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Add Unzipping deeparg db option #320

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Add Unzipping deeparg db option #320

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68b271a
Add unzipping support for deepARG db
jfy133 Nov 8, 2023
62869ef
Phrasing
jfy133 Nov 8, 2023
2741d46
Improve help test
jfy133 Nov 8, 2023
b2ece35
Update nextflow_schema.json
jfy133 Nov 10, 2023
66cc1f3
Update nextflow_schema.json
jfy133 Nov 10, 2023
cb1b8cf
Merge branch 'dev' into unzip-deeparg-db-option
jfy133 Jan 24, 2024
103247c
[automated] Fix linting with Prettier
nf-core-bot Jan 24, 2024
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8 changes: 4 additions & 4 deletions .devcontainer/devcontainer.json
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Original file line number Diff line number Diff line change
Expand Up @@ -18,11 +18,11 @@
"python.linting.flake8Path": "/opt/conda/bin/flake8",
"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
"python.linting.pylintPath": "/opt/conda/bin/pylint"
"python.linting.pylintPath": "/opt/conda/bin/pylint",
},

// Add the IDs of extensions you want installed when the container is created.
"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
}
}
"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"],
},
},
}
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#322](https://github.com/nf-core/funcscan/pull/322) Updated all modules: introduce environment.yml files. (by @jasmezz)
- [#324](https://github.com/nf-core/funcscan/pull/324) Removed separate DeepARG test profile because database download is now stable. (by @jasmezz)
- [#320](https://github.com/nf-core/funcscan/pull/320) Add support for supplying gzipped DeepARG database files as input (by @jfy133)

### `Fixed`

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2 changes: 1 addition & 1 deletion docs/usage.md
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Expand Up @@ -178,7 +178,7 @@ The downloaded database folder contains the AMR related files:

DeepARG requires a database of potential antimicrobial resistance gene sequences based on a consensus from UNIPROT, CARD, and ARDB.

nf-core/funcscan can download this database for you, however it is very slow and pipeline runtime will be improved if you download this separately and supply it to the pipeline.
nf-core/funcscan can download this database for you, however it is very slow and pipeline runtime will be improved if you download this separately and supply it to the pipeline. Furthermore, if you have problems downloading this from within the pipeline, we highly recommend using the Zenodo archive of the database (see direct download below).

You can either:

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5 changes: 5 additions & 0 deletions modules.json
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Expand Up @@ -175,6 +175,11 @@
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
},
"unzip": {
"branch": "master",
"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
"installed_by": ["modules"]
}
}
}
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6 changes: 6 additions & 0 deletions modules/nf-core/unzip/environment.yml
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37 changes: 37 additions & 0 deletions modules/nf-core/unzip/main.nf
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42 changes: 42 additions & 0 deletions modules/nf-core/unzip/meta.yml
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4 changes: 2 additions & 2 deletions nextflow_schema.json
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Expand Up @@ -598,8 +598,8 @@
"arg_deeparg_data": {
"type": "string",
"fa_icon": "fab fa-deezer",
"description": "Specify the path to the DeepARG database.",
"help_text": "Specify the path to a local version of the DeepARG database (see the pipelines' usage [documentation](https://nf-co.re/funcscan/usage)). If no input is given, the module will download the database for you, however this is not recommended, as the database is large and this will take time."
"description": "Specify the path to a directory or Zip archive of the DeepARG database.",
"help_text": "Specify the path to a local version of the DeepARG database (see the pipelines' usage [documentation](https://nf-co.re/funcscan/usage)). If no input is given, the module will download the database for you, however this is not recommended, as the database is large and this will take time. The input can be either an uncompressed directory, or a Zip file."
},
"arg_deeparg_data_version": {
"type": "integer",
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14 changes: 11 additions & 3 deletions subworkflows/local/arg.nf
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Expand Up @@ -6,6 +6,7 @@ include { ABRICATE_RUN } from '../../modules/nf-core/abricate/ru
include { AMRFINDERPLUS_UPDATE } from '../../modules/nf-core/amrfinderplus/update/main'
include { AMRFINDERPLUS_RUN } from '../../modules/nf-core/amrfinderplus/run/main'
include { FARGENE } from '../../modules/nf-core/fargene/main'
include { UNZIP } from '../../modules/nf-core/unzip/main'
include { DEEPARG_DOWNLOADDATA } from '../../modules/nf-core/deeparg/downloaddata/main'
include { DEEPARG_PREDICT } from '../../modules/nf-core/deeparg/predict/main'
include { RGI_MAIN } from '../../modules/nf-core/rgi/main/main'
Expand Down Expand Up @@ -91,9 +92,16 @@ workflow ARG {

// DeepARG prepare download
if ( !params.arg_skip_deeparg && params.arg_deeparg_data ) {
ch_deeparg_db = Channel
.fromPath( params.arg_deeparg_data )
.first()

if ( file(params.arg_deeparg_data).getExtension() == "zip") {
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UNZIP( [ [id: "deepargdb"], params.arg_deeparg_data ] )
ch_deeparg_db = UNZIP.out.unzipped_archive.map{meta, db -> [db]}
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@jasmezz jasmezz Nov 9, 2023 •
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Suggested change
ch_deeparg_db = UNZIP.out.unzipped_archive.map{meta, db -> [db]}
ch_deeparg_db = UNZIP.out.unzipped_archive.map{meta, db -> db}
.flatMap { it -> [ it + "/deeparg"] }

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The Zip file on Zenodo is a bit annoying because it contains a subfolder /deeparg which is the actual input we want. Hence the .flatMap line.

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Hmm I don't like that solution in case someone has made their own zip in the correct manner... So appending that may not always work... I guess we need to make update the module to find a file within it like is done in other modules like bwa/bowtie2

} else {
ch_deeparg_db = Channel
.fromPath( params.arg_deeparg_data )
.first()
}

} else if ( !params.arg_skip_deeparg && !params.arg_deeparg_data ) {
DEEPARG_DOWNLOADDATA( )
ch_versions = ch_versions.mix(DEEPARG_DOWNLOADDATA.out.versions)
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