From afe935c2d04c3950b01feb0613f508164c652005 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 15 Apr 2022 15:27:41 +0200
Subject: [PATCH 01/55] include stub profile

---
 conf/hasta.config                      | 22 +++++++++++++++++++---
 conf/pipeline/raredisease/hasta.config | 21 +++++++++++++++++++--
 2 files changed, 38 insertions(+), 5 deletions(-)

diff --git a/conf/hasta.config b/conf/hasta.config
index c5dd5e4..d12cc40 100644
--- a/conf/hasta.config
+++ b/conf/hasta.config
@@ -15,19 +15,35 @@ singularity {
 params {
     max_memory = 180.GB
     max_cpus   = 36
-    max_time   = 336.h    
+    max_time   = 336.h
 }
 
 process {
     executor = 'slurm'
-    clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''}" }    
+    clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''}" }
+}
+
+params {
+    max_memory = 180.GB
+    max_cpus   = 36
+    max_time   = 336.h
 }
 
 profiles {
-    dev_prio {
+    stub_prio {
         params {
            priority = 'development'
            clusterOptions = "--qos=low"
+           max_memory = 1.GB
+           max_cpus   = 1
+           max_time   = 1.h
+        }
+    }
+
+    dev_prio {
+        params {
+            priority = 'development'
+            clusterOptions = "--qos=low"
         }
     }
 
diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config
index 96e3332..9d6e0c9 100644
--- a/conf/pipeline/raredisease/hasta.config
+++ b/conf/pipeline/raredisease/hasta.config
@@ -1,5 +1,5 @@
 process {
-    
+
     withName:'PICARD_MARKDUPLICATES' {
         memory = { check_max( 90.GB  * task.attempt, 'memory' ) }
     }
@@ -7,4 +7,21 @@ process {
         cpus   = { check_max( 16      * task.attempt, 'cpus' ) }
         memory = { check_max( 80.GB   * task.attempt, 'memory' ) }
     }
-}
\ No newline at end of file
+    withname: BCFTOOLS_VIEW {
+        if (params.genome == 'GRCh37') {
+            ext.args = '--output-type v --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "'
+        } else if (params.genome == 'GRCh38') {
+            ext.args = '--output-type v --apply-filters PASS --exclude "INFO/swegenAF > 0.40"'
+        }
+        publishDir = [
+            enabled: false,
+        ]
+    }
+
+}
+
+params {
+
+    sentieon_install_dir = '/home/proj/bin/sentieon/sentieon-genomics-202010.02/bin'
+
+}

From 6fad232232c5fff70fc849092f7f9ba1374c6f39 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 19 Apr 2022 11:27:35 +0200
Subject: [PATCH 02/55] sentieon env variable

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

diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config
index 9d6e0c9..7beb3ba 100644
--- a/conf/pipeline/raredisease/hasta.config
+++ b/conf/pipeline/raredisease/hasta.config
@@ -22,6 +22,6 @@ process {
 
 params {
 
-    sentieon_install_dir = '/home/proj/bin/sentieon/sentieon-genomics-202010.02/bin'
+    sentieon_install_dir = "$SENTIEON_INSTALL_DIR/bin"
 
 }

From 32207a240273e86665c8ed072b3ec3ee358fdde1 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 19 Apr 2022 11:42:05 +0200
Subject: [PATCH 03/55] update path so that the sentieon version is explicit

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

diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config
index 7beb3ba..56c1a97 100644
--- a/conf/pipeline/raredisease/hasta.config
+++ b/conf/pipeline/raredisease/hasta.config
@@ -22,6 +22,6 @@ process {
 
 params {
 
-    sentieon_install_dir = "$SENTIEON_INSTALL_DIR/bin"
+    sentieon_install_dir = "$SENTIEON_INSTALL_DIR/sentieon-genomics-202010.02/bin"
 
 }

From d39bec05dcf0016d720ea73744283150c9e410c1 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 19 Apr 2022 13:21:51 +0200
Subject: [PATCH 04/55] fix typo

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

diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config
index 56c1a97..4e00c56 100644
--- a/conf/pipeline/raredisease/hasta.config
+++ b/conf/pipeline/raredisease/hasta.config
@@ -7,11 +7,11 @@ process {
         cpus   = { check_max( 16      * task.attempt, 'cpus' ) }
         memory = { check_max( 80.GB   * task.attempt, 'memory' ) }
     }
-    withname: BCFTOOLS_VIEW {
+    withName: BCFTOOLS_VIEW {
         if (params.genome == 'GRCh37') {
             ext.args = '--output-type v --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "'
         } else if (params.genome == 'GRCh38') {
-            ext.args = '--output-type v --apply-filters PASS --exclude "INFO/swegenAF > 0.40"'
+            ext.args = '--output-type v --apply-filters PASS --exclude "INFO/swegen_FRQ > 0.40"'
         }
         publishDir = [
             enabled: false,

From 3e3e2be04beda1477a26b53f94d9165aee9147d2 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 22 Apr 2022 00:09:29 +0200
Subject: [PATCH 05/55] remove duplicate entries

---
 conf/hasta.config | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/conf/hasta.config b/conf/hasta.config
index d12cc40..03e61b8 100644
--- a/conf/hasta.config
+++ b/conf/hasta.config
@@ -23,18 +23,12 @@ process {
     clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''}" }
 }
 
-params {
-    max_memory = 180.GB
-    max_cpus   = 36
-    max_time   = 336.h
-}
-
 profiles {
     stub_prio {
         params {
            priority = 'development'
            clusterOptions = "--qos=low"
-           max_memory = 1.GB
+           max_memory = 6.GB
            max_cpus   = 1
            max_time   = 1.h
         }

From 447b3ee05d5a696a39d222d1b1c703a2e77725a8 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 22 Apr 2022 11:03:09 +0200
Subject: [PATCH 06/55] add beforescript for sentieon

---
 conf/pipeline/raredisease/hasta.config | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config
index 4e00c56..18c7bab 100644
--- a/conf/pipeline/raredisease/hasta.config
+++ b/conf/pipeline/raredisease/hasta.config
@@ -7,6 +7,12 @@ process {
         cpus   = { check_max( 16      * task.attempt, 'cpus' ) }
         memory = { check_max( 80.GB   * task.attempt, 'memory' ) }
     }
+    withLabel:'sentieon' {
+        beforeScript = { [
+            "export SENTIEON_LICENSE=\$(echo -e \$SENTIEON_LICENSE_BASE64 | base64 -d)",
+            "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202010.02/bin"
+        ].join(";") }
+    }
     withName: BCFTOOLS_VIEW {
         if (params.genome == 'GRCh37') {
             ext.args = '--output-type v --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "'
@@ -20,8 +26,3 @@ process {
 
 }
 
-params {
-
-    sentieon_install_dir = "$SENTIEON_INSTALL_DIR/sentieon-genomics-202010.02/bin"
-
-}

From 9da85209f234e10d8e84b11d9bd7ee39a2a2fc4f Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 22 Apr 2022 11:05:56 +0200
Subject: [PATCH 07/55] change bcftools output format

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

diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config
index 18c7bab..1359522 100644
--- a/conf/pipeline/raredisease/hasta.config
+++ b/conf/pipeline/raredisease/hasta.config
@@ -15,9 +15,9 @@ process {
     }
     withName: BCFTOOLS_VIEW {
         if (params.genome == 'GRCh37') {
-            ext.args = '--output-type v --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "'
+            ext.args = '--output-type z --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "'
         } else if (params.genome == 'GRCh38') {
-            ext.args = '--output-type v --apply-filters PASS --exclude "INFO/swegen_FRQ > 0.40"'
+            ext.args = '--output-type z --apply-filters PASS --exclude "INFO/swegen_FRQ > 0.40"'
         }
         publishDir = [
             enabled: false,

From 40c965c76b612925d69087976644c1c0243ba46c Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 29 Apr 2022 00:20:57 +0200
Subject: [PATCH 08/55] fix sentieon errors

---
 conf/pipeline/raredisease/hasta.config | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config
index 1359522..fb4d94a 100644
--- a/conf/pipeline/raredisease/hasta.config
+++ b/conf/pipeline/raredisease/hasta.config
@@ -8,10 +8,7 @@ process {
         memory = { check_max( 80.GB   * task.attempt, 'memory' ) }
     }
     withLabel:'sentieon' {
-        beforeScript = { [
-            "export SENTIEON_LICENSE=\$(echo -e \$SENTIEON_LICENSE_BASE64 | base64 -d)",
-            "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202010.02/bin"
-        ].join(";") }
+        beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202010.02/bin" }
     }
     withName: BCFTOOLS_VIEW {
         if (params.genome == 'GRCh37') {

From df0429ce9d72ae02c0a319d4e14325707cc7b517 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Fri, 3 Jun 2022 14:20:39 +0200
Subject: [PATCH 09/55] Replace oracle specific _JAVA_OPTIONS to portable
 JAVA_TOOLS_OPTIONS

---
 conf/pipeline/eager/eva.config | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config
index f35f1ed..f633bae 100644
--- a/conf/pipeline/eager/eva.config
+++ b/conf/pipeline/eager/eva.config
@@ -9,7 +9,7 @@ params {
 // Specific nf-core/eager process configuration
 process {
 
-  beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
+  beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"'
 
   maxRetries = 2
 
@@ -69,17 +69,17 @@ process {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
     errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
    }
-   
+
   withName: fastqc_after_clipping {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
-    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
    }
 
   withName: adapter_removal {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
     errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
    }
-   
+
   withName: bwa {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
   }
@@ -188,19 +188,19 @@ process {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
     errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
    }
-   
+
   withName:get_software_versions {
     cache = false
     clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" }
-    beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
+    beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega())}M" }
     errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
   }
-  
+
   withName:eigenstrat_snp_coverage {
     beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
-  }  
-  
+  }
+
   withName:kraken_merge {
     beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
   }
@@ -226,7 +226,7 @@ profiles {
 
     process {
 
-        beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
+        beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"'
 
         maxRetries = 2
 
@@ -279,7 +279,7 @@ profiles {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
           errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
-        
+
         withName: fastqc_after_clipping {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
           errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
@@ -404,7 +404,7 @@ profiles {
 
     process {
 
-        beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
+        beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"'
 
         maxRetries = 2
 
@@ -457,7 +457,7 @@ profiles {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
           errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
-        
+
         withName: fastqc_after_clipping {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
           errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }

From c40ebb9acfa5f46b98654d3adeae5c8057d01a96 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Fri, 3 Jun 2022 14:21:41 +0200
Subject: [PATCH 10/55] Add overhead for get_software_versions

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

diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config
index f633bae..92ce500 100644
--- a/conf/pipeline/eager/eva.config
+++ b/conf/pipeline/eager/eva.config
@@ -192,8 +192,8 @@ process {
   withName:get_software_versions {
     cache = false
     clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" }
-    beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
-    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega())}M" }
+    beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
+    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 2)}M" }
     errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
   }
 

From 9ef52af084fd8b9fa21d047022bf993ffe55b55f Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Fri, 3 Jun 2022 14:24:27 +0200
Subject: [PATCH 11/55] Increase overhead

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

diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config
index 92ce500..55b254c 100644
--- a/conf/pipeline/eager/eva.config
+++ b/conf/pipeline/eager/eva.config
@@ -193,7 +193,7 @@ process {
     cache = false
     clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" }
     beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
-    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 2)}M" }
+    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 4)}M" }
     errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
   }
 

From 05cc8a08f133c66ff724b4032a3810d5549fe59b Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Fri, 3 Jun 2022 21:08:19 +0200
Subject: [PATCH 12/55] Update eva.config

---
 conf/pipeline/eager/eva.config | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config
index 55b254c..fa045b1 100644
--- a/conf/pipeline/eager/eva.config
+++ b/conf/pipeline/eager/eva.config
@@ -193,7 +193,7 @@ process {
     cache = false
     clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" }
     beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
-    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 4)}M" }
+    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 8)}M" }
     errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
   }
 
@@ -207,6 +207,7 @@ process {
 
   withName:multiqc {
     beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1;'
+    clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
   }
 }
 

From 46fba9c5970ca4ff7a235dfe3c9943ec58bd09d6 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Fri, 3 Jun 2022 21:10:48 +0200
Subject: [PATCH 13/55] Update eva.config

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

diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config
index fa045b1..a50c969 100644
--- a/conf/pipeline/eager/eva.config
+++ b/conf/pipeline/eager/eva.config
@@ -207,7 +207,7 @@ process {
 
   withName:multiqc {
     beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1;'
-    clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
+    clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga() * 2}G" }
   }
 }
 

From 72e995f32678c8a94c0a466f91b61973363d528b Mon Sep 17 00:00:00 2001
From: Emil Bertilsson <emil.bertilsson@hasta.scilifelab.se>
Date: Thu, 9 Jun 2022 10:28:20 +0200
Subject: [PATCH 14/55] Adds generic fix for java memory issue on slurm

---
 conf/pipeline/raredisease/hasta.config | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config
index a076dbc..c31b940 100644
--- a/conf/pipeline/raredisease/hasta.config
+++ b/conf/pipeline/raredisease/hasta.config
@@ -7,7 +7,13 @@ process {
         cpus   = { check_max( 16      * task.attempt, 'cpus' ) }
         memory = { check_max( 80.GB   * task.attempt, 'memory' ) }
     }
+
+    // Java memory fixes
     withName:'QUALIMAP_BAMQC' {
-        ext.args = { "--java-mem-size=${task.memory.giga / 1.15 as long}G" }
+        clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
     }
+    withName:'PICARD_MARKDUPLICATES' {
+        clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
+    }
+    
 }
\ No newline at end of file

From 58dd9d49c7532ca114ce7dba2b8d6182806a4419 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Wed, 15 Jun 2022 15:21:20 +0200
Subject: [PATCH 15/55] Move beforeScript exports to env scope

---
 conf/pipeline/eager/eva.config | 24 ++++++------------------
 1 file changed, 6 insertions(+), 18 deletions(-)

diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config
index 55b254c..a82257a 100644
--- a/conf/pipeline/eager/eva.config
+++ b/conf/pipeline/eager/eva.config
@@ -6,11 +6,15 @@ params {
   config_profile_description = 'nf-core/eager EVA profile provided by nf-core/configs'
 }
 
+env {
+    JAVA_TOOL_OPTIONS = "-XX:ParallelGCThreads=1"
+    OPENBLAS_NUM_THREADS = 1
+    OMP_NUM_THREADS = 1
+}
+
 // Specific nf-core/eager process configuration
 process {
 
-  beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"'
-
   maxRetries = 2
 
   // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
@@ -192,22 +196,10 @@ process {
   withName:get_software_versions {
     cache = false
     clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" }
-    beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 4)}M" }
     errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
   }
 
-  withName:eigenstrat_snp_coverage {
-    beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
-  }
-
-  withName:kraken_merge {
-    beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
-  }
-
-  withName:multiqc {
-    beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1;'
-  }
 }
 
 profiles {
@@ -226,8 +218,6 @@ profiles {
 
     process {
 
-        beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"'
-
         maxRetries = 2
 
         // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
@@ -404,8 +394,6 @@ profiles {
 
     process {
 
-        beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"'
-
         maxRetries = 2
 
         // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion

From acabcbd9e8779305bf7470e22c935900085615ce Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Wed, 15 Jun 2022 15:27:40 +0200
Subject: [PATCH 16/55] Use _JAVA_OPTIONS instead

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

diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config
index 9f1853f..8376719 100644
--- a/conf/pipeline/eager/eva.config
+++ b/conf/pipeline/eager/eva.config
@@ -7,7 +7,7 @@ params {
 }
 
 env {
-    JAVA_TOOL_OPTIONS = "-XX:ParallelGCThreads=1"
+    _JAVA_OPTIONS = "-XX:ParallelGCThreads=1"
     OPENBLAS_NUM_THREADS = 1
     OMP_NUM_THREADS = 1
 }

From bb35d8e5d18f7d99b16f6f209b0e0ba589b6842a Mon Sep 17 00:00:00 2001
From: Gwenna Breton <gwenna.breton@gu.se>
Date: Thu, 30 Jun 2022 11:42:36 +0200
Subject: [PATCH 17/55] Added conf file for medair

---
 conf/medair.config | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 conf/medair.config

diff --git a/conf/medair.config b/conf/medair.config
new file mode 100644
index 0000000..6cce6f9
--- /dev/null
+++ b/conf/medair.config
@@ -0,0 +1,39 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'Cluster profile for medair (local cluster of Clinical Genomics Gothenburg)'
+  config_profile_contact = 'Clinical Genomics, Gothenburg'
+  config_profile_url = 'https://www.scilifelab.se/units/clinical-genomics-goteborg/'
+}
+
+//Nextflow parameters
+singularity {
+    enabled = true
+}
+
+profiles {
+  
+  wgs {
+    process {
+      queue = 'wgs.q'
+      executor = 'sge'
+      penv = 'mpi'
+      process.clusterOptions = '-l excl=1'
+      params.max_cpus = 40
+      params.max_time = 48.h
+      params.max_memory = 128.GB
+    }
+  }
+
+  production {
+    process {
+      queue = 'production.q'
+      executor = 'sge'
+      penv = 'mpi'
+      process.clusterOptions = '-l excl=1'
+      params.max_cpus = 40
+      params.max_time = 480.h
+      params.max_memory = 128.GB
+    }
+  }
+}
+

From f718025e79a0e204c6339ce05a7c1915fcb2e66e Mon Sep 17 00:00:00 2001
From: Gwenna Breton <gwenna.breton@gu.se>
Date: Thu, 30 Jun 2022 11:43:04 +0200
Subject: [PATCH 18/55] Added doc file for medair

---
 docs/medair.md | 43 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 docs/medair.md

diff --git a/docs/medair.md b/docs/medair.md
new file mode 100644
index 0000000..3edcfc4
--- /dev/null
+++ b/docs/medair.md
@@ -0,0 +1,43 @@
+# nf-core/configs: Medair Configuration
+
+All nf-core pipelines have been successfully configured for use on the medair cluster at Clinical Genomics Gothenburg.
+
+To use, run the pipeline with `-profile medair`. This will download and launch the [`medair.config`](../conf/medair.config) which has been pre-configured with a setup suitable for the medair cluster. 
+It will enable Nextflow to manage the pipeline jobs via the `SGE` job scheduler.
+Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
+
+## Modules to load
+
+Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on medair. You can do this by issuing the commands below:
+
+```bash
+## Load Nextflow and Singularity environment modules
+module purge
+module load nextflow/21.10.5.5658
+module load singularity/v3.4.0
+```
+
+>Should we link to Confluence page about new modules? See something about updating modules? etc.
+>Is this a good location to mention the nf-core conda environment? module load miniconda; source activate nf-core
+
+## Storage of Singularity images
+
+When downloading a new nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. A central location for these images is: `/apps/bio/dependencies/nf-core/singularities`
+
+Cached Singularity images can be accessed by running (or adding to your `.bashrc`) the following line: `export NXF_SINGULARITY_CACHEDIR="/apps/bio/dependencies/nf-core/singularities"` #is that correct??
+
+## Different profiles depending on what you are running
+
+Depending on what you are running, you can choose between the `clinic`, `research`, `byss` and `qd_rnaseq` profiles. This specify for example which queue will be used.
+
+>NB: say more about the different queues?
+
+## iGenomes specific configuration
+
+>TODO modify this part. Do we want to have the iGenomes somewhere?
+
+A local copy of the iGenomes resource has been made available on PROFILE CLUSTER so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline.
+You can do this by simply using the `--genome <GENOME_ID>` parameter.
+
+>NB: You will need an account to use the HPC cluster on PROFILE CLUSTER in order to run the pipeline. If in doubt contact IT.
+>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.

From 77017e877af4c1de90bb0d37ff52586dcb0f739b Mon Sep 17 00:00:00 2001
From: Gwenna Breton <gwenna.breton@gu.se>
Date: Thu, 30 Jun 2022 11:48:34 +0200
Subject: [PATCH 19/55] Added medair configuration docs to the list

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index d86461c..94ce55c 100644
--- a/README.md
+++ b/README.md
@@ -120,6 +120,7 @@ Currently documentation is available for the following systems:
 - [LUGH](docs/lugh.md)
 - [MAESTRO](docs/maestro.md)
 - [MARVIN](docs/marvin.md)
+- [MEDAIR](docs/medair.md)
 - [MJOLNIR_GLOBE](docs/mjolnir_globe.md)
 - [MPCDF](docs/mpcdf.md)
 - [MUNIN](docs/munin.md)

From abccece8a38b8b18daebae8d6b8a82e21be5cc4d Mon Sep 17 00:00:00 2001
From: Gwenna Breton <gwenna.breton@gu.se>
Date: Thu, 30 Jun 2022 11:49:47 +0200
Subject: [PATCH 20/55] Added medair config file to the list

---
 nfcore_custom.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nfcore_custom.config b/nfcore_custom.config
index 4b44d8a..6f0ac6c 100644
--- a/nfcore_custom.config
+++ b/nfcore_custom.config
@@ -49,6 +49,7 @@ profiles {
   lugh         { includeConfig "${params.custom_config_base}/conf/lugh.config" }
   maestro      { includeConfig "${params.custom_config_base}/conf/maestro.config" }
   marvin       { includeConfig "${params.custom_config_base}/conf/marvin.config" }
+  medair       { includeConfig "${params.custom_config_base}/conf/medair.config" }
   mjolnir_globe { includeConfig "${params.custom_config_base}/conf/mjolnir_globe.config" }
   mpcdf        { includeConfig "${params.custom_config_base}/conf/mpcdf.config" }
   munin        { includeConfig "${params.custom_config_base}/conf/munin.config" }

From 77dba3256aa4b948dad9bad16036f8a621eff98b Mon Sep 17 00:00:00 2001
From: Gwenna Breton <gwenna.breton@gu.se>
Date: Thu, 30 Jun 2022 11:53:02 +0200
Subject: [PATCH 21/55] Add profile name to test scope

---
 .github/workflows/main.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index c142eb3..f5ba0d1 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -66,6 +66,7 @@ jobs:
           - "jax"
           - "lugh"
           - "marvin"
+          - "medair"
           - "mjolnir_globe"
           - "maestro"
           - "mpcdf"

From 22f73b06f9da47ebc1c96bf14dabecc4918be938 Mon Sep 17 00:00:00 2001
From: Gwenna Breton <gwenna.breton@gu.se>
Date: Thu, 30 Jun 2022 12:00:05 +0200
Subject: [PATCH 22/55] Updated info about the different profiles

---
 docs/medair.md | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/docs/medair.md b/docs/medair.md
index 3edcfc4..834ac1d 100644
--- a/docs/medair.md
+++ b/docs/medair.md
@@ -28,9 +28,7 @@ Cached Singularity images can be accessed by running (or adding to your `.bashrc
 
 ## Different profiles depending on what you are running
 
-Depending on what you are running, you can choose between the `clinic`, `research`, `byss` and `qd_rnaseq` profiles. This specify for example which queue will be used.
-
->NB: say more about the different queues?
+Depending on what you are running, you can choose between the `wgs` and `production` profiles. Jobs running with the `wgs` profile run on a queue with higher priority. Jobs running with the `production` profile can last longer (max time: 20 times, versus 2 days for the `wgs` profile).
 
 ## iGenomes specific configuration
 

From 2398110ea54f5f07ddecf5c6b08c52a1f308d3c6 Mon Sep 17 00:00:00 2001
From: Gwenna Breton <Gwenna.breton@gu.se>
Date: Thu, 30 Jun 2022 14:24:17 +0200
Subject: [PATCH 23/55] Added info on dowloading pipelines

---
 docs/medair.md | 49 +++++++++++++++++++++++++++++++++++++++----------
 1 file changed, 39 insertions(+), 10 deletions(-)

diff --git a/docs/medair.md b/docs/medair.md
index 834ac1d..9f2b51f 100644
--- a/docs/medair.md
+++ b/docs/medair.md
@@ -6,9 +6,43 @@ To use, run the pipeline with `-profile medair`. This will download and launch t
 It will enable Nextflow to manage the pipeline jobs via the `SGE` job scheduler.
 Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
 
-## Modules to load
+## Download nf-core pipelines
 
-Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on medair. You can do this by issuing the commands below:
+### Set-up
+
+First you need to load relevant softwares: Nextflow and nf-core tools. You can do it as follow:
+
+```bash
+## Load Nextflow
+module load nextflow/21.10.5.5658
+## Load nf-core tools
+module load miniconda
+source activate nf-core
+```
+
+### Download a pipeline
+
+We have started to download pipelines in the following location: `/apps/bio/repos/nf-core/`
+
+Use the `nf-core download --singularity-cache-only` command to start a downlonad. It will open an interactive menu. Choose `singularity` and `none` for the compression level.
+
+### Storage of Singularity images
+
+When downloading a new nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. A central location for these images is: `/apps/bio/dependencies/nf-core/singularities`
+
+Cached Singularity images can be accessed by running (or adding to your `.bashrc`) the following: 
+
+```
+export NXF_SINGULARITY_CACHEDIR="/apps/bio/dependencies/nf-core/singularities"
+```
+
+This was also added to cronuser.
+
+## Run nf-core pipelines
+
+### Set-up
+
+Before running a pipeline you will need to load Nextflow and Singularity using the environment module system on medair. You can do this by issuing the commands below:
 
 ```bash
 ## Load Nextflow and Singularity environment modules
@@ -18,18 +52,13 @@ module load singularity/v3.4.0
 ```
 
 >Should we link to Confluence page about new modules? See something about updating modules? etc.
->Is this a good location to mention the nf-core conda environment? module load miniconda; source activate nf-core
 
-## Storage of Singularity images
-
-When downloading a new nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. A central location for these images is: `/apps/bio/dependencies/nf-core/singularities`
-
-Cached Singularity images can be accessed by running (or adding to your `.bashrc`) the following line: `export NXF_SINGULARITY_CACHEDIR="/apps/bio/dependencies/nf-core/singularities"` #is that correct??
-
-## Different profiles depending on what you are running
+### Choose a profile
 
 Depending on what you are running, you can choose between the `wgs` and `production` profiles. Jobs running with the `wgs` profile run on a queue with higher priority. Jobs running with the `production` profile can last longer (max time: 20 times, versus 2 days for the `wgs` profile).
 
+>Usage: -profile medair,wgs ?? (Check)
+
 ## iGenomes specific configuration
 
 >TODO modify this part. Do we want to have the iGenomes somewhere?

From 84174043e4437338c1e11b218b71763de396bcd5 Mon Sep 17 00:00:00 2001
From: Gwenna Breton <Gwenna.breton@gu.se>
Date: Thu, 30 Jun 2022 16:41:50 +0200
Subject: [PATCH 24/55] Added details for nf-core pipelines download

---
 docs/medair.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/medair.md b/docs/medair.md
index 9f2b51f..727becb 100644
--- a/docs/medair.md
+++ b/docs/medair.md
@@ -24,7 +24,7 @@ source activate nf-core
 
 We have started to download pipelines in the following location: `/apps/bio/repos/nf-core/`
 
-Use the `nf-core download --singularity-cache-only` command to start a downlonad. It will open an interactive menu. Choose `singularity` and `none` for the compression level.
+Use the `nf-core download --singularity-cache-only` command to start a download. It will open an interactive menu. Choose `singularity` for the software container image, and `none` for the compression type.
 
 ### Storage of Singularity images
 

From abfa3f47f4a67884d4af82603b3ba886c23b054d Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Fri, 1 Jul 2022 15:55:44 +0200
Subject: [PATCH 25/55] lowered the job submit rate of vsc_ugent

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

diff --git a/conf/vsc_ugent.config b/conf/vsc_ugent.config
index f2558fc..169faab 100644
--- a/conf/vsc_ugent.config
+++ b/conf/vsc_ugent.config
@@ -7,9 +7,9 @@ workDir = "$scratch_dir/work"
 // Perform work directory cleanup when the run has succesfully completed
 // cleanup = true
 
-// Reduce the job submit rate to about 10 per second, this way the server won't be bombarded with jobs
+// Reduce the job submit rate to about 5 per second, this way the server won't be bombarded with jobs
 executor {
-    submitRateLimit = '10 sec'
+    submitRateLimit = '5 sec'
 }
 
 // Specify that singularity should be used and where the cache dir will be for the images

From fa949a069ef99aa002ce18d24b169f095e2377d7 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Fri, 1 Jul 2022 16:01:19 +0200
Subject: [PATCH 26/55] added queuesize

---
 conf/vsc_ugent.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conf/vsc_ugent.config b/conf/vsc_ugent.config
index 169faab..9837a54 100644
--- a/conf/vsc_ugent.config
+++ b/conf/vsc_ugent.config
@@ -10,6 +10,7 @@ workDir = "$scratch_dir/work"
 // Reduce the job submit rate to about 5 per second, this way the server won't be bombarded with jobs
 executor {
     submitRateLimit = '5 sec'
+    queueSize = 50
 }
 
 // Specify that singularity should be used and where the cache dir will be for the images

From 1e3459528053d41f18b6df38152b806ae138916b Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Fri, 1 Jul 2022 16:16:18 +0200
Subject: [PATCH 27/55] removed queue size limit

---
 conf/vsc_ugent.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/conf/vsc_ugent.config b/conf/vsc_ugent.config
index 9837a54..169faab 100644
--- a/conf/vsc_ugent.config
+++ b/conf/vsc_ugent.config
@@ -10,7 +10,6 @@ workDir = "$scratch_dir/work"
 // Reduce the job submit rate to about 5 per second, this way the server won't be bombarded with jobs
 executor {
     submitRateLimit = '5 sec'
-    queueSize = 50
 }
 
 // Specify that singularity should be used and where the cache dir will be for the images

From b202ad70ac95bfecd72256e809ac8e734df4debd Mon Sep 17 00:00:00 2001
From: Gwenna Breton <Gwenna.breton@gu.se>
Date: Wed, 6 Jul 2022 11:16:38 +0200
Subject: [PATCH 28/55] Removed mention of specific module versions

---
 docs/medair.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/medair.md b/docs/medair.md
index 727becb..7be38e6 100644
--- a/docs/medair.md
+++ b/docs/medair.md
@@ -14,7 +14,7 @@ First you need to load relevant softwares: Nextflow and nf-core tools. You can d
 
 ```bash
 ## Load Nextflow
-module load nextflow/21.10.5.5658
+module load nextflow
 ## Load nf-core tools
 module load miniconda
 source activate nf-core
@@ -47,8 +47,8 @@ Before running a pipeline you will need to load Nextflow and Singularity using t
 ```bash
 ## Load Nextflow and Singularity environment modules
 module purge
-module load nextflow/21.10.5.5658
-module load singularity/v3.4.0
+module load nextflow
+module load singularity
 ```
 
 >Should we link to Confluence page about new modules? See something about updating modules? etc.

From 1d7a34b11f3a657e3db0bc1f2f95a330ee7165a3 Mon Sep 17 00:00:00 2001
From: Gwenna Breton <Gwenna.breton@gu.se>
Date: Wed, 6 Jul 2022 11:17:58 +0200
Subject: [PATCH 29/55] Removed comment about internal doc

---
 docs/medair.md | 2 --
 1 file changed, 2 deletions(-)

diff --git a/docs/medair.md b/docs/medair.md
index 7be38e6..dd2b9aa 100644
--- a/docs/medair.md
+++ b/docs/medair.md
@@ -51,8 +51,6 @@ module load nextflow
 module load singularity
 ```
 
->Should we link to Confluence page about new modules? See something about updating modules? etc.
-
 ### Choose a profile
 
 Depending on what you are running, you can choose between the `wgs` and `production` profiles. Jobs running with the `wgs` profile run on a queue with higher priority. Jobs running with the `production` profile can last longer (max time: 20 times, versus 2 days for the `wgs` profile).

From 235097e58e545c182bd9d02b00a5e424f150b7bf Mon Sep 17 00:00:00 2001
From: Gwenna Breton <Gwenna.breton@gu.se>
Date: Wed, 6 Jul 2022 11:20:59 +0200
Subject: [PATCH 30/55] Addressed review comments

- removed mention of iGenomes
- clarified whom to contact for support
---
 docs/medair.md | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/docs/medair.md b/docs/medair.md
index dd2b9aa..0c54c81 100644
--- a/docs/medair.md
+++ b/docs/medair.md
@@ -57,12 +57,5 @@ Depending on what you are running, you can choose between the `wgs` and `product
 
 >Usage: -profile medair,wgs ?? (Check)
 
-## iGenomes specific configuration
-
->TODO modify this part. Do we want to have the iGenomes somewhere?
-
-A local copy of the iGenomes resource has been made available on PROFILE CLUSTER so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline.
-You can do this by simply using the `--genome <GENOME_ID>` parameter.
-
->NB: You will need an account to use the HPC cluster on PROFILE CLUSTER in order to run the pipeline. If in doubt contact IT.
->NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.
+>NB: You will need an account to use the HPC cluster on PROFILE CLUSTER in order to run the pipeline. If in doubt contact cgg-it.
+>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact cgg-it.

From 1d13dd9fbce6b3c8a7169e9d4f7be51ac717e49a Mon Sep 17 00:00:00 2001
From: Gwenna Breton <Gwenna.breton@gu.se>
Date: Wed, 6 Jul 2022 11:24:03 +0200
Subject: [PATCH 31/55] Changed where cgg-it is mentioned

---
 docs/medair.md | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/docs/medair.md b/docs/medair.md
index 0c54c81..96c44e3 100644
--- a/docs/medair.md
+++ b/docs/medair.md
@@ -6,6 +6,8 @@ To use, run the pipeline with `-profile medair`. This will download and launch t
 It will enable Nextflow to manage the pipeline jobs via the `SGE` job scheduler.
 Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
 
+You will need an account to use the Medair cluster in order to download or run pipelines. If in doubt, contact cgg-it.
+
 ## Download nf-core pipelines
 
 ### Set-up
@@ -40,6 +42,8 @@ This was also added to cronuser.
 
 ## Run nf-core pipelines
 
+Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands below will have to be executed on one of the login nodes. If in doubt contact cgg-it.
+
 ### Set-up
 
 Before running a pipeline you will need to load Nextflow and Singularity using the environment module system on medair. You can do this by issuing the commands below:
@@ -56,6 +60,3 @@ module load singularity
 Depending on what you are running, you can choose between the `wgs` and `production` profiles. Jobs running with the `wgs` profile run on a queue with higher priority. Jobs running with the `production` profile can last longer (max time: 20 times, versus 2 days for the `wgs` profile).
 
 >Usage: -profile medair,wgs ?? (Check)
-
->NB: You will need an account to use the HPC cluster on PROFILE CLUSTER in order to run the pipeline. If in doubt contact cgg-it.
->NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact cgg-it.

From 96fd2bf217b71c73f07552857c70569dbbcb4c55 Mon Sep 17 00:00:00 2001
From: Gwennid <gwenna.breton@gu.se>
Date: Wed, 6 Jul 2022 11:42:05 +0200
Subject: [PATCH 32/55] Fixed formatting

---
 docs/medair.md | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/docs/medair.md b/docs/medair.md
index 96c44e3..6185f64 100644
--- a/docs/medair.md
+++ b/docs/medair.md
@@ -1,8 +1,8 @@
 # nf-core/configs: Medair Configuration
 
-All nf-core pipelines have been successfully configured for use on the medair cluster at Clinical Genomics Gothenburg.
+All nf-core pipelines have been successfully configured for use on the Medair cluster at Clinical Genomics Gothenburg.
 
-To use, run the pipeline with `-profile medair`. This will download and launch the [`medair.config`](../conf/medair.config) which has been pre-configured with a setup suitable for the medair cluster. 
+To use, run the pipeline with `-profile medair`. This will download and launch the [`medair.config`](../conf/medair.config) which has been pre-configured with a setup suitable for the Medair cluster.
 It will enable Nextflow to manage the pipeline jobs via the `SGE` job scheduler.
 Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
 
@@ -10,7 +10,7 @@ You will need an account to use the Medair cluster in order to download or run p
 
 ## Download nf-core pipelines
 
-### Set-up
+### Set-up: load Nextflow and nf-core tools
 
 First you need to load relevant softwares: Nextflow and nf-core tools. You can do it as follow:
 
@@ -32,9 +32,9 @@ Use the `nf-core download --singularity-cache-only` command to start a download.
 
 When downloading a new nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. A central location for these images is: `/apps/bio/dependencies/nf-core/singularities`
 
-Cached Singularity images can be accessed by running (or adding to your `.bashrc`) the following: 
+Cached Singularity images can be accessed by running (or adding to your `.bashrc`) the following:
 
-```
+```bash
 export NXF_SINGULARITY_CACHEDIR="/apps/bio/dependencies/nf-core/singularities"
 ```
 
@@ -44,9 +44,9 @@ This was also added to cronuser.
 
 Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands below will have to be executed on one of the login nodes. If in doubt contact cgg-it.
 
-### Set-up
+### Set-up: load Nextflow and Singularity
 
-Before running a pipeline you will need to load Nextflow and Singularity using the environment module system on medair. You can do this by issuing the commands below:
+Before running a pipeline you will need to load Nextflow and Singularity using the environment module system on Medair. You can do this by issuing the commands below:
 
 ```bash
 ## Load Nextflow and Singularity environment modules
@@ -59,4 +59,4 @@ module load singularity
 
 Depending on what you are running, you can choose between the `wgs` and `production` profiles. Jobs running with the `wgs` profile run on a queue with higher priority. Jobs running with the `production` profile can last longer (max time: 20 times, versus 2 days for the `wgs` profile).
 
->Usage: -profile medair,wgs ?? (Check)
+> Usage: -profile medair,wgs ?? (Check)

From b6e2d03a02938b2eb6a1aff451140b43bf1835fa Mon Sep 17 00:00:00 2001
From: Gwennid <gwenna.breton@gu.se>
Date: Wed, 6 Jul 2022 13:59:35 +0200
Subject: [PATCH 33/55] Added Singularity cache dir

---
 conf/medair.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conf/medair.config b/conf/medair.config
index 6cce6f9..183d4f6 100644
--- a/conf/medair.config
+++ b/conf/medair.config
@@ -8,6 +8,7 @@ params {
 //Nextflow parameters
 singularity {
     enabled = true
+    cacheDir = "/apps/bio/dependencies/nf-core/singularities"
 }
 
 profiles {

From 746db14d4745ad3369d12d09b3b056db55c787f9 Mon Sep 17 00:00:00 2001
From: Gwenna Breton <Gwenna.breton@gu.se>
Date: Thu, 7 Jul 2022 11:42:46 +0200
Subject: [PATCH 34/55] Update medair.md

- updated text about storing singularity images
- updated text about using profiles
---
 docs/medair.md | 24 ++++++++++++++----------
 1 file changed, 14 insertions(+), 10 deletions(-)

diff --git a/docs/medair.md b/docs/medair.md
index 6185f64..5eb1c46 100644
--- a/docs/medair.md
+++ b/docs/medair.md
@@ -22,23 +22,23 @@ module load miniconda
 source activate nf-core
 ```
 
-### Download a pipeline
-
-We have started to download pipelines in the following location: `/apps/bio/repos/nf-core/`
-
-Use the `nf-core download --singularity-cache-only` command to start a download. It will open an interactive menu. Choose `singularity` for the software container image, and `none` for the compression type.
-
 ### Storage of Singularity images
 
-When downloading a new nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. A central location for these images is: `/apps/bio/dependencies/nf-core/singularities`
+When downloading a nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. A central location for these images is: `/apps/bio/dependencies/nf-core/singularities`.
 
-Cached Singularity images can be accessed by running (or adding to your `.bashrc`) the following:
+If you run or add the following to your `.bashrc`, Nexflow will know where to store the images:
 
 ```bash
 export NXF_SINGULARITY_CACHEDIR="/apps/bio/dependencies/nf-core/singularities"
 ```
 
-This was also added to cronuser.
+> Comment: This was also added to cronuser.
+
+### Download a pipeline
+
+We have started to download pipelines in the following location: `/apps/bio/repos/nf-core/`
+
+Use the `nf-core download --singularity-cache-only` command to start a download. It will open an interactive menu. Choose `singularity` for the software container image, and `none` for the compression type.
 
 ## Run nf-core pipelines
 
@@ -59,4 +59,8 @@ module load singularity
 
 Depending on what you are running, you can choose between the `wgs` and `production` profiles. Jobs running with the `wgs` profile run on a queue with higher priority. Jobs running with the `production` profile can last longer (max time: 20 times, versus 2 days for the `wgs` profile).
 
-> Usage: -profile medair,wgs ?? (Check)
+For example, the following job would run with the `wgs` profile:
+
+```bash
+run nextflow nf-core/raredisease -profile medair,wgs
+```

From 4538e8aa36d71b06cbf46a68f82596f513b1c506 Mon Sep 17 00:00:00 2001
From: Gwenna Breton <Gwenna.breton@gu.se>
Date: Thu, 7 Jul 2022 13:41:42 +0200
Subject: [PATCH 35/55] Update medair.config

- added path to singularity image for Sentieon
- harmonized alignment
---
 conf/medair.config | 36 +++++++++++++++++++++---------------
 1 file changed, 21 insertions(+), 15 deletions(-)

diff --git a/conf/medair.config b/conf/medair.config
index 183d4f6..eeda705 100644
--- a/conf/medair.config
+++ b/conf/medair.config
@@ -1,13 +1,13 @@
 //Profile config names for nf-core/configs
 params {
   config_profile_description = 'Cluster profile for medair (local cluster of Clinical Genomics Gothenburg)'
-  config_profile_contact = 'Clinical Genomics, Gothenburg'
-  config_profile_url = 'https://www.scilifelab.se/units/clinical-genomics-goteborg/'
+  config_profile_contact     = 'Clinical Genomics, Gothenburg'
+  config_profile_url         = 'https://www.scilifelab.se/units/clinical-genomics-goteborg/'
 }
 
 //Nextflow parameters
 singularity {
-    enabled = true
+    enabled  = true
     cacheDir = "/apps/bio/dependencies/nf-core/singularities"
 }
 
@@ -15,26 +15,32 @@ profiles {
   
   wgs {
     process {
-      queue = 'wgs.q'
-      executor = 'sge'
-      penv = 'mpi'
+      queue                  = 'wgs.q'
+      executor               = 'sge'
+      penv                   = 'mpi'
       process.clusterOptions = '-l excl=1'
-      params.max_cpus = 40
-      params.max_time = 48.h
-      params.max_memory = 128.GB
+      params.max_cpus        = 40
+      params.max_time        = 48.h
+      params.max_memory      = 128.GB
     }
   }
 
   production {
     process {
-      queue = 'production.q'
-      executor = 'sge'
-      penv = 'mpi'
+      queue                  = 'production.q'
+      executor               = 'sge'
+      penv                   = 'mpi'
       process.clusterOptions = '-l excl=1'
-      params.max_cpus = 40
-      params.max_time = 480.h
-      params.max_memory = 128.GB
+      params.max_cpus        = 40
+      params.max_time        = 480.h
+      params.max_memory      = 128.GB
     }
   }
 }
 
+//Specific parameter for pipelines that can use Sentieon (e.g. nf-core/sarek, nf-core/raredisease)
+process {
+  withLabel:'sentieon' {
+    container = "/apps/bio/singularities/sentieon-211204-peta.simg"
+  }
+}

From 6b9cdc8ef3c959cf7a4c2137a1b6bf80ee970a07 Mon Sep 17 00:00:00 2001
From: Gwenna Breton <Gwenna.breton@gu.se>
Date: Thu, 7 Jul 2022 14:24:15 +0200
Subject: [PATCH 36/55] Added info about Sentieon singularities

---
 docs/medair.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/docs/medair.md b/docs/medair.md
index 5eb1c46..7b0c7d7 100644
--- a/docs/medair.md
+++ b/docs/medair.md
@@ -64,3 +64,7 @@ For example, the following job would run with the `wgs` profile:
 ```bash
 run nextflow nf-core/raredisease -profile medair,wgs
 ```
+
+### Sentieon
+
+In some pipelines (sarek, raredisease) it is possible to use Sentieon for alignment and variant calling. If ones uses the label `sentieon` for running a process, the config file contains the path to the Sentieon singularity image on Medair.

From 2ab126fa4d2f235ad9dc949d2dfae6d1146cd468 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Mon, 11 Jul 2022 18:28:41 +0100
Subject: [PATCH 37/55] Update default Nextclade dataset to
 2022-06-14T12:00:00Z

---
 conf/pipeline/viralrecon/genomes.config | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/conf/pipeline/viralrecon/genomes.config b/conf/pipeline/viralrecon/genomes.config
index baad834..0d5e754 100644
--- a/conf/pipeline/viralrecon/genomes.config
+++ b/conf/pipeline/viralrecon/genomes.config
@@ -13,18 +13,18 @@ params {
       // Please use 'MN908947.3' if possible because all primer sets are available / have been pre-prepared relative to that assembly
       fasta            = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
       gff              = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.gff.gz'
-      nextclade_dataset           = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/nextclade_sars-cov-2_MN908947_2022-01-18T12_00_00Z.tar.gz'
+      nextclade_dataset           = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/nextclade_sars-cov-2_MN908947_2022-06-14T12_00_00Z.tar.gz'
       nextclade_dataset_name      = 'sars-cov-2'
       nextclade_dataset_reference = 'MN908947'
-      nextclade_dataset_tag       = '2022-01-18T12:00:00Z'
+      nextclade_dataset_tag       = '2022-06-14T12:00:00Z'
     }
     'MN908947.3' {
       fasta            = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz'
       gff              = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
-      nextclade_dataset           = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/nextclade_sars-cov-2_MN908947_2022-01-18T12_00_00Z.tar.gz'
+      nextclade_dataset           = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/nextclade_sars-cov-2_MN908947_2022-06-14T12_00_00Z.tar.gz'
       nextclade_dataset_name      = 'sars-cov-2'
       nextclade_dataset_reference = 'MN908947'
-      nextclade_dataset_tag       = '2022-01-18T12:00:00Z'
+      nextclade_dataset_tag       = '2022-06-14T12:00:00Z'
       primer_sets {
         artic {
           '1' {

From 5d7789792fee4ea42b04e71c7961ee3cd3343c6e Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Tue, 12 Jul 2022 09:57:20 +0200
Subject: [PATCH 38/55] Add CITATION.cff and update .editorconfig

---
 .editorconfig |  2 +-
 CITATION.cff  | 56 +++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 57 insertions(+), 1 deletion(-)
 create mode 100644 CITATION.cff

diff --git a/.editorconfig b/.editorconfig
index 835c83d..70c7a9a 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -8,5 +8,5 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml}]
+[*.{md,yml,yaml,cff}]
 indent_size = 2
diff --git a/CITATION.cff b/CITATION.cff
new file mode 100644
index 0000000..4533e2f
--- /dev/null
+++ b/CITATION.cff
@@ -0,0 +1,56 @@
+cff-version: 1.2.0
+message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication"
+authors:
+  - family-names: Ewels
+    given-names: Philip
+  - family-names: Peltzer
+    given-names: Alexander
+  - family-names: Fillinger
+    given-names: Sven
+  - family-names: Patel
+    given-names: Harshil
+  - family-names: Alneberg
+    given-names: Johannes
+  - family-names: Wilm
+    given-names: Andreas
+  - family-names: Ulysse Garcia
+    given-names: Maxime
+  - family-names: Di Tommaso
+    given-names: Paolo
+  - family-names: Nahnsen
+    given-names: Sven
+title: "The nf-core framework for community-curated bioinformatics pipelines."
+version: 2.4.1
+doi: 10.1038/s41587-020-0439-x
+date-released: 2022-05-16
+url: https://github.com/nf-core/tools
+prefered-citation:
+  type: article
+  authors:
+    - family-names: Ewels
+      given-names: Philip
+    - family-names: Peltzer
+      given-names: Alexander
+    - family-names: Fillinger
+      given-names: Sven
+    - family-names: Patel
+      given-names: Harshil
+    - family-names: Alneberg
+      given-names: Johannes
+    - family-names: Wilm
+      given-names: Andreas
+    - family-names: Ulysse Garcia
+      given-names: Maxime
+    - family-names: Di Tommaso
+      given-names: Paolo
+    - family-names: Nahnsen
+      given-names: Sven
+  doi: 10.1038/s41587-020-0439-x
+  journal: nature biotechnology
+  start: 276
+  end: 278
+  title: "The nf-core framework for community-curated bioinformatics pipelines."
+  issue: 3
+  volume: 38
+  year: 2020
+  url: https://dx.doi.org/10.1038/s41587-020-0439-x

From f40825ac142f3c13a8b1b01605193100f752a49d Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 14 Jul 2022 15:50:50 +0200
Subject: [PATCH 39/55] lower submission rate for vsc_ugent

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

diff --git a/conf/vsc_ugent.config b/conf/vsc_ugent.config
index e1e9418..0bc6ffd 100644
--- a/conf/vsc_ugent.config
+++ b/conf/vsc_ugent.config
@@ -9,7 +9,7 @@ workDir = "$scratch_dir/work"
 
 // Reduce the job submit rate to about 5 per second, this way the server won't be bombarded with jobs
 executor {
-    submitRateLimit = '5 sec'
+    submitRateLimit = '3 sec'
 }
 
 // Specify that singularity should be used and where the cache dir will be for the images

From 58508c4fbc27bd71c82a16f6ec2bee277bc53aea Mon Sep 17 00:00:00 2001
From: Priyanka Surana <ps22@sanger.ac.uk>
Date: Wed, 20 Jul 2022 13:14:42 +0100
Subject: [PATCH 40/55] Sanger profile update

---
 conf/sanger.config | 46 ++++++++++++++++++++++------------------------
 1 file changed, 22 insertions(+), 24 deletions(-)

diff --git a/conf/sanger.config b/conf/sanger.config
index 1955ca9..df2dee7 100644
--- a/conf/sanger.config
+++ b/conf/sanger.config
@@ -1,35 +1,33 @@
+// Profile details
 params {
-  config_profile_description = 'The Wellcome Sanger Institute HPC cluster profile'
-  config_profile_contact = 'Anthony Underwood (@aunderwo)'
-  config_profile_url = 'https://www.sanger.ac.uk/group/informatics-support-group/'
-}
-
-singularity {
-  enabled = true
-  cacheDir   = "${baseDir}/singularity"
-  runOptions = '--bind /lustre --bind /nfs/pathnfs01 --bind /nfs/pathnfs02 --bind /nfs/pathnfs03 --bind /nfs/pathnfs04 --bind /nfs/pathnfs05 --bind /nfs/pathnfs06 --no-home'
+    config_profile_description = 'The Wellcome Sanger Institute HPC cluster (farm5) profile'
+    config_profile_contact = 'Priyanka Surana (@priyanka-surana)'
+    config_profile_url = 'https://www.sanger.ac.uk'
 }
 
+// Queue and retry strategy
 process{
-  executor = 'lsf'
-  queue = 'normal'
-  errorStrategy = { task.attempt <= 5 ? "retry" : "finish" }
-  process.maxRetries = 5
-  withLabel:process_long {
-    queue = 'long'
-  }
+    executor = 'lsf'
+    queue = { task.time < 12.h ? 'normal' : task.time < 48.h ? 'long' : 'basement' }
+    errorStrategy = 'retry'
+    maxRetries = 5
 }
 
+// Executor details
 executor{
-  name = 'lsf'
-  perJobMemLimit = true
-  poolSize = 4
-  submitRateLimit = '5 sec'
-  killBatchSize = 50
+    name = 'lsf'
+    perJobMemLimit = true
+    poolSize = 4
+    submitRateLimit = '5 sec'
+    killBatchSize = 50
 }
 
+// Max resources
 params {
-  max_memory = 128.GB
-  max_cpus = 64
-  max_time = 48.h
+    max_memory = 683.GB
+    max_cpus = 256
+    max_time = 720.h
 }
+
+// For singularity
+singularity.runOptions = '--bind /lustre --bind /nfs'

From fd87fbcb9dadd51ed8dff1804f465132f1cc72e3 Mon Sep 17 00:00:00 2001
From: Priyanka Surana <ps22@sanger.ac.uk>
Date: Wed, 20 Jul 2022 13:22:51 +0100
Subject: [PATCH 41/55] Sanger profile update

---
 docs/sanger.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/sanger.md b/docs/sanger.md
index ee75755..3fa7ae3 100644
--- a/docs/sanger.md
+++ b/docs/sanger.md
@@ -14,7 +14,7 @@ The latest version of Nextflow is not installed by default on the cluster. You w
 A recommended place to move the `nextflow` executable to is `~/bin` so that it's in the `PATH`.
 
 Nextflow manages each process as a separate job that is submitted to the cluster by using the `bsub` command.
-Since the Nextflow pipeline will submit individual jobs for each process to the cluster and dependencies will be provided bu Singularity images you shoudl make sure that your account has access to the Singularity binary by adding these lines to your `.bashrc` file
+Since the Nextflow pipeline will submit individual jobs for each process to the cluster and dependencies will be provided by Singularity images you should make sure that your account has access to the Singularity binary by adding these lines to your `.bashrc` file
 
 ```bash
 [[ -f  /software/pathogen/farm5 ]] && module load ISG/singularity
@@ -26,7 +26,7 @@ To do so make a shell script with a similar structure to the following code and
 ```bash
 #!/bin/bash
 #BSUB -o /path/to/a/log/dir/%J.o
-#BSUB -e /path/to/a/log/dir//%J.e
+#BSUB -e /path/to/a/log/dir/%J.e
 #BSUB -M 8000
 #BSUB -q long
 #BSUB -n 4

From 2aad355fbfbb694a88727eaf0884d76ee40ffce2 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Wed, 20 Jul 2022 14:32:43 +0100
Subject: [PATCH 42/55] The config doesn't mandate Singularity any more (Conda
 is fine too)

---
 docs/sanger.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/sanger.md b/docs/sanger.md
index 3fa7ae3..f4c490c 100644
--- a/docs/sanger.md
+++ b/docs/sanger.md
@@ -2,8 +2,6 @@
 
 To use, run the pipeline with `-profile sanger`. This will download and launch the [`sanger.config`](../conf/sanger.config) which has been
 pre-configured with a setup suitable for the Wellcome Sanger Institute LSF cluster.
-Using this profile, either a docker image containing all of the required software will be downloaded, and converted to a Singularity image or
-a Singularity image downloaded directly before execution of the pipeline.
 
 ## Running the workflow on the Wellcome Sanger Institute cluster
 
@@ -14,7 +12,9 @@ The latest version of Nextflow is not installed by default on the cluster. You w
 A recommended place to move the `nextflow` executable to is `~/bin` so that it's in the `PATH`.
 
 Nextflow manages each process as a separate job that is submitted to the cluster by using the `bsub` command.
-Since the Nextflow pipeline will submit individual jobs for each process to the cluster and dependencies will be provided by Singularity images you should make sure that your account has access to the Singularity binary by adding these lines to your `.bashrc` file
+
+If asking Nextflow to use Singularity to run the individual jobs,
+you should make sure that your account has access to the Singularity binary by adding these lines to your `.bashrc` file
 
 ```bash
 [[ -f  /software/pathogen/farm5 ]] && module load ISG/singularity

From 1f1a9ac5f0fe13401d857adc5472bb7d8da21975 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Wed, 20 Jul 2022 14:34:25 +0100
Subject: [PATCH 43/55] ISG provide the module, not the pathogen informatics
 team

---
 docs/sanger.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/sanger.md b/docs/sanger.md
index f4c490c..a44acf3 100644
--- a/docs/sanger.md
+++ b/docs/sanger.md
@@ -17,7 +17,7 @@ If asking Nextflow to use Singularity to run the individual jobs,
 you should make sure that your account has access to the Singularity binary by adding these lines to your `.bashrc` file
 
 ```bash
-[[ -f  /software/pathogen/farm5 ]] && module load ISG/singularity
+[[ -f /software/modules/ISG/singularity ]] && module load ISG/singularity
 ```
 
 Nextflow shouldn't run directly on the submission node but on a compute node.

From 60dc451569971795c7f20b4c8ad7bc6517b53b7b Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Wed, 20 Jul 2022 14:34:59 +0100
Subject: [PATCH 44/55] The oversubscribed queue is recommended for workflow
 managers

---
 docs/sanger.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/sanger.md b/docs/sanger.md
index a44acf3..caf74bb 100644
--- a/docs/sanger.md
+++ b/docs/sanger.md
@@ -28,7 +28,7 @@ To do so make a shell script with a similar structure to the following code and
 #BSUB -o /path/to/a/log/dir/%J.o
 #BSUB -e /path/to/a/log/dir/%J.e
 #BSUB -M 8000
-#BSUB -q long
+#BSUB -q oversubscribed
 #BSUB -n 4
 
 export HTTP_PROXY='http://wwwcache.sanger.ac.uk:3128'

From 1ee20f0bb0d018f341067a27c9e05b66ae1b6ce4 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Wed, 20 Jul 2022 14:35:22 +0100
Subject: [PATCH 45/55] 2 cores should be enough for the nextflow manager
 itself

---
 docs/sanger.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/sanger.md b/docs/sanger.md
index caf74bb..a3b590f 100644
--- a/docs/sanger.md
+++ b/docs/sanger.md
@@ -29,7 +29,7 @@ To do so make a shell script with a similar structure to the following code and
 #BSUB -e /path/to/a/log/dir/%J.e
 #BSUB -M 8000
 #BSUB -q oversubscribed
-#BSUB -n 4
+#BSUB -n 2
 
 export HTTP_PROXY='http://wwwcache.sanger.ac.uk:3128'
 export HTTPS_PROXY='http://wwwcache.sanger.ac.uk:3128'

From dda1d810b1a772ea3947561a69de59299a677728 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Wed, 20 Jul 2022 14:35:39 +0100
Subject: [PATCH 46/55] Latest stable version (rather than an edge one)

---
 docs/sanger.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/sanger.md b/docs/sanger.md
index a3b590f..ac6df4d 100644
--- a/docs/sanger.md
+++ b/docs/sanger.md
@@ -35,7 +35,7 @@ export HTTP_PROXY='http://wwwcache.sanger.ac.uk:3128'
 export HTTPS_PROXY='http://wwwcache.sanger.ac.uk:3128'
 export NXF_ANSI_LOG=false
 export NXF_OPTS="-Xms8G -Xmx8G -Dnxf.pool.maxThreads=2000"
-export NXF_VER=21.04.0-edge
+export NXF_VER=22.04.0-5697
 
 
 nextflow run \

From 0b47849532ec03528fef5d551804a5fb330d4e8f Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 27 Jul 2022 14:23:29 +0200
Subject: [PATCH 47/55] Update mpcdf.config

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

diff --git a/conf/mpcdf.config b/conf/mpcdf.config
index ee33913..93e2924 100644
--- a/conf/mpcdf.config
+++ b/conf/mpcdf.config
@@ -61,7 +61,7 @@ profiles {
        
         params {
             config_profile_description = 'MPCDF raven profile (unofficially) provided by nf-core/configs.'
-            memory = 2000000.MB
+            max_memory = 2000000.MB
             max_cpus = 72
             max_time = 24.h
         }

From 648025c1ceea79460eb1f064d72d49d25f3ee942 Mon Sep 17 00:00:00 2001
From: Gwenna Breton <Gwenna.breton@gu.se>
Date: Mon, 8 Aug 2022 16:04:21 +0200
Subject: [PATCH 48/55] Clarified where to store singularity images

---
 docs/medair.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/medair.md b/docs/medair.md
index 7b0c7d7..48ad557 100644
--- a/docs/medair.md
+++ b/docs/medair.md
@@ -24,9 +24,9 @@ source activate nf-core
 
 ### Storage of Singularity images
 
-When downloading a nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. A central location for these images is: `/apps/bio/dependencies/nf-core/singularities`.
+When downloading a nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. We chose to have a central location for these images on medair: `/apps/bio/dependencies/nf-core/singularities`.
 
-If you run or add the following to your `.bashrc`, Nexflow will know where to store the images:
+For Nexflow to know where to store new images, run or add the following to your `.bashrc`:
 
 ```bash
 export NXF_SINGULARITY_CACHEDIR="/apps/bio/dependencies/nf-core/singularities"

From 2740b5efbfc62aed864c027396fd33cbc075d07a Mon Sep 17 00:00:00 2001
From: Gwenna Breton <Gwenna.breton@gu.se>
Date: Mon, 8 Aug 2022 16:08:05 +0200
Subject: [PATCH 49/55] Update docs/medair.md
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Fixed typo

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 docs/medair.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/medair.md b/docs/medair.md
index 48ad557..bd13e84 100644
--- a/docs/medair.md
+++ b/docs/medair.md
@@ -57,7 +57,7 @@ module load singularity
 
 ### Choose a profile
 
-Depending on what you are running, you can choose between the `wgs` and `production` profiles. Jobs running with the `wgs` profile run on a queue with higher priority. Jobs running with the `production` profile can last longer (max time: 20 times, versus 2 days for the `wgs` profile).
+Depending on what you are running, you can choose between the `wgs` and `production` profiles. Jobs running with the `wgs` profile run on a queue with higher priority. Jobs running with the `production` profile can last longer (max time: 20 days, versus 2 days for the `wgs` profile).
 
 For example, the following job would run with the `wgs` profile:
 

From ffefefe0ab95dec7e7ba45fbe7fb777972b276f6 Mon Sep 17 00:00:00 2001
From: Gwenna Breton <Gwenna.breton@gu.se>
Date: Mon, 8 Aug 2022 16:11:55 +0200
Subject: [PATCH 50/55] Added contact emails

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

diff --git a/conf/medair.config b/conf/medair.config
index eeda705..d147643 100644
--- a/conf/medair.config
+++ b/conf/medair.config
@@ -1,7 +1,7 @@
 //Profile config names for nf-core/configs
 params {
   config_profile_description = 'Cluster profile for medair (local cluster of Clinical Genomics Gothenburg)'
-  config_profile_contact     = 'Clinical Genomics, Gothenburg'
+  config_profile_contact     = 'Clinical Genomics, Gothenburg (cgg-rd@gu.se, cgg-it@gu.se)'
   config_profile_url         = 'https://www.scilifelab.se/units/clinical-genomics-goteborg/'
 }
 

From 0e4f2b40d3f0e2873a34569dc440858f871241e1 Mon Sep 17 00:00:00 2001
From: Gwenna Breton <Gwenna.breton@gu.se>
Date: Mon, 8 Aug 2022 16:14:17 +0200
Subject: [PATCH 51/55] Added email of IT group

---
 docs/medair.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/medair.md b/docs/medair.md
index bd13e84..706332f 100644
--- a/docs/medair.md
+++ b/docs/medair.md
@@ -42,7 +42,7 @@ Use the `nf-core download --singularity-cache-only` command to start a download.
 
 ## Run nf-core pipelines
 
-Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands below will have to be executed on one of the login nodes. If in doubt contact cgg-it.
+Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands below will have to be executed on one of the login nodes. If in doubt contact cgg-it (cgg-it[at]gu.se).
 
 ### Set-up: load Nextflow and Singularity
 

From 1c942759ea9e30822181fb9d854744f102c62e18 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Thu, 18 Aug 2022 15:52:31 +0200
Subject: [PATCH 52/55] update sentieon

---
 conf/pipeline/raredisease/hasta.config | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config
index fb4d94a..1bec159 100644
--- a/conf/pipeline/raredisease/hasta.config
+++ b/conf/pipeline/raredisease/hasta.config
@@ -8,7 +8,14 @@ process {
         memory = { check_max( 80.GB   * task.attempt, 'memory' ) }
     }
     withLabel:'sentieon' {
-        beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202010.02/bin" }
+        beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202112.02/bin" }
+    }
+    // Java memory fixes
+    withName:'QUALIMAP_BAMQC' {
+        clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
+    }
+    withName:'PICARD_MARKDUPLICATES' {
+        clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
     }
     withName: BCFTOOLS_VIEW {
         if (params.genome == 'GRCh37') {

From dd63dee7aa6422354311dcf4a55945ad18d01f1d Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Thu, 18 Aug 2022 15:56:41 +0200
Subject: [PATCH 53/55] update conf

---
 conf/pipeline/raredisease/hasta.config | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config
index 1bec159..d655bf7 100644
--- a/conf/pipeline/raredisease/hasta.config
+++ b/conf/pipeline/raredisease/hasta.config
@@ -10,13 +10,6 @@ process {
     withLabel:'sentieon' {
         beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202112.02/bin" }
     }
-    // Java memory fixes
-    withName:'QUALIMAP_BAMQC' {
-        clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
-    }
-    withName:'PICARD_MARKDUPLICATES' {
-        clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
-    }
     withName: BCFTOOLS_VIEW {
         if (params.genome == 'GRCh37') {
             ext.args = '--output-type z --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "'

From 8dcfcfd856f1e657752911ce4771fdf3d9fa2467 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 24 Aug 2022 12:13:17 +0100
Subject: [PATCH 54/55] Add monkeypox genome files to viralrecon genome config
 file

---
 conf/pipeline/viralrecon/genomes.config | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/conf/pipeline/viralrecon/genomes.config b/conf/pipeline/viralrecon/genomes.config
index 0d5e754..ce2cf72 100644
--- a/conf/pipeline/viralrecon/genomes.config
+++ b/conf/pipeline/viralrecon/genomes.config
@@ -8,6 +8,8 @@
 params {
   // Genome reference file paths
   genomes {
+
+    // SARS-CoV-2
     'NC_045512.2' {
       // This version of the reference has been kept here for backwards compatibility.
       // Please use 'MN908947.3' if possible because all primer sets are available / have been pre-prepared relative to that assembly
@@ -18,6 +20,8 @@ params {
       nextclade_dataset_reference = 'MN908947'
       nextclade_dataset_tag       = '2022-06-14T12:00:00Z'
     }
+
+    // SARS-CoV-2
     'MN908947.3' {
       fasta            = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz'
       gff              = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
@@ -66,5 +70,24 @@ params {
         }
       }
     }
+
+    // Monkeypox
+    'NC_063383.1' {
+      fasta            = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_063383.1/GCA_014621545.1_ASM1462154v1_genomic.220824.fna.gz'
+      gff              = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_063383.1/GCA_014621545.1_ASM1462154v1_genomic.220824.gff.gz'
+    }
+
+    // Monkeypox
+    'ON563414.3' {
+      fasta            = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/ON563414.3/GCA_023516015.3_ASM2351601v1_genomic.220824.fna.gz'
+      gff              = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/ON563414.3/GCA_023516015.3_ASM2351601v1_genomic.220824.gff.gz'
+    }
+
+    // Monkeypox
+    'MT903344.1' {
+      fasta            = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MT903344.1/GCA_014621585.1_ASM1462158v1_genomic.220824.fna.gz'
+      gff              = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MT903344.1/GCA_014621585.1_ASM1462158v1_genomic.220824.gff.gz'
+    }
+
   }
 }

From 8b9661825b9e1d99083bc1331eccec47967e05f1 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 24 Aug 2022 15:21:44 +0100
Subject: [PATCH 55/55] Replace NC_063383.1 fasta and gff and add Nextclade
 config

---
 conf/pipeline/viralrecon/genomes.config | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/conf/pipeline/viralrecon/genomes.config b/conf/pipeline/viralrecon/genomes.config
index ce2cf72..06c8577 100644
--- a/conf/pipeline/viralrecon/genomes.config
+++ b/conf/pipeline/viralrecon/genomes.config
@@ -73,8 +73,12 @@ params {
 
     // Monkeypox
     'NC_063383.1' {
-      fasta            = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_063383.1/GCA_014621545.1_ASM1462154v1_genomic.220824.fna.gz'
-      gff              = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_063383.1/GCA_014621545.1_ASM1462154v1_genomic.220824.gff.gz'
+      fasta            = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_063383.1/GCF_014621545.1_ASM1462154v1_genomic.220824.fna.gz'
+      gff              = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_063383.1/GCF_014621545.1_ASM1462154v1_genomic.220824.gff.gz'
+      nextclade_dataset           = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_063383.1/nextclade_hMPXV_NC_063383.1_2022-08-19T12_00_00Z.tar.gz'
+      nextclade_dataset_name      = 'hMPXV'
+      nextclade_dataset_reference = 'NC_063383.1'
+      nextclade_dataset_tag       = '2022-08-19T12:00:00Z'
     }
 
     // Monkeypox