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create a new test profile config for mOTUs.

This commit is contained in:
JIANHONG OU 2022-05-31 08:47:38 -04:00
parent e916c91de3
commit 4d77b47e8d
6 changed files with 56 additions and 3 deletions

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@ -42,6 +42,8 @@ jobs:
- "--perform_runmerging" - "--perform_runmerging"
- "--perform_runmerging --shortread_clipmerge_mergepairs" - "--perform_runmerging --shortread_clipmerge_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
@ -70,4 +72,4 @@ 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 test,docker --outdir ./results ${{ matrix.parameters }} nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results ${{ matrix.parameters }}

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@ -37,7 +37,7 @@ params {
run_metaphlan3 = true run_metaphlan3 = true
run_centrifuge = true run_centrifuge = true
run_diamond = true run_diamond = true
run_motus = true run_motus = false
} }
process { process {

41
conf/test_motus.config Normal file
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@ -0,0 +1,41 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running minimal tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Defines input files and everything required to run a fast and simple pipeline test.
Use as follows:
nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
----------------------------------------------------------------------------------------
*/
params {
config_profile_name = 'mOTUs Test profile'
config_profile_description = 'Minimal test to check mOTUs function'
// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'
// Input data
// 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
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
perform_shortread_clipmerge = false
perform_longread_clip = false
perform_shortread_complexityfilter = false
perform_shortread_hostremoval = false
perform_longread_hostremoval = false
perform_runmerging = false
hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
run_kaiju = false
run_kraken2 = false
run_malt = false
run_metaphlan3 = false
run_centrifuge = false
run_diamond = false
run_motus = true
}

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@ -37,7 +37,7 @@ params {
run_metaphlan3 = true run_metaphlan3 = true
run_centrifuge = true run_centrifuge = true
run_diamond = true run_diamond = true
run_motus = true run_motus = false
} }
process { process {

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@ -77,6 +77,7 @@ kraken2,db1,,/<path>/<to>/kraken2/testdb-kraken2.tar.gz
kraken2,db2,--quick,/<path>/<to>/kraken2/testdb-kraken2.tar.gz kraken2,db2,--quick,/<path>/<to>/kraken2/testdb-kraken2.tar.gz
centrifuge,db1,,/<path>/<to>/centrifuge/minigut_cf.tar.gz centrifuge,db1,,/<path>/<to>/centrifuge/minigut_cf.tar.gz
metaphlan3,db1,,/<path>/<to>/metaphlan3/metaphlan_database/ metaphlan3,db1,,/<path>/<to>/metaphlan3/metaphlan_database/
motus,db_mOTU,,/<path>/<to>/motus/motus_database/
``` ```
Column specifications are as follows: Column specifications are as follows:
@ -131,6 +132,14 @@ Expected (uncompressed) database files for each tool are as follows:
- **DIAMOND** output of `diamond makedb`. Note: requires building with taxonomy files - **DIAMOND** output of `diamond makedb`. Note: requires building with taxonomy files
to generate taxonomic profile. See [DIAMOND documentation](https://github.com/bbuchfink/diamond/wiki/3.-Command-line-options#makedb-options). A file named: to generate taxonomic profile. See [DIAMOND documentation](https://github.com/bbuchfink/diamond/wiki/3.-Command-line-options#makedb-options). A file named:
- `<database_name>.dmnd` - `<database_name>.dmnd`
- **mOTUs** is composed of code and database together. The mOTUs tools
[`downloadDB`](https://github.com/motu-tool/mOTUs/blob/master/motus/downloadDB.py)
is used to prepare the mOTUs database and create a file with the version information.
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
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
`download_motus_db` and let the pipeline download the database automatically.
## Running the pipeline ## Running the pipeline

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@ -193,6 +193,7 @@ profiles {
test_full { includeConfig 'conf/test_full.config' } test_full { includeConfig 'conf/test_full.config' }
test_noprofiling { includeConfig 'conf/test_noprofiling.config' } test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' } test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' }
test_motus { includeConfig 'conf/test_motus.config' }
} }
// Load igenomes.config if required // Load igenomes.config if required