Get database to work on github actions by reduceing kmers

nf-core · May 23, 2024 · c721c85 · c721c85
1 parent ad97077
commit c721c85
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Showing 3 changed files with 6 additions and 11 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -51,8 +51,4 @@ process {
         ext.args   = { "--sequenceType ${params.malt_sequencetype}" }
     }
 
-    withName: 'KRAKENUNIQ_BUILD' {
-        ext.args   = { "--jellyfish-bin \$(which jellyfish)" }
-    }
-
 }
diff --git a/conf/test.config b/conf/test.config
@@ -16,7 +16,7 @@ params {
 
     // Limit resources so that this can run on GitHub Actions
     max_cpus   = 2
-    max_memory = '24.GB'
+    max_memory = '14.GB'
     max_time   = '6.h'
 
     // Input data
@@ -41,8 +41,7 @@ params {
 
 process {
     withName:'KRAKENUNIQ_BUILD'{
-        memory = { check_max( 24.GB * task.attempt, 'memory'  ) }
-        ext.args ="--work-on-disk"
-
+        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
+        ext.args = "--work-on-disk --max-db-size 14 --kmer-len 15 --minimizer-len 13 --jellyfish-bin \$(which jellyfish)"
     }
 }
diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap
@@ -14,8 +14,8 @@
             "taxo.k2d:md5,cd8170a8c5a1b763a9ac1ffa2107cc88",
             true,
             "database.idx",
-            "database.kdb:md5,5b807ed9faead95a8893a52ec187bb7b",
-            "taxDB:md5,1aed1afa948daffc236deba1c5d635db",
+            "database.kdb:md5,a24fce43bedbc6c420f6e36d10c112a3",
+            "taxDB:md5,dad63877a3e5731d4fb5bff26bd1b8c4",
             true,
             "index0.idx:md5,876139dc930e68992cd2625e08bba48a",
             "ref.db:md5,377073f58a9f9b85acca59fcf21744a9",
@@ -29,6 +29,6 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.1"
         },
-        "timestamp": "2024-05-23T11:44:12.499883078"
+        "timestamp": "2024-05-23T12:52:21.949823939"
     }
 }