Merge pull request #42 from sanger-tol/runner-testing

try free runner
sanger-tol · May 7, 2024 · f4701f1 · f4701f1
2 parents 271885e + 0458cd4
commit f4701f1
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/conf/test_github.config b/conf/test_github.config
@@ -14,8 +14,8 @@ params {
     config_profile_name        = 'Github test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    max_cpus   = 2
-    max_memory = '6.GB'
+    max_cpus   = 4
+    max_memory = '15.GB'
     max_time   = '6.h'
     // Limit resources so that this can run on GitHub Actions
 

diff --git a/modules/local/bamtobed_sort.nf b/modules/local/bamtobed_sort.nf
@@ -22,7 +22,7 @@ process BAMTOBED_SORT {
     script:
     def prefix      = args.ext.prefix ?: "${meta.id}"
     def st_cores    = task.cpus > 4 ? 4 : "${task.cpus}"
-    def buffer_mem  = task.memory.toGiga() / 2
+    def buffer_mem  = (task.memory.toGiga() / 2).round()
     """
     samtools view -@${st_cores} -u -F0x400 ${bam} | bamToBed | sort -k4 --parallel=${task.cpus} -S ${buffer_mem}G -T . > ${prefix}_merged_sorted.bed