From 460f3ca157bd618dde7dbc20f5c99bdd2bda731b Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Mon, 12 Dec 2022 11:03:40 +0100
Subject: [PATCH] Add database sheet validation

---
 subworkflows/local/db_check.nf  | 31 ++++++++++++++++++++-----------
 subworkflows/local/profiling.nf | 10 +++++-----
 2 files changed, 25 insertions(+), 16 deletions(-)

diff --git a/subworkflows/local/db_check.nf b/subworkflows/local/db_check.nf
index ce26905..4ed786d 100644
--- a/subworkflows/local/db_check.nf
+++ b/subworkflows/local/db_check.nf
@@ -11,14 +11,22 @@ workflow DB_CHECK {
     main:
     ch_versions = Channel.empty()
 
-    // TODO: make database sheet check
-    // Checks:
-    // 1) no duplicates,
+    // special check to check _between_ rows, for which we must group rows together
+    Channel.fromPath(dbsheet)
+            .splitCsv ( header:true, sep:',' )
+            .map {[it.tool, it.db_name] }
+            .groupTuple()
+            .map {
+                tool, db_name ->
+                    def unique_names = db_name.unique(false)
+                    if ( unique_names.size() < db_name.size() ) exit 1, "[nf-core/taxprofiler] ERROR: Each database for a tool must have a unique name, duplicated detected. Tool: ${tool}, Database name: ${unique_names}"
+            }
 
+    // normal checks for within-row validity, so can be moved to separate functions
     parsed_samplesheet = Channel.fromPath(dbsheet)
         .splitCsv ( header:true, sep:',' )
         .map {
-            validate_db_sheet(it)
+            validate_db_rows(it)
             create_db_channels(it)
         }
 
@@ -40,21 +48,22 @@ workflow DB_CHECK {
     versions = ch_versions                   // channel: [ versions.yml ]
 }
 
-def validate_db_sheet(LinkedHashMap row){
+def validate_db_rows(LinkedHashMap row){
 
         // check minimum number of columns
-        if (row.size() < 4) exit 1, "[nf-core/taxprofiler] error:  Invalid database input sheet - malformed row (e.g. missing column). See documentation for more information. Error in: ${row}, "
+        if (row.size() < 4) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database input sheet - malformed row (e.g. missing column). See documentation for more information. Error in: ${row}"
 
         // all columns there
         def expected_headers = ['tool', 'db_name', 'db_params', 'db_path']
-        if ( !row.keySet().containsAll(expected_headers) ) exit 1, "[nf-core/taxprofiler] error: Invalid database input sheet - malformed column names. Please check input TSV. Column names should be: ${expected_keys.join(", ")}"
+        if ( !row.keySet().containsAll(expected_headers) ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database input sheet - malformed column names. Please check input TSV. Column names should be: ${expected_keys.join(", ")}"
 
         // valid tools specified// TIFNISIH LIST
-        def expected_tools = [ "bracken", "centrifuge", "diamond", "kaiju",  "kraken2", "malt", "metaphlan3"  ]
+        def expected_tools = [ "bracken", "centrifuge", "diamond", "kaiju",  "kraken2", "krakenuniq", "malt", "metaphlan3", "motus" ]
+        if ( !expected_tools.contains(row.tool) ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid tool name. Please see documentation for all supported profilers. Error in: ${row}"
 
         // detect quotes in params
-        if ( row.db_params.contains('"') ) exit 1, "[nf-core/taxprofiler] error: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
-        if ( row.db_params.contains("'") ) exit 1, "[nf-core/taxprofiler] error: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
+        if ( row.db_params.contains('"') ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
+        if ( row.db_params.contains("'") ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
 
 }
 
@@ -66,7 +75,7 @@ def create_db_channels(LinkedHashMap row) {
 
     def array = []
     if (!file(row.db_path, type: 'dir').exists()) {
-        exit 1, "ERROR: Please check input samplesheet -> database could not be found!\n${row.db_path}"
+        exit 1, "ERROR: Please check input samplesheet -> database path could not be found!\n${row.db_path}"
     }
     array = [ meta, file(row.db_path) ]
 
diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
index f5c970c..6613648 100644
--- a/subworkflows/local/profiling.nf
+++ b/subworkflows/local/profiling.nf
@@ -41,14 +41,14 @@ workflow PROFILING {
             }
             .combine(databases)
             .branch {
-                malt:    it[2]['tool'] == 'malt'
-                kraken2: it[2]['tool'] == 'kraken2' || it[2]['tool'] == 'bracken' // to reuse the kraken module to produce the input data for bracken
-                metaphlan3: it[2]['tool'] == 'metaphlan3'
                 centrifuge: it[2]['tool'] == 'centrifuge'
-                kaiju: it[2]['tool'] == 'kaiju'
                 diamond: it[2]['tool'] == 'diamond'
-                motus: it[2]['tool'] == 'motus'
+                kaiju: it[2]['tool'] == 'kaiju'
+                kraken2: it[2]['tool'] == 'kraken2' || it[2]['tool'] == 'bracken' // to reuse the kraken module to produce the input data for bracken
                 krakenuniq: it[2]['tool'] == 'krakenuniq'
+                malt:    it[2]['tool'] == 'malt'
+                metaphlan3: it[2]['tool'] == 'metaphlan3'
+                motus: it[2]['tool'] == 'motus'
                 unknown: true
             }