From c2af30ebe99d1b626f265fd5c87d7a0c0a31794b Mon Sep 17 00:00:00 2001
From: Jim Downie <jd42@sanger.ac.uk>
Date: Fri, 29 Nov 2024 15:40:24 +0000
Subject: [PATCH] Fix taxonomy WF, add resource requirements for GTDB

---
 conf/base.config                   | 15 +++++++++++++--
 subworkflows/local/bin_taxonomy.nf |  9 ++++-----
 2 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/conf/base.config b/conf/base.config
index 22c5ffc..ed45d3e 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -10,7 +10,6 @@
 
 process {
 
-    // TODO nf-core: Check the defaults for all processes
     cpus   = { 1      * task.attempt }
     memory = { 6.GB   * task.attempt }
     time   = { 4.h    * task.attempt }
@@ -24,39 +23,51 @@ process {
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
-    // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
         cpus   = { 1                   }
         memory = { 6.GB * task.attempt }
         time   = { 4.h  * task.attempt }
     }
+
     withLabel:process_low {
         cpus   = { 2     * task.attempt }
         memory = { 12.GB * task.attempt }
         time   = { 4.h   * task.attempt }
     }
+
     withLabel:process_medium {
         cpus   = { 6     * task.attempt }
         memory = { 36.GB * task.attempt }
         time   = { 8.h   * task.attempt }
     }
+
     withLabel:process_high {
         cpus   = { 12    * task.attempt }
         memory = { 72.GB * task.attempt }
         time   = { 16.h  * task.attempt }
     }
+
     withLabel:process_long {
         time   = { 20.h  * task.attempt }
     }
+
     withLabel:process_high_memory {
         memory = { 200.GB * task.attempt }
     }
+
     withLabel:error_ignore {
         errorStrategy = 'ignore'
     }
+
     withLabel:error_retry {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
+
+    withName: GTDBTK_CLASSIFYWF {
+        cpus   = { 10 * task.attempt }
+        memory = { 128.GB * task.attempt }
+        time   = { 12.h * task.attempt }
+    }
 }
diff --git a/subworkflows/local/bin_taxonomy.nf b/subworkflows/local/bin_taxonomy.nf
index 2e5cf1d..c0e1d19 100644
--- a/subworkflows/local/bin_taxonomy.nf
+++ b/subworkflows/local/bin_taxonomy.nf
@@ -11,10 +11,10 @@ workflow BIN_TAXONOMY {
     if(checkm2_summary) {
         ch_bin_scores = checkm2_summary
             | splitCsv(header: true, sep: '\t')
-            | map { row ->
+            | map { meta, row ->
                 def completeness  = Double.parseDouble(row.'Completeness')
                 def contamination = Double.parseDouble(row.'Contamination')
-                [row.'Bin Id' + ".fa", completeness, contamination]
+                [row.'Name' + ".fa", completeness, contamination]
             }
 
         ch_filtered_bins = bins
@@ -31,9 +31,8 @@ workflow BIN_TAXONOMY {
     }
 
     if(params.enable_gtdbtk && params.gtdbtk_db) {
-        gtdbtk_db = Channel.of(
-            [ "GTDBTk", file(params.gtdbtk_db, checkIfExists: true) ]
-        )
+        gtdbtk_db = Channel.of(file(params.gtdbtk_db, checkIfExists: true).listFiles())
+            | collect | map { ["gtdb" ,it] }
         gtdbtk_mash = params.gtdbtk_mash_db ? file(params.gtdbtk_mash_db, checkIfExists: true) : []
 
         GTDBTK_CLASSIFYWF(