Updated GTDBTK

Author: olabiyi

Metagenomics/Illumina/Workflow_Documentation/SW_MGIllumina/workflow_code/modules/summarize_MAG.nf

@@ -92,7 +92,7 @@ process  GTDBTK_ON_MAGS {
                         -x fasta \\
                         --out_dir gtdbtk-out/ \\
                         --cpus ${task.cpus} \\
-                        --pplacer_cpus 1
+                        --skip_ani_screen 
 
             else
 
@@ -101,7 +101,7 @@ process  GTDBTK_ON_MAGS {
                        -x fasta \\
                        --out_dir gtdbtk-out/ \\
                        --cpus ${task.cpus} \\
-                       --pplacer_cpus 1
+                       --skip_ani_screen
 
             fi
 

Metagenomics/Illumina/Workflow_Documentation/SW_MGIllumina/workflow_code/nextflow.config

@@ -156,7 +156,7 @@ profiles {
 
 // Maximum number of jobs to submit in parallel
 executor.queueSize = 20
-params.DB_ROOT = "../Reference_DBs"
+params.DB_ROOT = "/full/path/to/Reference_DBs"
 
 
 // Mount the databases to their predefined locations in the Biobakery container
@@ -402,7 +402,7 @@ process {
 
     withName: GTDBTK_ON_MAGS {
                   conda = {params.conda.gtdbtk != null ? params.conda.gtdbtk : "envs/gtdb-tk.yaml.yaml"}
-                  container = "quay.io/biocontainers/gtdbtk:1.5.0--pyhdfd78af_0"
+                  container =  "quay.io/biocontainers/gtdbtk:2.4.0--pyhdfd78af_1" // "quay.io/biocontainers/gtdbtk:1.5.0--pyhdfd78af_0"
                   containerOptions = { params.containerEngine == "singularity" ? "-B \${PWD}:/data -B ${gtdbtk_db_dir}:/refdata" : "-v \${PWD}:/data -v ${gtdbtk_db_dir}:/refdata" } 
                   cpus = 8
                   memory = "600 GB"