Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 9 additions & 0 deletions workflows/amplicon/qiime2/qiime2-II-denoising/CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,14 @@
# Changelog

## [0.4] - 2025-07-21

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_single/qiime2__dada2__denoise_single/2024.10.0+q2galaxy.2024.10.0` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_single/qiime2__dada2__denoise_single/2025.7.0+q2galaxy.2025.7.0`
- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2024.10.0+q2galaxy.2024.10.0` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2025.7.0+q2galaxy.2025.7.0`
- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2024.10.0+q2galaxy.2024.10.0` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2025.7.0+q2galaxy.2025.7.0`
- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__summarize/qiime2__feature_table__summarize/2024.10.0+q2galaxy.2024.10.0` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__summarize/qiime2__feature_table__summarize/2025.7.0+q2galaxy.2025.7.0`
- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_paired/qiime2__dada2__denoise_paired/2024.10.0+q2galaxy.2024.10.0` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_paired/qiime2__dada2__denoise_paired/2025.7.0+q2galaxy.2025.7.0`

## [0.3] - 2024-11-04

### Automatic update
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -9,13 +9,12 @@
"name": "Debjyoti Ghosh"
},
{
"address": "Permoserstra\u00dfe 15, 04318 Leipzig",
"address": "Permoserstraße 15, 04318 Leipzig",
"class": "Organization",
"name": "Helmholtz-Zentrum f\u00fcr Umweltforschung - UFZ"
"name": "Helmholtz-Zentrum für Umweltforschung - UFZ"
}
],
"format-version": "0.1",
"release": "0.3",
"license": "MIT",
"name": "QIIME2 IIa: Denoising (sequence quality control) and feature table creation (single-end)",
"steps": {
Expand Down Expand Up @@ -93,7 +92,7 @@
"top": 387.6692612809613
},
"tool_id": null,
"tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}",
"tool_state": "{\"validators\": [], \"parameter_type\": \"integer\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "02f3a9bf-0e92-4682-b6b3-ab6b5a332937",
Expand All @@ -120,7 +119,7 @@
"top": 519.0800476074219
},
"tool_id": null,
"tool_state": "{\"parameter_type\": \"integer\", \"optional\": true}",
"tool_state": "{\"validators\": [], \"parameter_type\": \"integer\", \"optional\": true}",
"tool_version": null,
"type": "parameter_input",
"uuid": "8d947f65-cb01-4477-b833-4e446f2a92d5",
Expand All @@ -129,7 +128,7 @@
},
"4": {
"annotation": "qiime2 dada2 denoise-paired\nDenoise and dereplicate paired-end sequences\nSmall insight: if the denoising percentage is lower or poorer, reduce 'trunc_q: Int' from 2 to 1.",
"content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_single/qiime2__dada2__denoise_single/2024.10.0+q2galaxy.2024.10.0",
"content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_single/qiime2__dada2__denoise_single/2025.7.0+q2galaxy.2025.7.0",
"errors": null,
"id": 4,
"input_connections": {
Expand Down Expand Up @@ -173,15 +172,15 @@
"top": 133.89925462837766
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_single/qiime2__dada2__denoise_single/2024.10.0+q2galaxy.2024.10.0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_single/qiime2__dada2__denoise_single/2025.7.0+q2galaxy.2025.7.0",
"tool_shed_repository": {
"changeset_revision": "354f63459d37",
"changeset_revision": "be83e72c1ee9",
"name": "qiime2__dada2__denoise_single",
"owner": "q2d2",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"trim_left\": {\"__class__\": \"ConnectedValue\"}, \"max_ee\": \"2.0\", \"trunc_q\": \"2\", \"pooling_method\": \"independent\", \"chimera_method\": \"consensus\", \"min_fold_parent_over_abundance\": \"1.0\", \"allow_one_off\": false, \"n_reads_learn\": \"1000000\", \"hashed_feature_ids\": true, \"retain_all_samples\": true}, \"demultiplexed_seqs\": {\"__class__\": \"ConnectedValue\"}, \"trunc_len\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2024.10.0+q2galaxy.2024.10.0",
"tool_version": "2025.7.0+q2galaxy.2025.7.0",
"type": "tool",
"uuid": "a6369693-372e-4258-9e81-b7085746e441",
"when": null,
Expand All @@ -205,7 +204,7 @@
},
"5": {
"annotation": "qiime2 feature-table tabulate-seqs\nView sequence associated with each feature",
"content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2024.10.0+q2galaxy.2024.10.0",
"content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2025.7.0+q2galaxy.2025.7.0",
"errors": null,
"id": 5,
"input_connections": {
Expand Down Expand Up @@ -241,15 +240,15 @@
"output_name": "visualization"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2024.10.0+q2galaxy.2024.10.0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2025.7.0+q2galaxy.2025.7.0",
"tool_shed_repository": {
"changeset_revision": "c4570ced1d88",
"changeset_revision": "2df6f241b583",
"name": "qiime2__feature_table__tabulate_seqs",
"owner": "q2d2",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"taxonomy\": {\"__class__\": \"RuntimeValue\"}, \"metadata\": [], \"merge_method\": \"strict\"}, \"data\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2024.10.0+q2galaxy.2024.10.0",
"tool_version": "2025.7.0+q2galaxy.2025.7.0",
"type": "tool",
"uuid": "221fe314-49e9-48bd-979e-1b6d0c2f4192",
"when": null,
Expand All @@ -263,7 +262,7 @@
},
"6": {
"annotation": "qiime2 metadata tabulate\nInteractively explore Metadata in a table",
"content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2024.10.0+q2galaxy.2024.10.0",
"content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2025.7.0+q2galaxy.2025.7.0",
"errors": null,
"id": 6,
"input_connections": {
Expand Down Expand Up @@ -294,15 +293,15 @@
"output_name": "visualization"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2024.10.0+q2galaxy.2024.10.0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2025.7.0+q2galaxy.2025.7.0",
"tool_shed_repository": {
"changeset_revision": "9857be21dcaf",
"changeset_revision": "8bf2391cf240",
"name": "qiime2__metadata__tabulate",
"owner": "q2d2",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"page_size\": \"100\"}, \"input\": [{\"__index__\": 0, \"__q2galaxy__GUI__conditional__input__\": {\"type\": \"qza\", \"__current_case__\": 1, \"source\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2024.10.0+q2galaxy.2024.10.0",
"tool_version": "2025.7.0+q2galaxy.2025.7.0",
"type": "tool",
"uuid": "082c2df8-422c-4661-b39d-181ef7ff3072",
"when": null,
Expand All @@ -316,7 +315,7 @@
},
"7": {
"annotation": "qiime2 feature-table summarize\nSummarize table\n",
"content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__summarize/qiime2__feature_table__summarize/2024.10.0+q2galaxy.2024.10.0",
"content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__summarize/qiime2__feature_table__summarize/2025.7.0+q2galaxy.2025.7.0",
"errors": null,
"id": 7,
"input_connections": {
Expand Down Expand Up @@ -351,15 +350,15 @@
"output_name": "visualization"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__summarize/qiime2__feature_table__summarize/2024.10.0+q2galaxy.2024.10.0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__summarize/qiime2__feature_table__summarize/2025.7.0+q2galaxy.2025.7.0",
"tool_shed_repository": {
"changeset_revision": "d0f2249afe30",
"changeset_revision": "93efdc769465",
"name": "qiime2__feature_table__summarize",
"owner": "q2d2",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"sample_metadata\": [{\"__index__\": 0, \"__q2galaxy__GUI__conditional__sample_metadata__\": {\"type\": \"tsv\", \"__current_case__\": 0, \"source\": {\"__class__\": \"ConnectedValue\"}}}]}, \"table\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2024.10.0+q2galaxy.2024.10.0",
"tool_version": "2025.7.0+q2galaxy.2025.7.0",
"type": "tool",
"uuid": "f6376403-1be3-4bc0-af85-d5e2e04984b2",
"when": null,
Expand All @@ -373,6 +372,7 @@
}
},
"tags": [],
"uuid": "718df5b9-9cbb-4792-be50-604e18ef0548",
"version": 2
"uuid": "f3df0d3b-5731-4fe9-96fa-26e19afb5d44",
"version": 1,
"release": "0.4"
}
Loading