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13 changes: 13 additions & 0 deletions workflows/amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md
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# Changelog

## [0.3] - 2025-11-03

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__fragment_insertion__sepp/qiime2__fragment_insertion__sepp/2024.10.0+q2galaxy.2024.10.0` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__fragment_insertion__sepp/qiime2__fragment_insertion__sepp/2025.10.0+q2galaxy.2025.10.0`
- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2024.10.0+q2galaxy.2024.10.0` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2025.10.0+q2galaxy.2025.10.0`
- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2024.10.0+q2galaxy.2024.10.0` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2025.10.0+q2galaxy.2025.10.0`
- `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/2025.10.0+q2galaxy.2025.10.0`
- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2024.10.0+q2galaxy.2024.10.0` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2025.10.0+q2galaxy.2025.10.0`
- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.10.0+dist.h3d8a7e27` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2025.10.0+dist.hbfe50fe0`
- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2024.10.0+q2galaxy.2024.10.0` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2025.10.0+q2galaxy.2025.10.0`
- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2024.10.0+q2galaxy.2024.10.0` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2025.10.0+q2galaxy.2025.10.0`
- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2024.10.0+q2galaxy.2024.10.0` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2025.10.0+q2galaxy.2025.10.0`

## [0.2] - 2024-11-04

### Automatic update
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Expand All @@ -624,7 +623,7 @@
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Expand All @@ -690,7 +689,7 @@
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Expand All @@ -743,7 +742,7 @@
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Expand All @@ -1073,6 +1072,7 @@
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