create a new test profile config for mOTUs.

.github/workflows/ci.yml

@@ -42,6 +42,8 @@ jobs:
           - "--perform_runmerging"
           - "--perform_runmerging --shortread_clipmerge_mergepairs"
           - "--shortread_complexityfilter false --perform_shortread_hostremoval"
+        # Test different profiles
+        profile: ["test", "test_motus"]
 
     steps:
       - name: Check out pipeline code
@@ -70,4 +72,4 @@ jobs:
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results ${{ matrix.parameters }}

conf/test.config

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

conf/test_motus.config

@@ -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
+}

conf/test_nopreprocessing.config

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

docs/usage.md

@@ -77,6 +77,7 @@ kraken2,db1,,/<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
 metaphlan3,db1,,/<path>/<to>/metaphlan3/metaphlan_database/
+motus,db_mOTU,,/<path>/<to>/motus/motus_database/
 ```
 
 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
   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`
+- **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
 

nextflow.config

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