaxy.2024.10.0`
- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2024.10.0+q2galaxy.2024.10.0`
- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_paired/qiime2__demux__emp_paired/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_paired/qiime2__demux__emp_paired/2024.10.0+q2galaxy.2024.10.0`

## [0.2] 2024-05-23
Fix dockstore.yml and test.

## [0.1] 2024-04-08
First release.
## [0.2] 2024-05-23
Fix dockstore.yml and test.
59 changes: 36 additions & 23 deletions workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ia-multiplexed-data-single-end.ga
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Expand Up @@ -15,7 +15,7 @@
],
"format-version": "0.1",
"license": "MIT",
"release": "0.2",
"release": "0.3",
"name": "QIIME2 Ia: multiplexed data (single-end)",
"steps": {
"0": {
Expand Down Expand Up @@ -73,7 +73,7 @@
"workflow_outputs": []
},
"2": {
"annotation": "Metadata",
"annotation": "A tab separated metadata file",
"content_id": null,
"errors": null,
"id": 2,
Expand Down Expand Up @@ -127,7 +127,7 @@
"workflow_outputs": []
},
"4": {
"annotation": "Reverse complement barcodes",
"annotation": "If reverse complement of barcodes is necessary for the analysis, choose Yes.",
"content_id": null,
"errors": null,
"id": 4,
Expand Down Expand Up @@ -155,7 +155,7 @@
},
"5": {
"annotation": "qiime2 tools input\nThis step allows the input of the files to be analysed and then generate a qza output, necessary for the QIIME2 pipeline.",
"content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3",
"content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.10.0+dist.h3d8a7e27",
"errors": null,
"id": 5,
"input_connections": {
Expand Down Expand Up @@ -195,23 +195,23 @@
"output_name": "imported_data"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3",
"tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.10.0+dist.h3d8a7e27",
"tool_shed_repository": {
"changeset_revision": "10447a4b0cc3",
"changeset_revision": "8a0db69428c7",
"name": "qiime2_core__tools__import",
"owner": "q2d2",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"import_root\": {\"type\": \"EMPSingleEndSequences\", \"__current_case__\": 5, \"__q2galaxy__GUI__cond__format__\": {\"format\": \"EMPSingleEndDirFmt\", \"__current_case__\": 1, \"import_sequences\": {\"name\": \"sequences.fastq.gz\", \"data\": {\"__class__\": \"ConnectedValue\"}}, \"import_barcodes\": {\"name\": \"barcodes.fastq.gz\", \"data\": {\"__class__\": \"ConnectedValue\"}}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2023.5.0+dist.h193f7cc9.3",
"tool_state": "{\"import_root\": {\"type\": \"EMPSingleEndSequences\", \"__current_case__\": 17, \"__q2galaxy__GUI__cond__format__\": {\"format\": \"EMPSingleEndDirFmt\", \"__current_case__\": 1, \"import_sequences\": {\"name\": \"sequences.fastq.gz\", \"data\": {\"__class__\": \"ConnectedValue\"}}, \"import_barcodes\": {\"name\": \"barcodes.fastq.gz\", \"data\": {\"__class__\": \"ConnectedValue\"}}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2024.10.0+dist.h3d8a7e27",
"type": "tool",
"uuid": "b39f05da-9f23-47ff-9695-b21bb61f18a2",
"when": null,
"workflow_outputs": []
},
"6": {
"annotation": "Import the metadata as artifact",
"content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3",
"content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.10.0+dist.h3d8a7e27",
"errors": null,
"id": 6,
"input_connections": {
Expand Down Expand Up @@ -247,23 +247,23 @@
"output_name": "imported_data"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3",
"tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.10.0+dist.h3d8a7e27",
"tool_shed_repository": {
"changeset_revision": "10447a4b0cc3",
"changeset_revision": "8a0db69428c7",
"name": "qiime2_core__tools__import",
"owner": "q2d2",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"import_root\": {\"type\": \"ImmutableMetadata\", \"__current_case__\": 29, \"__q2galaxy__GUI__cond__format__\": {\"format\": \"ImmutableMetadataFormat\", \"__current_case__\": 0, \"import\": {\"name\": \"__q2galaxy__::literal::None\", \"data\": {\"__class__\": \"ConnectedValue\"}}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2023.5.0+dist.h193f7cc9.3",
"tool_state": "{\"import_root\": {\"type\": \"ImmutableMetadata\", \"__current_case__\": 58, \"__q2galaxy__GUI__cond__format__\": {\"format\": \"ImmutableMetadataFormat\", \"__current_case__\": 0, \"import\": {\"name\": \"__q2galaxy__::literal::None\", \"data\": {\"__class__\": \"ConnectedValue\"}}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2024.10.0+dist.h3d8a7e27",
"type": "tool",
"uuid": "9caaabce-3a1a-4bf9-9fa0-d6fbe24a4bb4",
"when": null,
"workflow_outputs": []
},
"7": {
"annotation": "qiime2 demux emp-single\nDemultiplex sequence data generated with the EMP protocol.",
"content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_single/qiime2__demux__emp_single/2023.5.0+q2galaxy.2023.5.0.2",
"content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_single/qiime2__demux__emp_single/2024.10.0+q2galaxy.2024.10.0",
"errors": null,
"id": 7,
"input_connections": {
Expand All @@ -284,7 +284,20 @@
"output_name": "imported_data"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool qiime2 demux emp-single",
"name": "__q2galaxy__GUI__section__extra_opts__"
},
{
"description": "runtime parameter for tool qiime2 demux emp-single",
"name": "barcodes"
},
{
"description": "runtime parameter for tool qiime2 demux emp-single",
"name": "barcodes"
}
],
"label": "Demultiplex single-end data",
"name": "qiime2 demux emp-single",
"outputs": [
Expand Down Expand Up @@ -322,15 +335,15 @@
"output_name": "per_sample_sequences"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_single/qiime2__demux__emp_single/2023.5.0+q2galaxy.2023.5.0.2",
"tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_single/qiime2__demux__emp_single/2024.10.0+q2galaxy.2024.10.0",
"tool_shed_repository": {
"changeset_revision": "75b07a996ac0",
"changeset_revision": "8e01d149bcdb",
"name": "qiime2__demux__emp_single",
"owner": "q2d2",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"golay_error_correction\": true, \"rev_comp_barcodes\": false, \"rev_comp_mapping_barcodes\": {\"__class__\": \"ConnectedValue\"}, \"ignore_description_mismatch\": false}, \"barcodes\": {\"type\": \"qza\", \"__current_case__\": 1, \"source\": {\"__class__\": \"ConnectedValue\"}, \"column\": {\"__class__\": \"ConnectedValue\"}}, \"seqs\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2023.5.0+q2galaxy.2023.5.0.2",
"tool_version": "2024.10.0+q2galaxy.2024.10.0",
"type": "tool",
"uuid": "23dd9199-b8aa-4daf-893f-1ca504ee0292",
"when": null,
Expand All @@ -344,7 +357,7 @@
},
"8": {
"annotation": "qiime2 demux summarize\nSummarize counts per sample.\n(Galaxy Version 2023.5.0+q2galaxy.2023.5.0.2)",
"content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2023.5.0+q2galaxy.2023.5.0.2",
"content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2024.10.0+q2galaxy.2024.10.0",
"errors": null,
"id": 8,
"input_connections": {
Expand Down Expand Up @@ -375,15 +388,15 @@
"output_name": "visualization"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2023.5.0+q2galaxy.2023.5.0.2",
"tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2024.10.0+q2galaxy.2024.10.0",
"tool_shed_repository": {
"changeset_revision": "d8a9f74f1a6d",
"changeset_revision": "1a13e87462a0",
"name": "qiime2__demux__summarize",
"owner": "q2d2",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"n\": \"10000\"}, \"data\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2023.5.0+q2galaxy.2023.5.0.2",
"tool_version": "2024.10.0+q2galaxy.2024.10.0",
"type": "tool",
"uuid": "3b70c32e-3cd7-4444-b5e8-3ecf0916a14f",
"when": null,
Expand All @@ -399,4 +412,4 @@
"tags": [],
"uuid": "951c418e-f57e-491d-af38-f2c44c6089ce",
"version": 45
}
}
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