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Merged
jfy133 merged 6 commits into from
May 14, 2025
Merged

Update fastqc #804

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a5ad0d4
Update FASTQC module to fix memory definition issue
jfy133 May 14, 2025
7dd5938
Update CHANGELOG
jfy133 May 14, 2025
6f580c9
Update CHANGELOG.md
jfy133 May 14, 2025
91d77eb
Fix typo
jfy133 May 14, 2025
49bdf1b
Merge branch 'update-fastqc' of github.com:nf-core/mag into update-fa…
jfy133 May 14, 2025
04b6e30
Split previous BUSCO to make clearer of major change
jfy133 May 14, 2025
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9 changes: 6 additions & 3 deletions CHANGELOG.md
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Expand Up @@ -7,9 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Added`

- [#730](https://github.com/nf-core/mag/pull/730) - Added `--busco_db_lineage` to allow specifying a specific lineage for BUSCO database and remove `--busco_auto_lineage_prok` (added by @jfy133, @dialvarezs).
- [#784](https://github.com/nf-core/mag/pull/784) - Added `--bin_min_size` and `--bin_max_size` parameters to filter out bins based on size (requested by @maxibor, @alexhbnr, added by @jfy133, @prototaxites).
- [#793](https://github.com/nf-core/mag/pull/793) - Document use of a SquashFS image with `--gtdb_db`, useful for limited inode infrastructure (by @muniheart).
- [#730](https://github.com/nf-core/mag/pull/730) - Added `--busco_db_lineage` to allow specifying a specific lineage for BUSCO database (added by @jfy133, @dialvarezs)
- [#784](https://github.com/nf-core/mag/pull/784) - Added `--bin_min_size` and `--bin_max_size` parameters to filter out bins based on size (requested by @maxibor, @alexhbnr, added by @jfy133, @prototaxites)
- [#793](https://github.com/nf-core/mag/pull/793) - Document use of a SquashFS image with `--gtdb_db`, useful for limited inode infrastructure (by @muniheart)

### `Changed`

Expand All @@ -22,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#789](https://github.com/nf-core/mag/pull/789) - Improve `--bowtie2_mode` description to clarify default settings (reported by @IceGreb, fix by @jfy133)
- [#798](https://github.com/nf-core/mag/pull/798) - Fix overly strict database validation for `--metauk_db` and improve documentation (reported by @ruqse, fix by @jfy133)
- [#804](https://github.com/nf-core/mag/pull/804) - Fix broken memory specification for FASTQC (reported by @jmichaelegana, fix by @awgymer & @jfy133)

### `Dependencies`

Expand All @@ -32,6 +33,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Deprecated`

- [#730](https://github.com/nf-core/mag/pull/730) - Remove `--busco_auto_lineage_prok` due to update and simplified usage of BUSCO (added by @jfy133, @dialvarezs)

## 3.4.0 [2025-04-04]

### `Added`
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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -129,7 +129,7 @@
},
"fastqc": {
"branch": "master",
"git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
"git_sha": "b1966f36ec9de31927b2603d8f499960b2a4c294",
"installed_by": ["modules"]
},
"filtlong": {
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2 changes: 2 additions & 0 deletions modules/nf-core/fastqc/environment.yml
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2 changes: 1 addition & 1 deletion modules/nf-core/fastqc/main.nf
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