gtdbtk update

replikation · Nov 20, 2023 · e72cc54 · e72cc54
1 parent 5fc0612
commit e72cc54
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Showing 4 changed files with 6 additions and 9 deletions.
diff --git a/configs/docker.config b/configs/docker.config
@@ -19,7 +19,7 @@ process {
     withLabel: filtlong     { container = 'nanozoo/filtlong:v0.2.0--afa175e' }
     withLabel: flye         { container = 'nanozoo/flye:2.8.3--2769e9b' } 
     withLabel: ggplot2      { container = 'nanozoo/ggplot2:3.3.1--303f617' }
-    withLabel: gtdbtk       { container = 'nanozoo/gtdb:1.6.0--5383545' }     
+    withLabel: gtdbtk       { container = 'nanozoo/gtdbtk:2.3.2--641ec99' }     
     withLabel: kraken2      { container = 'nanozoo/kraken2:2.1.1--d5ded30'}
     withLabel: krakentools  { container = 'nanozoo/krakentools:1.2--13d5ba5'}
     withLabel: krona        { container = 'nanozoo/krona:2.7.1--e7615f7'}

diff --git a/modules/fargene.nf b/modules/fargene.nf
@@ -1,9 +1,7 @@
 process fargene {
     label 'fargene'
-    errorStrategy 'ignore'
-    validExitStatus 0,1
   input:
-    tuple val(name), val(splitname), val(type), path(fasta) 
+    tuple val(name), val(splitname), val(type), path(fasta) optional true 
     each method
   output:
     path("${method}_${type}_${name}_*.fargene") 
@@ -19,7 +17,6 @@ process fargene {
 
 process fargene_plasmid_screen {
     label 'fargene'
-    validExitStatus 0,1
     //publishDir "${params.output}/fargene/", mode: 'copy'
   input:
     tuple val(name), path(fasta) 

diff --git a/modules/gtdbtk.nf b/modules/gtdbtk.nf
@@ -21,6 +21,6 @@ process gtdbtk {
       # file suffix get
       SUFFIXNAME=\$(ls ${dir} | head -1 | rev | cut -f1 -d "." | rev)
 
-      gtdbtk classify_wf  --genome_dir ${dir} --cpus 1 --out_dir ${name}-results -x \${SUFFIXNAME} --scratch_dir scratch_dir
+      gtdbtk classify_wf  --genome_dir ${dir} --skip_ani_screen --pplacer_cpus 1 --out_dir ${name}-results -x \${SUFFIXNAME} --scratch_dir scratch_dir
       """
 }
diff --git a/nextflow.config b/nextflow.config
@@ -116,9 +116,9 @@ profiles {
         google {  
             project = 'case-dev-302214'
             zone = 'europe-west1-b'
-            lifeSciences.preemptible = false
-            lifeSciences.bootDiskSize = 50.GB
-            }
+            lifeSciences {  preemptible = false
+                            bootDiskSize = 100.GB
+        }    }               
         includeConfig 'configs/docker.config'
         includeConfig 'configs/gcloud.config'