From b1a8b45aa06fe5b09c7de7f7bbbb4275de2bea95 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@users.noreply.github.com>
Date: Thu, 5 Dec 2019 17:52:53 +0100
Subject: [PATCH 1/4] Maybe typo?

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

diff --git a/conf/pipeline/eager/shh.config b/conf/pipeline/eager/shh.config
index 3dd95ed..afe0871 100644
--- a/conf/pipeline/eager/shh.config
+++ b/conf/pipeline/eager/shh.config
@@ -8,7 +8,7 @@ params {
 
 // Specific nf-core/eager process configuration
 process {
-  withName: malt {
+  withName:malt {
     memory = { check_max( 756.GB * task.attempt, 'memory' ) }
     cpus = { check_max(64 * task.attempt, 'cpus') }
     time = 1440.h

From dc0f1dfb401cf02223512441375e6f467d3ffbb3 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@users.noreply.github.com>
Date: Thu, 5 Dec 2019 17:58:49 +0100
Subject: [PATCH 2/4] Update shh.config

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

diff --git a/conf/pipeline/eager/shh.config b/conf/pipeline/eager/shh.config
index afe0871..2315fce 100644
--- a/conf/pipeline/eager/shh.config
+++ b/conf/pipeline/eager/shh.config
@@ -9,8 +9,8 @@ params {
 // Specific nf-core/eager process configuration
 process {
   withName:malt {
-    memory = { check_max( 756.GB * task.attempt, 'memory' ) }
-    cpus = { check_max(64 * task.attempt, 'cpus') }
+    memory = {  756.GB * task.attempt ]
+    cpus = { 64 * task.attempt }
     time = 1440.h
     queue = { task.memory > 756.GB ? 'supercruncher': 'long' }
   }

From 0033b74e4e27020f8716bd560cb2901ef2dd2213 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@users.noreply.github.com>
Date: Thu, 5 Dec 2019 18:08:39 +0100
Subject: [PATCH 3/4] Update shh.config

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

diff --git a/conf/pipeline/eager/shh.config b/conf/pipeline/eager/shh.config
index 2315fce..9a54c2b 100644
--- a/conf/pipeline/eager/shh.config
+++ b/conf/pipeline/eager/shh.config
@@ -12,6 +12,6 @@ process {
     memory = {  756.GB * task.attempt ]
     cpus = { 64 * task.attempt }
     time = 1440.h
-    queue = { task.memory > 756.GB ? 'supercruncher': 'long' }
+    queue = { task.memory > 756.GB ? 'supercruncher' : 'long' }
   }
 }

From e8b4675692ae1634965ff248f9b42201c6b0987d Mon Sep 17 00:00:00 2001
From: jfy133 <jfy133@gmail.com>
Date: Fri, 6 Dec 2019 13:17:31 +0100
Subject: [PATCH 4/4] Cleanup and tweaking

---
 conf/pipeline/eager/shh.config | 1 +
 conf/shh.config                | 1 -
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/pipeline/eager/shh.config b/conf/pipeline/eager/shh.config
index 9a54c2b..b333f09 100644
--- a/conf/pipeline/eager/shh.config
+++ b/conf/pipeline/eager/shh.config
@@ -4,6 +4,7 @@ params {
   // Specific nf-core/configs params
   config_profile_contact = 'James Fellows Yates (@jfy133)'
   config_profile_description = 'nf-core/eager SHH profile provided by nf-core/configs'
+  igenomes_base = "/projects1/public_data/igenomes/"
 }
 
 // Specific nf-core/eager process configuration
diff --git a/conf/shh.config b/conf/shh.config
index 190caad..91ea734 100644
--- a/conf/shh.config
+++ b/conf/shh.config
@@ -29,7 +29,6 @@ params {
   igenomes_base = "/projects1/public_data/igenomes/"
 }
 
-
 profiles {
   cdag {
       config_profile_description = 'MPI-SHH CDAG profile, provided by nf-core/configs.'