millironx/taxprofiler
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Merge pull request #294 from nf-core/patch

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Patch release 1.0.1
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James A. Fellows Yates 2023-05-15 11:05:37 +02:00 committed by GitHub
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12
CHANGELOG.md
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@ -3,6 +3,18 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## v1.0.1 - Dodgy Dachshund Patch [2023-05-15]
### `Added`
### `Fixed`
- [#291](https://github.com/nf-core/taxprofiler/pull/291) - Fix Taxpasta not receiving taxonomy directory (❤️ to SannaAb for reporting, fix by @jfy133)
### `Dependencies`
### `Deprecated`
## v1.0.0 - Dodgy Dachshund [2023-03-13] ## v1.0.0 - Dodgy Dachshund [2023-03-13]
Initial release of nf-core/taxprofiler, created with the [nf-core](https://nf-co.re/) template. Initial release of nf-core/taxprofiler, created with the [nf-core](https://nf-co.re/) template.

1
conf/modules.config
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@ -543,7 +543,6 @@ process {
ext.args = { ext.args = {
[ [
"-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}", "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
params.taxpasta_taxonomy_dir ? "--taxonomy ${params.taxpasta_taxonomy_dir}" : "",
params.taxpasta_add_name ? "--add-name" : "", params.taxpasta_add_name ? "--add-name" : "",
params.taxpasta_add_rank ? "--add-rank" : "", params.taxpasta_add_rank ? "--add-rank" : "",
params.taxpasta_add_lineage ? "--add-lineage" : "", params.taxpasta_add_lineage ? "--add-lineage" : "",

2
nextflow.config
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@ -305,7 +305,7 @@ manifest {
description = """Taxonomic classification and profiling of shotgun metagenomic data""" description = """Taxonomic classification and profiling of shotgun metagenomic data"""
mainScript = 'main.nf' mainScript = 'main.nf'
nextflowVersion = '!>=22.10.1' nextflowVersion = '!>=22.10.1'
version = '1.0.0' version = '1.0.1'
doi = '10.5281/zenodo.7728364' doi = '10.5281/zenodo.7728364'
} }

4
subworkflows/local/standardisation_profiles.nf
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@ -33,7 +33,9 @@ workflow STANDARDISATION_PROFILES {
.groupTuple () .groupTuple ()
.map { [ it[0], it[1].flatten() ] } .map { [ it[0], it[1].flatten() ] }
TAXPASTA_MERGE (ch_input_for_taxpasta, [], []) ch_taxpasta_tax_dir = params.taxpasta_taxonomy_dir ? Channel.fromPath(params.taxpasta_taxonomy_dir, checkIfExists: true).collect() : []
TAXPASTA_MERGE (ch_input_for_taxpasta, ch_taxpasta_tax_dir, [])
/* /*
Split profile results based on tool they come from Split profile results based on tool they come from