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Update taxpasta #355

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merged 5 commits into from
Aug 26, 2023
Merged

Update taxpasta #355

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7f9315f
Update taxpasta
sofstam Aug 25, 2023
027dddf
Update changelog dependencies
sofstam Aug 25, 2023
026ed22
Add rank lineage parameter and fix mistakes in schema docs
jfy133 Aug 26, 2023
b85d397
Apply suggestions from code review
jfy133 Aug 26, 2023
071e488
Update CHANGELOG.md [skip ci]
jfy133 Aug 26, 2023
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#319](https://github.com/nf-core/taxprofiler/pull/319) Added support for virus hit expansion in Kaiju (❤️ to @dnlrxn for requesting, added by @jfy133)
- [#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)

### `Fixed`

Expand Down Expand Up @@ -46,7 +47,7 @@ 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 | 0.4.1 |
| TAXPASTA | 0.2.3 | 0.5.0 |
| 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 @@ -730,7 +730,8 @@ process {
params.taxpasta_add_name ? "--add-name" : "",
params.taxpasta_add_rank ? "--add-rank" : "",
params.taxpasta_add_lineage ? "--add-lineage" : "",
params.taxpasta_add_idlineage ? "--add-id-lineage" : ""
params.taxpasta_add_idlineage ? "--add-id-lineage" : "",
params.taxpasta_add_ranklineage ? "--add-rank-lineage" : ""
].join(' ').trim()
}
publishDir = [
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4 changes: 2 additions & 2 deletions modules.json
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Expand Up @@ -239,12 +239,12 @@
},
"taxpasta/merge": {
"branch": "master",
"git_sha": "72230a81d2a1e61d171dbfc427d48d53ac7b1d86",
"git_sha": "3af710fef2aa46a913b3cce7bd2a728976164e56",
"installed_by": ["modules"]
},
"taxpasta/standardise": {
"branch": "master",
"git_sha": "72230a81d2a1e61d171dbfc427d48d53ac7b1d86",
"git_sha": "3af710fef2aa46a913b3cce7bd2a728976164e56",
"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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3 changes: 2 additions & 1 deletion nextflow.config
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Expand Up @@ -180,6 +180,7 @@ params {
taxpasta_add_rank = false
taxpasta_add_lineage = false
taxpasta_add_idlineage = false
taxpasta_add_ranklineage = false
standardisation_motus_generatebiom = false
}

Expand Down Expand Up @@ -302,7 +303,7 @@ profiles {
test_fastp { includeConfig 'conf/test_fastp.config' }
test_adapterremoval { includeConfig 'conf/test_adapterremoval.config' }
test_bbduk { includeConfig 'conf/test_bbduk.config' }
test_prinseqplusplus { includeConfig 'conf/test_prinseqplusplus.config' }
test_prinseqplusplus { includeConfig 'conf/test_prinseqplusplus.config' }

}

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14 changes: 10 additions & 4 deletions nextflow_schema.json
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Expand Up @@ -615,25 +615,31 @@
"taxpasta_add_name": {
"type": "boolean",
"description": "Add the taxon name to the output.",
"help_text": "The standard output format of taxpasta is a two-column table including the read counts and the integer taxonomic ID. The taxon name can be added as additional information to the output table.\n\nModifies tool parameter(s):\n- taxpasta: `--taxpasta_add_name`",
"help_text": "The standard output format of taxpasta is a two-column table including the read counts and the integer taxonomic ID. The taxon name can be added as additional information to the output table in addition to the taxon ID.\n\nModifies tool parameter(s):\n- taxpasta: `--add-name`",
"fa_icon": "fas fa-tag"
},
"taxpasta_add_rank": {
"type": "boolean",
"description": "Add the taxon rank to the output.",
"help_text": "The standard output format of taxpasta is a two-column table including the read counts and the integer taxonomic ID. The taxon rank can be added as additional information to the output table.\n\nModifies tool parameter(s):\n- taxpasta: `--taxpasta_add_rank`",
"help_text": "The standard output format of taxpasta is a two-column table including the read counts and the integer taxonomic ID. The taxon rank of the given taxonomic entry can be added as additional information to the output table.\n\nModifies tool parameter(s):\n- taxpasta: `--add-rank`",
"fa_icon": "fas fa-sort-amount-down-alt"
},
"taxpasta_add_lineage": {
"type": "boolean",
"description": "Add the taxon's entire name 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 taxon's entire lineage with the taxon names separated by semi-colons can be added as additional information to the output table.\n\nModifies tool parameter(s):\n- taxpasta: `--taxpasta_add_lineage`\n",
"help_text": "\nThe standard output format of taxpasta is a two-column table including the read counts and the integer taxonomic ID. The taxon's entire taxonomic lineage with the taxon names separated by semi-colons can be added as additional information to the output table.\n\nModifies tool parameter(s):\n- taxpasta: `--add-lineage`\n",
"fa_icon": "fas fa-link"
},
"taxpasta_add_idlineage": {
"type": "boolean",
"description": "Add the taxon's entire ID 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 taxon's entire lineage with the taxon identifiers separated by semi-colons can be added as additional information to the output table.\n\nModifies tool parameter(s):\n- taxpasta: `--taxpasta_add_idlineage`\n",
"help_text": "\nThe standard output format of taxpasta is a two-column table including the read counts and the integer taxonomic ID. The taxon's entire taxonomic lineage with the taxon identifiers separated by semi-colons can be added as additional information to the output table.\n\nModifies tool parameter(s):\n- taxpasta: `--add-id-lineage`\n",
"fa_icon": "fas fa-link"
},
"taxpasta_add_ranklineage": {
"type": "boolean",
"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"
}
},
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