Lets see if SPAdes now works with fusion with the new container...

conf/test_full.config

@@ -16,30 +16,30 @@ params {
 
     // Input data for full size test
     // hg19 reference with highly conserved and low-complexity regions masked by Brian Bushnell
-    host_fasta    = "s3://ngi-igenomes/test-data/mag/hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz"
-    input         = "s3://ngi-igenomes/test-data/mag/samplesheets/samplesheet.full.csv"
+    host_fasta                 = "s3://ngi-igenomes/test-data/mag/hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz"
+    input                      = "s3://ngi-igenomes/test-data/mag/samplesheets/samplesheet.full.csv"
 
     //centrifuge_db = "s3://ngi-igenomes/test-data/mag/p_compressed+h+v.tar.gz"
-    kraken2_db    = "s3://ngi-igenomes/test-data/mag/minikraken_8GB_202003.tgz"
-    cat_db        = "s3://ngi-igenomes/test-data/mag/CAT_prepare_20210107.tar.gz"
+    kraken2_db                 = "s3://ngi-igenomes/test-data/mag/minikraken_8GB_202003.tgz"
+    cat_db                     = "s3://ngi-igenomes/test-data/mag/CAT_prepare_20210107.tar.gz"
     // gtdb_db       = "s3://ngi-igenomes/test-data/mag/gtdbtk_r214_data.tar.gz" ## This should be updated to release 220, once we get GTDB-Tk working again
-    skip_gtdbtk   = true
+    skip_gtdbtk                = true
 
     // TODO TEMPORARY: deactivate SPAdes due to incompatibility of container with fusion file system
-    skip_spades       = true
-    skip_spadeshybrid = true
+    skip_spades                = false
+    skip_spadeshybrid          = false
 
     // reproducibility options for assembly
-    spades_fix_cpus       = 10
-    spadeshybrid_fix_cpus = 10
-    megahit_fix_cpu_1     = true
+    spades_fix_cpus            = 10
+    spadeshybrid_fix_cpus      = 10
+    megahit_fix_cpu_1          = true
 
     // available options to enable reproducibility for BUSCO (--busco_db) not used here
     // to allow detection of possible problems in automated lineage selection mode using public databases
 
     // test CAT with official taxonomic ranks only
-    cat_official_taxonomy         = true
+    cat_official_taxonomy      = true
 
     // Skip CONCOCT due to timeout issues
-    skip_concoct                  = true
+    skip_concoct               = true
 }