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create a new test profile config for mOTUs.
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parent
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6 changed files with 56 additions and 3 deletions
4
.github/workflows/ci.yml
vendored
4
.github/workflows/ci.yml
vendored
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@ -42,6 +42,8 @@ jobs:
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- "--perform_runmerging"
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- "--perform_runmerging"
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- "--perform_runmerging --shortread_clipmerge_mergepairs"
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- "--perform_runmerging --shortread_clipmerge_mergepairs"
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- "--shortread_complexityfilter false --perform_shortread_hostremoval"
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- "--shortread_complexityfilter false --perform_shortread_hostremoval"
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# Test different profiles
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profile: ["test", "test_motus"]
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steps:
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steps:
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- name: Check out pipeline code
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- name: Check out pipeline code
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@ -70,4 +72,4 @@ jobs:
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# For example: adding multiple test runs with different parameters
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# For example: adding multiple test runs with different parameters
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# Remember that you can parallelise this by using strategy.matrix
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# Remember that you can parallelise this by using strategy.matrix
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run: |
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
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nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results ${{ matrix.parameters }}
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@ -37,7 +37,7 @@ params {
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run_metaphlan3 = true
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run_metaphlan3 = true
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run_centrifuge = true
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run_centrifuge = true
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run_diamond = true
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run_diamond = true
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run_motus = true
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run_motus = false
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}
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}
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process {
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process {
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41
conf/test_motus.config
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41
conf/test_motus.config
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@ -0,0 +1,41 @@
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running minimal tests
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Defines input files and everything required to run a fast and simple pipeline test.
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Use as follows:
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nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
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----------------------------------------------------------------------------------------
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*/
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params {
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config_profile_name = 'mOTUs Test profile'
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config_profile_description = 'Minimal test to check mOTUs function'
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// Limit resources so that this can run on GitHub Actions
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max_cpus = 2
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max_memory = '6.GB'
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max_time = '6.h'
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// Input data
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// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
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perform_shortread_clipmerge = false
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perform_longread_clip = false
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perform_shortread_complexityfilter = false
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perform_shortread_hostremoval = false
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perform_longread_hostremoval = false
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perform_runmerging = false
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hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
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run_kaiju = false
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run_kraken2 = false
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run_malt = false
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run_metaphlan3 = false
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run_centrifuge = false
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run_diamond = false
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run_motus = true
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}
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@ -37,7 +37,7 @@ params {
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run_metaphlan3 = true
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run_metaphlan3 = true
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run_centrifuge = true
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run_centrifuge = true
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run_diamond = true
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run_diamond = true
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run_motus = true
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run_motus = false
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}
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}
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process {
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process {
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@ -77,6 +77,7 @@ kraken2,db1,,/<path>/<to>/kraken2/testdb-kraken2.tar.gz
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kraken2,db2,--quick,/<path>/<to>/kraken2/testdb-kraken2.tar.gz
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kraken2,db2,--quick,/<path>/<to>/kraken2/testdb-kraken2.tar.gz
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centrifuge,db1,,/<path>/<to>/centrifuge/minigut_cf.tar.gz
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centrifuge,db1,,/<path>/<to>/centrifuge/minigut_cf.tar.gz
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metaphlan3,db1,,/<path>/<to>/metaphlan3/metaphlan_database/
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metaphlan3,db1,,/<path>/<to>/metaphlan3/metaphlan_database/
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motus,db_mOTU,,/<path>/<to>/motus/motus_database/
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```
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```
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Column specifications are as follows:
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Column specifications are as follows:
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@ -131,6 +132,14 @@ Expected (uncompressed) database files for each tool are as follows:
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- **DIAMOND** output of `diamond makedb`. Note: requires building with taxonomy files
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- **DIAMOND** output of `diamond makedb`. Note: requires building with taxonomy files
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to generate taxonomic profile. See [DIAMOND documentation](https://github.com/bbuchfink/diamond/wiki/3.-Command-line-options#makedb-options). A file named:
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to generate taxonomic profile. See [DIAMOND documentation](https://github.com/bbuchfink/diamond/wiki/3.-Command-line-options#makedb-options). A file named:
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- `<database_name>.dmnd`
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- `<database_name>.dmnd`
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- **mOTUs** is composed of code and database together. The mOTUs tools
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[`downloadDB`](https://github.com/motu-tool/mOTUs/blob/master/motus/downloadDB.py)
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is used to prepare the mOTUs database and create a file with the version information.
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The database download step can be time consuming and the database will be consisting
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with same release version of the mOTUs tools. The database for same version tools
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can be thus reused for multiple runs. Users can download the database once and
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assign the database with the table. User can also set the parameter
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`download_motus_db` and let the pipeline download the database automatically.
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## Running the pipeline
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## Running the pipeline
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@ -193,6 +193,7 @@ profiles {
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test_full { includeConfig 'conf/test_full.config' }
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test_full { includeConfig 'conf/test_full.config' }
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test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
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test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
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test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' }
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test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' }
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test_motus { includeConfig 'conf/test_motus.config' }
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}
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}
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// Load igenomes.config if required
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// Load igenomes.config if required
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