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Update Taxpasta update to reduce pipeline failures from overly strict profile validation #495

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Merged
merged 2 commits into from
Jun 19, 2024
Merged

Update Taxpasta update to reduce pipeline failures from overly strict profile validation #495

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d749769
Update Taxpasta, which stops overly strict failures
jfy133 Jun 12, 2024
0a3ce1c
Update CHANGELOG.md
jfy133 Jun 13, 2024
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10 changes: 6 additions & 4 deletions CHANGELOG.md
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Expand Up @@ -13,13 +13,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#484](https://github.com/nf-core/taxprofiler/pull/484) Improved input validation to immediately fail if run accession IDs within a given sample ID are not unique (❤️ to @sofstam for reporting, fixed by @jfy133)
- [#491](https://github.com/nf-core/taxprofiler/pull/491) Added flag to publish intermediate bracken files (❤️ to @ewissel for reporting, fixed by @sofstam and @jfy133)
- [489](https://github.com/nf-core/taxprofiler/pull/489) Fix KrakenUniq classified reads output format mismatch (❤️ to @SannaAb for reporting, fixed by @jfy133)
- [#489](https://github.com/nf-core/taxprofiler/pull/489) Fix KrakenUniq classified reads output format mismatch (❤️ to @SannaAb for reporting, fixed by @jfy133)
- [#495](https://github.com/nf-core/taxprofiler/pull/495) Stop TAXPASTA failures when profiles do not have exact compositionality (fixes by @Midnighter, @jfy133)

### `Dependencies`

| Tool | Previous version | New version |
| ---- | ---------------- | ----------- |
| KMCP | 0.9.1 | 0.9.4 |
| Tool | Previous version | New version |
| -------- | ---------------- | ----------- |
| KMCP | 0.9.1 | 0.9.4 |
| TAXPASTA | 0.6.1 | 0.7.0 |

### `Deprecated`

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18 changes: 9 additions & 9 deletions conf/modules.config
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Expand Up @@ -754,15 +754,14 @@ process {

withName: TAXPASTA_MERGE {
tag = { "${meta.tool}|${meta.id}" }
ext.prefix = { "${meta.tool}_${meta.id}" }
ext.args = {
[
"-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
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_ranklineage ? "--add-rank-lineage" : "",
params.taxpasta_ignore_errors ? "--ignore-errors" : ""
].join(' ').trim()
}
publishDir = [
Expand All @@ -774,14 +773,15 @@ process {

withName: TAXPASTA_STANDARDISE {
tag = { "${meta.tool}|${meta.id}" }
ext.prefix = { "${meta.tool}_${meta.id}" }
ext.args = {
[
"-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
params.taxpasta_add_name ? "--add-name" : "",
params.taxpasta_add_rank ? "--add-rank" : "",
params.taxpasta_add_lineage ? "--add-lineage" : "",
params.taxpasta_add_idlineage ? "--add-id-lineage" : ""
].join(' ').trim()
[
params.taxpasta_add_name ? "--add-name" : "",
params.taxpasta_add_rank ? "--add-rank" : "",
params.taxpasta_add_lineage ? "--add-lineage" : "",
params.taxpasta_add_idlineage ? "--add-id-lineage" : "",
params.taxpasta_add_ranklineage ? "--add-rank-lineage" : ""
].join(' ').trim()
}
publishDir = [
path: { "${params.outdir}/taxpasta/" },
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4 changes: 2 additions & 2 deletions modules.json
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Expand Up @@ -228,12 +228,12 @@
},
"taxpasta/merge": {
"branch": "master",
"git_sha": "48019785051ba491e82dce910273c2eca61bd5b7",
"git_sha": "4fd9089d3cf904e0b870d5a6a7ab903ee5e1004d",
"installed_by": ["modules"]
},
"taxpasta/standardise": {
"branch": "master",
"git_sha": "48019785051ba491e82dce910273c2eca61bd5b7",
"git_sha": "4fd9089d3cf904e0b870d5a6a7ab903ee5e1004d",
"installed_by": ["modules"]
},
"untar": {
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7 changes: 7 additions & 0 deletions modules/nf-core/taxpasta/merge/environment.yml
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30 changes: 21 additions & 9 deletions modules/nf-core/taxpasta/merge/main.nf
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27 changes: 16 additions & 11 deletions modules/nf-core/taxpasta/merge/meta.yml
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111 changes: 111 additions & 0 deletions modules/nf-core/taxpasta/merge/tests/main.nf.test
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83 changes: 83 additions & 0 deletions modules/nf-core/taxpasta/merge/tests/main.nf.test.snap
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2 changes: 2 additions & 0 deletions modules/nf-core/taxpasta/merge/tests/tags.yml
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