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nf-core · Jun 30, 2023 · 6472f93 · 6472f93
1 parent 4f4d2ee
commit 6472f93
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Showing 5 changed files with 30 additions and 22 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -665,7 +665,8 @@ process {
             path: { "${params.outdir}/kmcp/${meta.db_name}/" },
             mode: params.publish_dir_mode,
             pattern: '*.{profile}'
-
+        ]
+    }
 
     withName: GANON_CLASSIFY {
         ext.args = params.ganon_save_readclassifications ? { "${meta.db_params} --output-all --output-lca --output-unclassified" } : { "${meta.db_params}" }

diff --git a/nextflow.config b/nextflow.config
@@ -152,6 +152,12 @@ params {
     motus_remove_ncbi_ids           = false
     motus_save_mgc_read_counts      = false
 
+    // kmcp
+    run_kmcp     = false
+    kmcp_taxdump = null
+    kmcp_taxid   = null
+    kmcp_mode    = 3      // default  kmcp profiling value
+
     // ganon
     run_ganon                       = false
     ganon_report_type               = 'reads'
@@ -165,12 +171,6 @@ params {
     run_krona                  = false
     krona_taxonomy_directory   = null
 
-    // kmcp
-    run_kmcp     = false
-    kmcp_taxdump = null
-    kmcp_taxid   = null
-    kmcp_mode    = 3      // default  kmcp profiling value
-
     // profile standardisation
     run_profile_standardisation             = false
     standardisation_taxpasta_format         = 'tsv'

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -493,7 +493,8 @@
                 "motus_remove_ncbi_ids": {
                     "type": "boolean",
                     "description": "Turn on removing NCBI taxonomic IDs.",
-                    "fa_icon": "fas fa-address-card"
+                    "fa_icon": "fas fa-address-card",
+                    "help_text": "By default mOTUs will report species names rather than NCBI Taxon IDs. In nf-core/taxprofiler we prefer taxon IDs due to interoperatbility and comparability with the output of other classifiers and profilers. If you prefer to have just species names, you can specify this to remove the IDs.\n\n> Modifies tool parameter(s):\n- mOTUs: `-p` (removed from the default nf-core/taxprofiler command)"
                 },
                 "run_kmcp": {
                     "type": "boolean",
@@ -519,8 +520,6 @@
                     "description": "Profiling mode.",
                     "help_text": "Available values: \n0 (for pathogen detection)\n1 (higherrecall)\n2 (high recall)\n3 (default)\n4 (high precision)\n5 (higher precision)",
                     "fa_icon": "fas fa-check-square"
-                    "fa_icon": "fas fa-address-card",
-                    "help_text": "By default mOTUs will report species names rather than NCBI Taxon IDs. In nf-core/taxprofiler we prefer taxon IDs due to interoperatbility and comparability with the output of other classifiers and profilers. If you prefer to have just species names, you can specify this to remove the IDs.\n\n> Modifies tool parameter(s):\n- mOTUs: `-p` (removed from the default nf-core/taxprofiler command)"
                 },
                 "run_ganon": {
                     "type": "boolean",

diff --git a/subworkflows/local/db_check.nf b/subworkflows/local/db_check.nf
@@ -62,9 +62,8 @@ def validate_db_rows(LinkedHashMap row) {
     if ( !row.keySet().containsAll(expected_headers) ) error("[nf-core/taxprofiler] ERROR: Invalid database input sheet - malformed column names. Please check input TSV. Column names should be: ${expected_headers.join(", ")}")
 
     // valid tools specified
-    def expected_tools = [ "bracken", "centrifuge", "diamond", "kaiju", "kmcp","kraken2", "krakenuniq", "malt", "metaphlan3", "motus" ]
     def expected_tools = [ "bracken", "centrifuge", "diamond", "kaiju", "kraken2", "krakenuniq", "malt", "metaphlan3", "motus", "ganon", "metaphlan", "kmcp" ]
-    
+
     if ( !expected_tools.contains(row.tool) ) error("[nf-core/taxprofiler] ERROR: Invalid tool name. Please see documentation for all supported profilers. Error in: ${row}")
 
     // detect quotes in params

diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
@@ -353,20 +353,13 @@ workflow PROFILING {
                                     meta, reads, meta_db, db ->
                                         if ( meta['instrument_platform'] == 'OXFORD_NANOPORE' ) log.warn "[nf-core/taxprofiler] Kmcp is only suitable for short-read metagenomic profiling, with much lower sensitivity on long-read datasets. Skipping kmcp for sample ${meta.id}."
                                         meta_db['tool'] == 'kmcp' && meta['instrument_platform'] != 'OXFORD_NANOPORE'
-    if ( params.run_ganon ) {
-
-        ch_input_for_ganonclassify = ch_input_for_profiling.ganon
-                                .filter {
-                                    meta, reads, meta_db, db ->
-                                        if ( meta['instrument_platform'] == 'OXFORD_NANOPORE' ) log.warn "[nf-core/taxprofiler] Ganon has not been evaluated for Nanopore data. Skipping Ganon for sample ${meta.id}."
-                                        meta_db['tool'] == 'ganon' && meta['instrument_platform'] != 'OXFORD_NANOPORE'
-                                }
-                                .multiMap {
+                                    }
+                                    .multiMap {
                                     it ->
                                         reads: [ it[0] + it[2], it[1] ]
                                         db: it[3]
                                 }
-                                
+
             ch_input_for_kmcpcompute.db
             KMCP_COMPUTE (ch_input_for_kmcpcompute.db)
             KMCP_INDEX (KMCP_COMPUTE.out.outdir)
@@ -377,6 +370,22 @@ workflow PROFILING {
             ch_raw_profiles    = ch_raw_profiles.mix( KMCP_PROFILE.out.profile )
             ch_multiqc_files   = ch_multiqc_files.mix( KMCP_PROFILE.out.profile )
 
+    }
+
+    if ( params.run_ganon ) {
+
+        ch_input_for_ganonclassify = ch_input_for_profiling.ganon
+                                .filter {
+                                    meta, reads, meta_db, db ->
+                                        if ( meta['instrument_platform'] == 'OXFORD_NANOPORE' ) log.warn "[nf-core/taxprofiler] Ganon has not been evaluated for Nanopore data. Skipping Ganon for sample ${meta.id}."
+                                        meta_db['tool'] == 'ganon' && meta['instrument_platform'] != 'OXFORD_NANOPORE'
+                                }
+                                .multiMap {
+                                    it ->
+                                        reads: [ it[0] + it[2], it[1] ]
+                                        db: it[3]
+                                }
+
         ch_input_for_ganonclassify.reads
 
         GANON_CLASSIFY( ch_input_for_ganonclassify.reads, ch_input_for_ganonclassify.db )