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 01/20] 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 02/20] 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 03/20] 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 04/20] 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 05/20] 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 06/20] 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 07/20] 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 08/20] 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 d8c27759761232798ce6a295a98426b66adb39ee Mon Sep 17 00:00:00 2001
From: Andrew Frank <andrew.m.frank@gmail.com>
Date: Tue, 7 Jun 2022 09:41:41 -0400
Subject: [PATCH 09/20] Update google.config to fix custom VM memory error

---
 conf/google.config | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/conf/google.config b/conf/google.config
index 41f0e1f..6e8a45a 100644
--- a/conf/google.config
+++ b/conf/google.config
@@ -19,4 +19,6 @@ google.lifeSciences.preemptible = params.google_preemptible
 if (google.lifeSciences.preemptible) {
   process.errorStrategy = { task.exitStatus in [8,10,14] ? 'retry' : 'terminate' }
   process.maxRetries = 5
-}
\ No newline at end of file
+}
+
+process.machineType = { task.memory > task.cpus * 6.GB ? ['custom', task.cpus, task.cpus * 6656].join('-') : null }

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 10/20] 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 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 11/20] 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 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 12/20] 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 13/20] 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 8d5ae4c3ab53c8892bce378c58fb0e881c2e6cd0 Mon Sep 17 00:00:00 2001
From: Austyn Trull <atrull@uab.edu>
Date: Tue, 23 Aug 2022 15:30:13 -0500
Subject: [PATCH 14/20] Committing changes made by Brandon Wilk so that
 singularity containers will use scratch space

---
 conf/cheaha.config | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/conf/cheaha.config b/conf/cheaha.config
index 323a625..578259c 100644
--- a/conf/cheaha.config
+++ b/conf/cheaha.config
@@ -5,9 +5,15 @@ params {
     config_profile_url = 'https://www.uab.edu/cores/ircp/bds'
 }
 
+env {
+    TMPDIR="$USER_SCRATCH"
+    SINGULARITY_TMPDIR="$USER_SCRATCH"
+}
+
 singularity {
     enabled = true
     autoMounts = true
+    runOptions = "--contain --workdir $USER_SCRATCH"
 }
 
 process {

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 15/20] 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 16/20] 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

From 90f638d3761a6b8fa6560e1a3d09a6a62a6ee44a Mon Sep 17 00:00:00 2001
From: Austyn Trull <atrull@uab.edu>
Date: Mon, 29 Aug 2022 10:47:46 -0500
Subject: [PATCH 17/20] Updating the cheaha documentation to clarify that
 /data/temporary-scratch/atrull will be used as storage for files that would
 normally go into one of the temporary locations when using Singularity

---
 docs/cheaha.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/cheaha.md b/docs/cheaha.md
index 9d871c3..fb04c88 100644
--- a/docs/cheaha.md
+++ b/docs/cheaha.md
@@ -13,6 +13,8 @@ module load Singularity
 module load Nextflow
 ```
 
+Various tasks will be run inside of Singularity containers and all temp files typically written to `/tmp` and `/var/tmp` are instead written to the path pointed to by the `USER_SCRATCH` environment variable. This means that these temp files are stored in a user specific location, making them inaccessible to other users for pipeline reruns. Some of these temp files can be large and cleanup is also the responsibility of the user.
+
 All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
 
 > NB: You will need an account to use the HPC cluster on Cheaha in order to run the pipeline. If in doubt contact UAB IT Research Computing.</br></br>

From 51871ea6fca317ed6fca37597cabea895d62cbba Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 31 Aug 2022 11:32:01 +0200
Subject: [PATCH 18/20] rnafusion setup for hasta usage

---
 conf/pipeline/rnafusion/hasta.config | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 conf/pipeline/rnafusion/hasta.config

diff --git a/conf/pipeline/rnafusion/hasta.config b/conf/pipeline/rnafusion/hasta.config
new file mode 100644
index 0000000..fdd7475
--- /dev/null
+++ b/conf/pipeline/rnafusion/hasta.config
@@ -0,0 +1,7 @@
+// rnafusion/hasta specific profile config for Clinical Genomics Stockholm usage
+
+params {
+    all = true
+    trim = true
+    fusioninspector_filter = true
+}

From 0851903f66068d4e05b43f6a296134098063a5a1 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 31 Aug 2022 14:19:07 +0200
Subject: [PATCH 19/20] include new config in pipeline configs file

---
 README.md                        |  1 +
 docs/pipeline/rnafusion/hasta.md | 19 +++++++++++++++++++
 pipeline/rnafusion.config        |  4 +++-
 3 files changed, 23 insertions(+), 1 deletion(-)
 create mode 100644 docs/pipeline/rnafusion/hasta.md

diff --git a/README.md b/README.md
index 94ce55c..ae45869 100644
--- a/README.md
+++ b/README.md
@@ -198,6 +198,7 @@ Currently documentation is available for the following pipelines within specific
 - mag
   - [EVA](docs/pipeline/mag/eva.md)
 - rnafusion
+  - [HASTA](docs/pipeline/rnafusion/hasta.md)
   - [MUNIN](docs/pipeline/rnafusion/munin.md)
 - rnavar
   - [MUNIN](docs/pipeline/rnavar/munin.md)
diff --git a/docs/pipeline/rnafusion/hasta.md b/docs/pipeline/rnafusion/hasta.md
new file mode 100644
index 0000000..9f7813d
--- /dev/null
+++ b/docs/pipeline/rnafusion/hasta.md
@@ -0,0 +1,19 @@
+# nf-core/configs: HASTA rnafusion specific configuration
+
+Extra specific configuration for rnafusion pipeline
+
+## Usage
+
+To use, run the pipeline with `-profile hasta`.
+
+This will download and launch the rnafusion specific [`hasta.config`](../../../conf/pipeline/rnafusion/munin.config) which has been pre-configured with a setup suitable for the `HASTA` cluster.
+
+Example: `nextflow run nf-core/rnafusion -profile hasta`
+
+## rnafusion specific configurations for HASTA
+
+Specific configurations for `HASTA` has been made for rnafusion.
+
+- Always run all the analysis steps (all = true)
+- Use trimming (trim = true)
+- Take the fusions identified by at least 2 fusion detection tools to the fusioninspector analysis (fusioninspector_filter = true)
diff --git a/pipeline/rnafusion.config b/pipeline/rnafusion.config
index 2d86d89..f5a4e47 100644
--- a/pipeline/rnafusion.config
+++ b/pipeline/rnafusion.config
@@ -9,5 +9,7 @@
  */
 
 profiles {
+  hasta { includeConfig "${params.custom_config_base}/conf/pipeline/rnafusion/hasta.config" }
   munin { includeConfig "${params.custom_config_base}/conf/pipeline/rnafusion/munin.config" }
-}
\ No newline at end of file
+
+}

From 242101db16a342a45ef806e00ab20243327c4322 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 31 Aug 2022 14:26:32 +0200
Subject: [PATCH 20/20] fix extra space

---
 pipeline/rnafusion.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pipeline/rnafusion.config b/pipeline/rnafusion.config
index f5a4e47..894f6ab 100644
--- a/pipeline/rnafusion.config
+++ b/pipeline/rnafusion.config
@@ -11,5 +11,4 @@
 profiles {
   hasta { includeConfig "${params.custom_config_base}/conf/pipeline/rnafusion/hasta.config" }
   munin { includeConfig "${params.custom_config_base}/conf/pipeline/rnafusion/munin.config" }
-
 }