1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-10 22:53:08 +00:00

remove the database auto-download for mOTUs.

This commit is contained in:
JIANHONG OU 2022-06-03 14:13:58 -04:00
parent 53c4399052
commit c8a59adbce
10 changed files with 53 additions and 121 deletions

View file

@ -42,8 +42,6 @@ jobs:
- "--perform_runmerging" - "--perform_runmerging"
- "--perform_runmerging --shortread_qc_mergepairs" - "--perform_runmerging --shortread_qc_mergepairs"
- "--shortread_complexityfilter false --perform_shortread_hostremoval" - "--shortread_complexityfilter false --perform_shortread_hostremoval"
# Test different profiles
profile: ["test", "test_motus"]
steps: steps:
- name: Check out pipeline code - name: Check out pipeline code
@ -72,4 +70,54 @@ jobs:
# For example: adding multiple test runs with different parameters # For example: adding multiple test runs with different parameters
# Remember that you can parallelise this by using strategy.matrix # Remember that you can parallelise this by using strategy.matrix
run: | run: |
nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results ${{ matrix.parameters }} nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
motus:
name: Test mOTUs with workflow parameters
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
runs-on: ubuntu-latest
env:
NXF_VER: ${{ matrix.nxf_ver }}
NXF_ANSI_LOG: false
strategy:
matrix:
# Nextflow versions
include:
# Test pipeline minimum Nextflow version
- NXF_VER: "21.10.3"
NXF_EDGE: ""
# Test latest edge release of Nextflow
- NXF_VER: ""
NXF_EDGE: "1"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.NXF_VER }}
# Uncomment only if the edge release is more recent than the latest stable release
# See https://github.com/nextflow-io/nextflow/issues/2467
# NXF_EDGE: ${{ matrix.NXF_EDGE }}
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Show current locale
run: locale
- name: Set UTF-8 enabled locale
run: |
sudo locale-gen en_US.UTF-8
sudo update-locale LANG=en_US.UTF-8
- name: Prepare the database
run: |
wget https://github.com/motu-tool/mOTUs/blob/master/motus/downloadDB.py
python downloadDB.py
echo 'tool,db_name,db_params,db_path\nmotus,db_mOTU,,db_mOTU' > 'database_motus.csv'
- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_motus,docker --outdir ./results --databases ./database_motus.csv

View file

@ -353,13 +353,6 @@ process {
] ]
} }
withName: MOTUS_DOWNLOADDB {
publishDir = [
path: { "${params.outdir}/motus/db/${meta.db_name}" },
mode: params.publish_dir_mode
]
}
withName: MOTUS_PROFILE { withName: MOTUS_PROFILE {
publishDir = [ publishDir = [
path: { "${params.outdir}/motus/${meta.db_name}" }, path: { "${params.outdir}/motus/${meta.db_name}" },

View file

@ -23,7 +23,7 @@ params {
// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
// TODO nf-core: Give any required params for the test so that command line flags are not needed // TODO nf-core: Give any required params for the test so that command line flags are not needed
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv' input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv' databases = 'database_motus.csv'
perform_shortread_clipmerge = false perform_shortread_clipmerge = false
perform_longread_clip = false perform_longread_clip = false
perform_shortread_complexityfilter = false perform_shortread_complexityfilter = false

View file

@ -138,8 +138,7 @@ Expected (uncompressed) database files for each tool are as follows:
The database download step can be time consuming and the database will be consisting The database download step can be time consuming and the database will be consisting
with same release version of the mOTUs tools. The database for same version tools with same release version of the mOTUs tools. The database for same version tools
can be thus reused for multiple runs. Users can download the database once and can be thus reused for multiple runs. Users can download the database once and
assign the database with the table. User can also set the parameter assign the database with the table.
`download_motus_db` and let the pipeline download the database automatically.
## Running the pipeline ## Running the pipeline

View file

@ -63,9 +63,6 @@
"minimap2/index": { "minimap2/index": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
}, },
"motus/downloaddb": {
"git_sha": "6393a085c5fcea11963774c041808df169907487"
},
"motus/profile": { "motus/profile": {
"git_sha": "6b960f0e75bbb4d5bd301cd3875fa078d0eab4d1" "git_sha": "6b960f0e75bbb4d5bd301cd3875fa078d0eab4d1"
}, },

View file

@ -1,39 +0,0 @@
process MOTUS_DOWNLOADDB {
label 'process_low'
conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
input:
path motus_downloaddb_script
output:
path "db_mOTU/" , emit: db
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def software = "${motus_downloaddb_script.simpleName}_copy.py"
"""
## must copy script file to working directory,
## otherwise the reference_db will be download to bin folder
## other than current directory
cp $motus_downloaddb_script ${software}
python ${software} \\
$args \\
-t $task.cpus
## mOTUs version number is not available from command line.
## mOTUs save the version number in index database folder.
## mOTUs will check the database version is same version as exec version.
cat <<-END_VERSIONS > versions.yml
"${task.process}":
mOTUs: \$(grep motus db_mOTU/db_mOTU_versions | sed 's/motus\\t//g')
END_VERSIONS
"""
}

View file

@ -1,39 +0,0 @@
name: "motus_downloaddb"
description: Download the mOTUs database
keywords:
- classify
- metagenomics
- fastq
- taxonomic profiling
- database
- download
tools:
- "motus":
description: "The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data."
homepage: "None"
documentation: "https://github.com/motu-tool/mOTUs/wiki"
tool_dev_url: "https://github.com/motu-tool/mOTUs"
doi: "10.1038/s41467-019-08844-4"
licence: "['GPL v3']"
input:
- motus_downloaddb:
type: directory
description: |
The mOTUs downloadDB script source file.
It is the source file installed or
remote source in github such as https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py
pattern: "downloadDB.py"
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- db:
type: directory
description: The mOTUs database directory
pattern: "db_mOTU"
authors:
- "@jianhong"

View file

@ -126,8 +126,6 @@ params {
// mOTUs // mOTUs
run_motus = false run_motus = false
download_motus_db = true
motus_downloaddb_script = 'https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py'
} }
// Load base.config by default for all pipelines // Load base.config by default for all pipelines

View file

@ -430,14 +430,6 @@
}, },
"run_motus": { "run_motus": {
"type": "boolean" "type": "boolean"
},
"download_motus_db": {
"type": "boolean"
},
"motus_downloaddb_script": {
"type": "string",
"default": "https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py",
"description": "mOTUs database download script path."
} }
} }
} }

View file

@ -4,7 +4,6 @@
include { DATABASE_CHECK } from '../../modules/local/database_check' include { DATABASE_CHECK } from '../../modules/local/database_check'
include { UNTAR } from '../../modules/nf-core/modules/untar/main' include { UNTAR } from '../../modules/nf-core/modules/untar/main'
include { MOTUS_DOWNLOADDB } from '../../modules/nf-core/modules/motus/downloaddb/main'
workflow DB_CHECK { workflow DB_CHECK {
take: take:
@ -21,22 +20,6 @@ workflow DB_CHECK {
.splitCsv ( header:true, sep:',' ) .splitCsv ( header:true, sep:',' )
.map { create_db_channels(it) } .map { create_db_channels(it) }
// Download database for mOTUs
if( params.run_motus ){
check_motus_db =
parsed_samplesheet.filter{ it[0].tool == "motus" }
.ifEmpty{[]}
if( params.download_motus_db ){
MOTUS_DOWNLOADDB( params.motus_downloaddb_script )
check_motus_db = MOTUS_DOWNLOADDB.out.db
.map{[
[tool: "motus", db_name: "db_mOTU", db_params: ''],
it
]}
}
parsed_samplesheet = parsed_samplesheet.mix(check_motus_db)
}
ch_dbs_for_untar = parsed_samplesheet ch_dbs_for_untar = parsed_samplesheet
.branch { .branch {
untar: it[1].toString().endsWith(".tar.gz") untar: it[1].toString().endsWith(".tar.gz")