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Update Taxpasta to v0.6.0 #368

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merged 5 commits into from
Sep 11, 2023
Merged

Update Taxpasta to v0.6.0 #368

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778eaa2
Update Taxpasta to v0.6.0
LilyAnderssonLee Sep 11, 2023
0040cf2
Add PR info
LilyAnderssonLee Sep 11, 2023
3081538
Update CHANGELOG.md
LilyAnderssonLee Sep 11, 2023
5382789
Update CHANGELOG.md
LilyAnderssonLee Sep 11, 2023
9d030a8
Update nextflow_schema.json
LilyAnderssonLee Sep 11, 2023
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#323](https://github.com/nf-core/taxprofiler/pull/323) Add ability to skip sequencing quality control tools (❤️ to @vinisalazar for requesting, added by @jfy133)
- [#345](https://github.com/nf-core/taxprofiler/pull/345) Add simple tutorial to explain how to get up and running with an nf-core/taxprofiler run (added by @jfy133)
- [#355](https://github.com/nf-core/taxprofiler/pull/355) Add support for TAXPASTA's `--add-rank-lineage` to output (❤️ to @MajoroMask for request, added by @Midnighter, @sofstam, @jfy133)
- [#368](https://github.com/nf-core/taxprofiler/pull/368/) Add the ability to ignore profile errors caused by empty profiles and other validation errors when merging multiple profiles using TAXPASTA (added by @Midnighter and @LilyAnderssonLee)

### `Fixed`

Expand Down Expand Up @@ -48,7 +49,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
| Tool | Previous version | New version |
| --------- | ---------------- | ----------- |
| MultiQC | 1.13 | 1.14 |
| TAXPASTA | 0.2.3 | 0.5.0 |
| TAXPASTA | 0.2.3 | 0.6.0 |
| MetaPhlAn | 3.0.12 | 4.0.6 |

### `Deprecated`
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3 changes: 2 additions & 1 deletion conf/modules.config
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Expand Up @@ -731,7 +731,8 @@ process {
params.taxpasta_add_rank ? "--add-rank" : "",
params.taxpasta_add_lineage ? "--add-lineage" : "",
params.taxpasta_add_idlineage ? "--add-id-lineage" : "",
params.taxpasta_add_ranklineage ? "--add-rank-lineage" : ""
params.taxpasta_add_ranklineage ? "--add-rank-lineage" : "",
params.taxpasta_ignore_errors ? "--ignore-errors" : ""
].join(' ').trim()
}
publishDir = [
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4 changes: 2 additions & 2 deletions modules.json
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Expand Up @@ -234,12 +234,12 @@
},
"taxpasta/merge": {
"branch": "master",
"git_sha": "3af710fef2aa46a913b3cce7bd2a728976164e56",
"git_sha": "7edce7d8425ebdf3975d22c2c4fe741d7b5dd899",
"installed_by": ["modules"]
},
"taxpasta/standardise": {
"branch": "master",
"git_sha": "3af710fef2aa46a913b3cce7bd2a728976164e56",
"git_sha": "7edce7d8425ebdf3975d22c2c4fe741d7b5dd899",
"installed_by": ["modules"]
},
"untar": {
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6 changes: 3 additions & 3 deletions modules/nf-core/taxpasta/merge/main.nf
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6 changes: 3 additions & 3 deletions modules/nf-core/taxpasta/standardise/main.nf
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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -181,6 +181,7 @@ params {
taxpasta_add_lineage = false
taxpasta_add_idlineage = false
taxpasta_add_ranklineage = false
taxpasta_ignore_errors = false
standardisation_motus_generatebiom = false
}

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6 changes: 6 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -641,6 +641,12 @@
"description": "Add the taxon's entire rank lineage to the output.",
"help_text": "\nThe standard output format of taxpasta is a two-column table including the read counts and the integer taxonomic ID. The taxonomic ranks categories of the taxon's entire lineage separated by semi-colons can be added as additional information to the output table. This complements `--taxpasta_add_lineage` by telling you which taxonomic rank level each entry in the lineage refers to.\n\nModifies tool parameter(s):\n- taxpasta: `--add-rank-lineage`\n",
"fa_icon": "fas fa-link"
},
"taxpasta_ignore_errors": {
"type": "boolean",
"description": "Ignore individual profiles that cause errors.",
"help_text": "\nIgnore any metagenomic profiles with errors when running `taxpasta merge`. At least two profiles without errors are needed to merge.\n\nModifies tool parameter(s):\n- taxpasta: `--ignore-errors`\n",
"fa_icon": "fas fa-link"
}
},
"fa_icon": "fas fa-chart-line"
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