From eed1e42eace5da9ae89d22a34ca37bbf1e26e6e8 Mon Sep 17 00:00:00 2001
From: Guoying Qi <729395+gq1@users.noreply.github.com>
Date: Tue, 7 May 2024 11:21:20 +0100
Subject: [PATCH 1/6] try free runner

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8ba25e9..2f60ef3 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -22,7 +22,7 @@ jobs:
     name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'sanger-tol/genomeassembly') }}"
-    runs-on: ubuntu2204-4c
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         NXF_VER:

From 8c7dab549d95a4e8259972a1447154be4877409f Mon Sep 17 00:00:00 2001
From: Guoying Qi <729395+gq1@users.noreply.github.com>
Date: Tue, 7 May 2024 11:36:59 +0100
Subject: [PATCH 2/6] increase resource for the testing

---
 conf/test_github.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/test_github.config b/conf/test_github.config
index ee83537..8086af2 100644
--- 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
 

From f6c31306477715a511b63807fc1852995524b344 Mon Sep 17 00:00:00 2001
From: Guoying Qi <729395+gq1@users.noreply.github.com>
Date: Tue, 7 May 2024 12:03:56 +0100
Subject: [PATCH 3/6] change the memory to even number

---
 conf/test_github.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/test_github.config b/conf/test_github.config
index 8086af2..9eedc93 100644
--- a/conf/test_github.config
+++ b/conf/test_github.config
@@ -15,7 +15,7 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     max_cpus   = 4
-    max_memory = '15.GB'
+    max_memory = '14.GB'
     max_time   = '6.h'
     // Limit resources so that this can run on GitHub Actions
 

From da7a1b3fd970f23c761aa65fad495b73b185fe30 Mon Sep 17 00:00:00 2001
From: Guoying Qi <729395+gq1@users.noreply.github.com>
Date: Tue, 7 May 2024 13:40:55 +0100
Subject: [PATCH 4/6] roll back to the paid version of large runner with more
 storage

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2f60ef3..8ba25e9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -22,7 +22,7 @@ jobs:
     name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'sanger-tol/genomeassembly') }}"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu2204-4c
     strategy:
       matrix:
         NXF_VER:

From 6aeae6a845255ea6663ad7d417a3bf1fecfff87c Mon Sep 17 00:00:00 2001
From: Ksenia Krasheninnikova <kk16@sanger.ac.uk>
Date: Tue, 7 May 2024 15:04:38 +0100
Subject: [PATCH 5/6] Round up the buffer size estimate

---
 modules/local/bamtobed_sort.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/bamtobed_sort.nf b/modules/local/bamtobed_sort.nf
index c4d1db6..2f89d16 100644
--- 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
 

From 0458cd4dc61a63fb192f17de3ec659cf15e1d4c5 Mon Sep 17 00:00:00 2001
From: Guoying Qi <729395+gq1@users.noreply.github.com>
Date: Tue, 7 May 2024 15:31:21 +0100
Subject: [PATCH 6/6] more memory for CI profile and test round working or not.

---
 conf/test_github.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/test_github.config b/conf/test_github.config
index 9eedc93..8086af2 100644
--- a/conf/test_github.config
+++ b/conf/test_github.config
@@ -15,7 +15,7 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     max_cpus   = 4
-    max_memory = '14.GB'
+    max_memory = '15.GB'
     max_time   = '6.h'
     // Limit resources so that this can run on GitHub Actions