Include memory reduction from nf-core#7074

Co-authored-by: MartinPippel <[email protected]>
MartinPippel · Dec 4, 2024 · 0b1f640 · 0b1f640
1 parent 773a6fc
commit 0b1f640
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Showing 3 changed files with 19 additions and 19 deletions.
diff --git a/modules/nf-core/merqury/merqury/tests/main.nf.test.snap b/modules/nf-core/merqury/merqury/tests/main.nf.test.snap
@@ -417,7 +417,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.completeness.stats:md5,58b3933129832d64652babd80688eec3"
+                    "test.completeness.stats:md5,a8c7089c212e9dca2e0c47199b3002f9"
                 ]
             ],
             [
@@ -477,18 +477,18 @@
             [
                 "versions.yml:md5,825a4c61369638389227eee16dfb08b5"
             ],
-            "test.genome.read.test2_1.spectra-cn.fl.png,test.genome.read.test2_2.spectra-cn.fl.png,test.genome.spectra-cn.fl.png",
-            "test.genome.read.test2_1.spectra-cn.ln.png,test.genome.read.test2_2.spectra-cn.ln.png,test.genome.spectra-cn.ln.png",
-            "test.genome.read.test2_1.spectra-cn.st.png,test.genome.read.test2_2.spectra-cn.st.png,test.genome.spectra-cn.st.png",
+            "test.genome.spectra-cn.fl.png,test.genome.test.test2_1.spectra-cn.fl.png,test.genome.test.test2_2.spectra-cn.fl.png",
+            "test.genome.spectra-cn.ln.png,test.genome.test.test2_1.spectra-cn.ln.png,test.genome.test.test2_2.spectra-cn.ln.png",
+            "test.genome.spectra-cn.st.png,test.genome.test.test2_1.spectra-cn.st.png,test.genome.test.test2_2.spectra-cn.st.png",
             "test.spectra-asm.fl.png",
             "test.spectra-asm.ln.png",
             "test.spectra-asm.st.png",
             "test.hapmers.blob.png"
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-04T12:43:51.143935902"
+        "timestamp": "2024-12-04T20:06:48.980375307"
     }
 }
diff --git a/modules/nf-core/meryl/count/main.nf b/modules/nf-core/meryl/count/main.nf
@@ -21,15 +21,16 @@ process MERYL_COUNT {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def reduced_mem = task.memory.multiply(0.9).toGiga()
     """
-    for READ in $reads; do
+    for READ in ${reads}; do
         meryl count \\
-            k=$kvalue \\
-            threads=$task.cpus \\
-            memory=${task.memory.toGiga()} \\
-            $args \\
+            k=${kvalue} \\
+            threads=${task.cpus} \\
+            memory=${reduced_mem} \\
+            ${args} \\
             \$READ \\
-            output read.\${READ%.f*}.meryl
+            output ${prefix}.\${READ%.f*}.meryl
     done
 
     cat <<-END_VERSIONS > versions.yml
@@ -39,11 +40,10 @@ process MERYL_COUNT {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    for READ in $reads; do
-        touch read.\${READ%.f*}.meryl
+    for READ in ${reads}; do
+        touch ${prefix}.\${READ%.f*}.meryl
     done
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/meryl/count/tests/main.nf.test.snap b/modules/nf-core/meryl/count/tests/main.nf.test.snap
@@ -303,7 +303,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "read.test1_1.meryl:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.test1_1.meryl:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -315,7 +315,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "read.test1_1.meryl:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.test1_1.meryl:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -327,6 +327,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-04T12:28:06.856825599"
+        "timestamp": "2024-12-04T20:07:50.042776716"
     }
 }