Added an option to skip filtering hits from the same species

sanger-tol · Aug 22, 2024 · e9d3a64 · e9d3a64
1 parent 70f961c
commit e9d3a64
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Showing 5 changed files with 45 additions and 21 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,13 +15,16 @@ The pipeline has now been validated for draft (unpublished) assemblies.
   automatically selecting based on the taxonomy.
 - All parameters are now passed the regular Nextflow way. There is no support
   for the original Yaml configuration files of the Snakemake version.
+- New option `--skip_taxon_filtering` to skip the taxon filtering in blast searches.
+  Mostly relevant for draft assemblies.
 
 ### Parameters
 
-| Old parameter | New parameter    |
-| ------------- | ---------------- |
-| --yaml        |                  |
-|               | --busco_lineages |
+| Old parameter | New parameter          |
+| ------------- | ---------------------- |
+| --yaml        |                        |
+|               | --busco_lineages       |
+|               | --skip_taxon_filtering |
 
 > **NB:** Parameter has been **updated** if both old and new parameter information is present. </br> **NB:** Parameter has been **added** if just the new parameter information is present. </br> **NB:** Parameter has been **removed** if new parameter information isn't present.
 

diff --git a/nextflow.config b/nextflow.config
@@ -33,6 +33,7 @@ params {
     blastp                     = null
     blastx                     = null
     blastn                     = null
+    skip_taxon_filtering       = false
 
     // MultiQC options
     multiqc_config             = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -32,6 +32,11 @@
                     "description": "Turn on optional genome masking if needed.",
                     "fa_icon": "fas fa-toggle-off"
                 },
+                "skip_taxon_filtering": {
+                    "type": "boolean",
+                    "description": "Skip filtering out hits from the same species in blast* searches.",
+                    "fa_icon": "fas fa-toggle-off"
+                },
                 "fetchngs_samplesheet": {
                     "type": "boolean",
                     "description": "Turn on the conversion from a nf-core/fetchngs samplesheet.",

diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
@@ -87,9 +87,10 @@ workflow INPUT_CHECK {
 
 
     //
-    // Get the taxon ID
+    // Get the taxon ID if we do taxon filtering in blast* searches
     //
     ch_parsed_csv.taxon_id
+    | map { params.skip_taxon_filtering ? '' : it }
     | first
     | set { ch_taxon_id }
 

diff --git a/subworkflows/local/run_blastn.nf b/subworkflows/local/run_blastn.nf
@@ -47,23 +47,37 @@ workflow RUN_BLASTN {
     | set { ch_chunks }
 
     // Run blastn search
-    // run blastn excluding taxon_id
-    BLASTN_TAXON ( ch_chunks, blastn, taxon_id )
-    ch_versions = ch_versions.mix ( BLASTN_TAXON.out.versions.first() )
-
-    // check if blastn output table is empty
-    BLASTN_TAXON.out.txt
-    | branch { meta, txt ->
-        empty:     txt.isEmpty()
-        not_empty: true
-    }
-    | set { ch_blastn_taxon_out }
+    if (params.skip_taxon_filtering) {
+
+        // skip BLASTN_TAXON
+        ch_blast_blastn_input = ch_chunks
+
+        // fake ch_blastn_taxon_out.not_empty
+        ch_blastn_taxon_out = [
+            not_empty: Channel.empty()
+        ]
+
+    } else {
 
-    // repeat the blastn search without excluding taxon_id
-    ch_blastn_taxon_out.empty
-    | join ( ch_chunks )
-    | map { meta, txt, fasta -> [meta, fasta] }
-    | set { ch_blast_blastn_input }
+        // run blastn excluding taxon_id
+        BLASTN_TAXON ( ch_chunks, blastn, taxon_id )
+        ch_versions = ch_versions.mix ( BLASTN_TAXON.out.versions.first() )
+
+        // check if blastn output table is empty
+        BLASTN_TAXON.out.txt
+        | branch { meta, txt ->
+            empty:     txt.isEmpty()
+            not_empty: true
+        }
+        | set { ch_blastn_taxon_out }
+
+        // repeat the blastn search without excluding taxon_id
+        ch_blastn_taxon_out.empty
+        | join ( ch_chunks )
+        | map { meta, txt, fasta -> [meta, fasta] }
+        | set { ch_blast_blastn_input }
+
+    }
 
     BLAST_BLASTN ( ch_blast_blastn_input, blastn, [] )
     ch_versions = ch_versions.mix ( BLAST_BLASTN.out.versions.first() )