Merge pull request #42 from EBI-Metagenomics/bugfix/ips-unipro-docker…

…-mounts-fix

Fixes for ref dbs mounts for docker in ips and unifire. Mem limit to emapper --dbmem flag

modules/local/eggnog.nf

@@ -17,17 +17,25 @@ process EGGNOG_MAPPER {
     path "versions.yml", emit: versions
 
     script:
+    def db_mem_flag = ""
+    /*
+    The required memory of the executor needs to be greater than 44GB
+    to be able to load the eggnog SQLite database into memory.
+    Docs: https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.12#a-few-recipes
+    */
+    if ( task.memory >= 44.GB ) {
+        db_mem_flag = "--dbmem"
+    }
     if ( mode == "mapper" )
         """
         emapper.py -i ${fasta} \
         --database ${eggnog_db_dir}/eggnog.db \
         --dmnd_db ${eggnog_db_dir}/eggnog_proteins.dmnd \
         --data_dir ${eggnog_db_dir} \
-        --dbmem \
         -m diamond \
         --no_file_comments \
         --cpu ${task.cpus} \
-        --no_annot \
+        --no_annot ${db_mem_flag} \
         -o ${meta.prefix}
 
         cat <<-END_VERSIONS > versions.yml
@@ -43,8 +51,7 @@ process EGGNOG_MAPPER {
         --no_file_comments \
         --cpu ${task.cpus} \
         --tax_scope 'prokaryota_broad' \
-        --dbmem \
-        --annotate_hits_table ${annotation_hit_table} \
+        --annotate_hits_table ${annotation_hit_table} ${db_mem_flag} \
         -o ${meta.prefix}
 
         cat <<-END_VERSIONS > versions.yml

modules/local/interproscan.nf

@@ -11,7 +11,7 @@ process INTERPROSCAN {
         if (workflow.containerEngine == 'singularity') {
             return "--bind ${interproscan_db}/data:/opt/interproscan-5.62-94.0/data"
         } else {
-            return "-v ${interproscan_db}/data:/opt/interproscan-5.62-94.0/data"
+            return "-v ./${interproscan_db}/data:/opt/interproscan-5.62-94.0/data"
         }
     }
 

modules/local/unifire.nf

@@ -5,11 +5,12 @@ process UNIFIRE {
     label 'error_retry'
 
     container "dockerhub.ebi.ac.uk/uniprot-public/unifire:2023.4"
+
     containerOptions {
         if (workflow.containerEngine == 'singularity') {
             return "--bind unifire:/volume"
         } else {
-            return "-v unifire:/volume"
+            return "-v ./unifire:/volume"
         }
     }
 

nextflow.config

@@ -175,6 +175,14 @@ profiles {
     }
     test      { includeConfig 'conf/test.config'      }
 
+    local {
+        params {
+            // Any modern laptop / desktop should have at least...
+            max_memory = "12GB"
+            max_cpus   = 8
+        }
+    }
+
     ebi {
         params.workdir = "/hps/nobackup/rdf/metagenomics/service-team/nextflow-workdir/mett-pipeline"
         params.singularity_cachedir = "/hps/nobackup/rdf/metagenomics/service-team/singularity-cache/"