From 6c5a5c8bcb5b548c00cb25a5ee9016853a809603 Mon Sep 17 00:00:00 2001
From: Marc Hoeppner <mphoeppner@gmail.com>
Date: Mon, 24 Feb 2020 12:01:43 +0100
Subject: [PATCH 01/22] Removing old CCGA profile from docs and linting

Removing CCGA profile from master config

Removing CCGA profile from master config
---
 .github/workflows/main.yml |  2 +-
 README.md                  |  1 -
 conf/ccga.config           | 41 --------------------------------------
 docs/ccga.md               | 18 -----------------
 nfcore_custom.config       |  1 -
 5 files changed, 1 insertion(+), 62 deletions(-)
 delete mode 100644 conf/ccga.config
 delete mode 100644 docs/ccga.md

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 5fb2601..6f96a98 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh']
+          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow
diff --git a/README.md b/README.md
index 3011a00..7634409 100644
--- a/README.md
+++ b/README.md
@@ -98,7 +98,6 @@ Currently documentation is available for the following systems:
 * [BIGPURPLE](docs/bigpurple.md)
 * [BINAC](docs/binac.md)
 * [CBE](docs/cbe.md)
-* [CCGA](docs/ccga.md)
 * [CCGA_DX](docs/ccga_dx.md)
 * [CCGA_MED](docs/ccga_med.md)
 * [CFC](docs/binac.md)
diff --git a/conf/ccga.config b/conf/ccga.config
deleted file mode 100644
index 6163626..0000000
--- a/conf/ccga.config
+++ /dev/null
@@ -1,41 +0,0 @@
-//Profile config names for nf-core/configs
-params {
-  config_profile_description = 'CCGA cluster profile provided by nf-core/configs.'
-  config_profile_contact = 'Marc Hoeppner (@marchoeppner)'
-  config_profile_url = 'https://www.ccga.uni-kiel.de/'
-}
-
-/*
- * -------------------------------------------------
- *  Nextflow config file for CCGA cluster in Kiel
- * -------------------------------------------------
- */
-
-singularity {
-  enabled = true
-  runOptions = "-B /ifs -B /scratch -B /work_beegfs"
-  cacheDir = "/ifs/data/nfs_share/ikmb_repository/singularity_cache/"
-}
-
-executor {
-  queueSize=100
-}
-
-process {
-
-  // Global process config
-  executor = 'slurm'
-  queue = 'ikmb_a'
-
-  clusterOptions = { "--qos=ikmb_a" }
-
-}
-
-params {
-  // illumina iGenomes reference file paths on RZCluster
-  igenomes_base = '/ifs/data/nfs_share/ikmb_repository/references/iGenomes/references/'
-  saveReference = true
-  max_memory = 128.GB
-  max_cpus = 16
-  max_time = 120.h
-}
diff --git a/docs/ccga.md b/docs/ccga.md
deleted file mode 100644
index 798df29..0000000
--- a/docs/ccga.md
+++ /dev/null
@@ -1,18 +0,0 @@
-# nf-core/configs: CCGA Configuration
-
-Deployment and testing of nf-core pipelines at the CCGA cluster is on-going.
-
-To use, run the pipeline with `-profile ccga`. This will download and launch the [`ccga.config`](../conf/ccga.config) which has been pre-configured with a setup suitable for the CCGA cluster. 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.
-
-Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on the cluster. You can do this by issuing the commands below:
-
-```bash
-## Load Nextflow and Singularity environment modules
-module purge
-module load IKMB
-module load Java/1.8.0
-module load Nextflow
-module load singularity3.1.0
-```
-
->NB: Access to the CCGA cluster is restricted to IKMB/CCGA employes. Please talk to Marc Hoeppner to get access (@marchoeppner).
diff --git a/nfcore_custom.config b/nfcore_custom.config
index 8b4a3a9..0fcbe66 100644
--- a/nfcore_custom.config
+++ b/nfcore_custom.config
@@ -17,7 +17,6 @@ profiles {
   bigpurple    { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }
   binac        { includeConfig "${params.custom_config_base}/conf/binac.config" }
   cbe          { includeConfig "${params.custom_config_base}/conf/cbe.config" }
-  ccga         { includeConfig "${params.custom_config_base}/conf/ccga.config" }
   ccga_dx      { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" }
   ccga_med     { includeConfig "${params.custom_config_base}/conf/ccga_med.config" }
   cfc          { includeConfig "${params.custom_config_base}/conf/cfc.config" }

From e2e4dd05d318c6a537f5dd17f6a1ec82c5a32167 Mon Sep 17 00:00:00 2001
From: phue <patrick.huether@gmi.oeaw.ac.at>
Date: Thu, 5 Mar 2020 16:34:20 +0100
Subject: [PATCH 02/22] cbe: move container cache to different filesystem

this is a workaround for squashfs errors that occur when containers are run from beeGFS
---
 conf/cbe.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/cbe.config b/conf/cbe.config
index ea24e5b..5888202 100755
--- a/conf/cbe.config
+++ b/conf/cbe.config
@@ -14,7 +14,7 @@ process {
 
 singularity {
   enabled = true
-  cacheDir = '/scratch-cbe/shared/containers'
+  cacheDir = '/resources/containers'
 }
 
 params {

From 8a9d3ad8a0ca66ef35276adacc1facac4d1b0129 Mon Sep 17 00:00:00 2001
From: Evan Floden <evanfloden@gmail.com>
Date: Fri, 6 Mar 2020 05:47:29 +0000
Subject: [PATCH 03/22] First commit of Google Cloud config

---
 .github/workflows/main.yml        |   2 +-
 README.md                         |   1 +
 conf/google.config                |  21 +++++++++++++++++++++
 docs/google.md                    |  30 ++++++++++++++++++++++++++++++
 docs/images/google-cloud-logo.png | Bin 0 -> 13226 bytes
 nfcore_custom.config              |   1 +
 6 files changed, 54 insertions(+), 1 deletion(-)
 create mode 100644 conf/google.config
 create mode 100644 docs/google.md
 create mode 100644 docs/images/google-cloud-logo.png

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 5fb2601..d68f44f 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh']
+          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'google', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow
diff --git a/README.md b/README.md
index 0e58b09..b49edb7 100644
--- a/README.md
+++ b/README.md
@@ -108,6 +108,7 @@ Currently documentation is available for the following systems:
 * [GENOTOUL](docs/genotoul.md)
 * [GENOUEST](docs/genouest.md)
 * [GIS](docs/gis.md)
+* [GOOGLE](docs/google.md)
 * [HEBBE](docs/hebbe.md)
 * [KRAKEN](docs/kraken.md)
 * [MUNIN](docs/munin.md)
diff --git a/conf/google.config b/conf/google.config
new file mode 100644
index 0000000..4333d86
--- /dev/null
+++ b/conf/google.config
@@ -0,0 +1,21 @@
+// Nextflow config file for running on Google Cloud Life Sciences
+params {
+  config_profile_description = 'Google Cloud Life Sciences Profile'
+  config_profile_contact = 'Evan Floden, Seqera Labs (@evanfloden)'
+  config_profile_url = 'https://cloud.google.com/life-sciences'
+
+  google_zone = 'europe-west2-c'
+  google_bucket = false
+  google_debug = false
+  google_preemptible = true
+}
+
+process.executor = 'google-lifesciences'
+google.zone = params.google_zone
+google.lifeSciences.debug = params.google_debug
+workDir = params.google_bucket
+google.lifeSciences.preemptible = params.google_preemptible
+if (google.lifeSciences.preemptible) {
+  process.errorStrategy = { task.exitStatus==14 ? 'retry' : 'terminate' }
+  process.maxRetries = 5
+}
\ No newline at end of file
diff --git a/docs/google.md b/docs/google.md
new file mode 100644
index 0000000..d2b0f51
--- /dev/null
+++ b/docs/google.md
@@ -0,0 +1,30 @@
+# nf-core/configs: Google Cloud Life Sciences Configuration
+![Google Cloud](images/google-cloud-logo.png "https://cloud.google.com/life-sciences/docs/tutorials/nextflow")
+
+To be used with the `google` profile by specifying the `-profile google` when running nf-core pipelines.
+
+## Quick Start
+```
+GOOGLE_APPLICATION_CREDENTIALS=<your_key>.json
+NXF_MODE=google
+nextflow run nf-core/rnaseq -profile google,test --google_bucket <gs://your_bucket/work>
+```
+
+## Required Parameters
+#### `--google-bucket`
+The Google Cloud Storage bucket location to be used as a Nextflow work directory. Can also be specified with (`-w gs://your_bucket/work`).
+
+## Optional Parameters
+#### `--google-zone`
+The Google zone where the computation is executed in Compute Engine VMs. Multiple zones can be provided separating them by a comma. Default (`europe-west2-c`).
+
+#### `--google-preemptible`
+Enables the usage of preemptible virtual machines with a retry error statergy for up to 5 retries. Default (`true`)
+
+#### `--google-debug`
+Copies the /google debug directory from the VM to the task bucket directory. Useful for debugging. Default (`false`).
+
+## Google Cloud Life Sciences Setup
+Please refer to the [Google Cloud](https://cloud.google.com/life-sciences/docs/tutorials/nextflow) and [Nextflow](https://www.nextflow.io/docs/latest/google.html#cloud-life-sciences) documentation which describe how to setup the Google Cloud environment.
+
+
diff --git a/docs/images/google-cloud-logo.png b/docs/images/google-cloud-logo.png
new file mode 100644
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diff --git a/nfcore_custom.config b/nfcore_custom.config
index 72a4ee8..1c391f5 100644
--- a/nfcore_custom.config
+++ b/nfcore_custom.config
@@ -24,6 +24,7 @@ profiles {
                  includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config";
                  includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config"}
   genotoul     { includeConfig "${params.custom_config_base}/conf/genotoul.config" }
+  google       { includeConfig "${params.custom_config_base}/conf/google.config" }
   denbi_qbic   { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" }
   genouest     { includeConfig "${params.custom_config_base}/conf/genouest.config" }
   gis          { includeConfig "${params.custom_config_base}/conf/gis.config" }

From 87e8da61a4467d8a55a0944995809899e3a59bb5 Mon Sep 17 00:00:00 2001
From: Evan Floden <evanfloden@gmail.com>
Date: Fri, 6 Mar 2020 05:58:59 +0000
Subject: [PATCH 04/22] Readme formatting

---
 docs/google.md                    |  14 +++--
 docs/images/google-cloud-logo.png | Bin 13226 -> 0 bytes
 docs/images/google-cloud-logo.svg |  96 ++++++++++++++++++++++++++++++
 3 files changed, 105 insertions(+), 5 deletions(-)
 delete mode 100644 docs/images/google-cloud-logo.png
 create mode 100644 docs/images/google-cloud-logo.svg

diff --git a/docs/google.md b/docs/google.md
index d2b0f51..d3a65f5 100644
--- a/docs/google.md
+++ b/docs/google.md
@@ -1,8 +1,11 @@
 # nf-core/configs: Google Cloud Life Sciences Configuration
-![Google Cloud](images/google-cloud-logo.png "https://cloud.google.com/life-sciences/docs/tutorials/nextflow")
 
 To be used with the `google` profile by specifying the `-profile google` when running nf-core pipelines.
 
+
+![Google Cloud](images/google-cloud-logo.svg "https://cloud.google.com/life-sciences/docs/tutorials/nextflow")
+
+
 ## Quick Start
 ```
 GOOGLE_APPLICATION_CREDENTIALS=<your_key>.json
@@ -10,21 +13,22 @@ NXF_MODE=google
 nextflow run nf-core/rnaseq -profile google,test --google_bucket <gs://your_bucket/work>
 ```
 
-## Required Parameters
+### Required Parameters
 #### `--google-bucket`
 The Google Cloud Storage bucket location to be used as a Nextflow work directory. Can also be specified with (`-w gs://your_bucket/work`).
 
-## Optional Parameters
+### Optional Parameters
 #### `--google-zone`
 The Google zone where the computation is executed in Compute Engine VMs. Multiple zones can be provided separating them by a comma. Default (`europe-west2-c`).
 
 #### `--google-preemptible`
-Enables the usage of preemptible virtual machines with a retry error statergy for up to 5 retries. Default (`true`)
+Enables the usage of preemptible virtual machines with a retry error statergy for up to 5 retries. Default (`true`).
 
 #### `--google-debug`
 Copies the /google debug directory from the VM to the task bucket directory. Useful for debugging. Default (`false`).
 
-## Google Cloud Life Sciences Setup
+
+## Cloud Life Sciences Setup
 Please refer to the [Google Cloud](https://cloud.google.com/life-sciences/docs/tutorials/nextflow) and [Nextflow](https://www.nextflow.io/docs/latest/google.html#cloud-life-sciences) documentation which describe how to setup the Google Cloud environment.
 
 
diff --git a/docs/images/google-cloud-logo.png b/docs/images/google-cloud-logo.png
deleted file mode 100644
index 07c9a325b254d93f3fe4e94abb5cbdd9162afd92..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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diff --git a/docs/images/google-cloud-logo.svg b/docs/images/google-cloud-logo.svg
new file mode 100644
index 0000000..18b0e48
--- /dev/null
+++ b/docs/images/google-cloud-logo.svg
@@ -0,0 +1,96 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- Generator: Adobe Illustrator 23.0.1, SVG Export Plug-In . SVG Version: 6.00 Build 0)  -->
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd" [
+	<!ENTITY ns_extend "http://ns.adobe.com/Extensibility/1.0/">
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+	<!ENTITY ns_graphs "http://ns.adobe.com/Graphs/1.0/">
+	<!ENTITY ns_vars "http://ns.adobe.com/Variables/1.0/">
+	<!ENTITY ns_imrep "http://ns.adobe.com/ImageReplacement/1.0/">
+	<!ENTITY ns_sfw "http://ns.adobe.com/SaveForWeb/1.0/">
+	<!ENTITY ns_custom "http://ns.adobe.com/GenericCustomNamespace/1.0/">
+	<!ENTITY ns_adobe_xpath "http://ns.adobe.com/XPath/1.0/">
+]>
+<svg version="1.1" id="Art" xmlns:x="&ns_extend;" xmlns:i="&ns_ai;" xmlns:graph="&ns_graphs;"
+	 xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px" viewBox="0 0 8986.8 1407.9"
+	 style="enable-background:new 0 0 8986.8 1407.9;" xml:space="preserve">
+<style type="text/css">
+	.st0{fill:#EA4335;}
+	.st1{fill:#4285F4;}
+	.st2{fill:#34A853;}
+	.st3{fill:#FBBC05;}
+	.st4{fill:#5F6368;}
+</style>
+<metadata>
+	<sfw  xmlns="&ns_sfw;">
+		<slices></slices>
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From 44cd3089def3f47cc1a53a6f7536c4d203e05fab Mon Sep 17 00:00:00 2001
From: Evan Floden <evanfloden@gmail.com>
Date: Fri, 6 Mar 2020 09:48:00 +0100
Subject: [PATCH 05/22] Alphabetical ordering of GitHub workflows

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

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index d68f44f..5e9676d 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'google', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh']
+          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

From 8e42bbd7d055acae8fff3ed8fca372979a96adfa Mon Sep 17 00:00:00 2001
From: mseybold <matthias.seybold@uni-tuebingen.de>
Date: Fri, 6 Mar 2020 10:25:08 +0100
Subject: [PATCH 06/22] Update cfc.config

We just added some new HighMem nodes to the cfc, Partition/queue name is qbic, each node has 128Cores and 2TB of RAM.
The old queue (Name compute) is set to default by slurm.
Each process over 60GB of RAM or over 20cpus should run on those new nodes.
So added the queue State and adjusted the max_memory and max_cpu setting.
---
 conf/cfc.config | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/conf/cfc.config b/conf/cfc.config
index 763dcf0..99917ba 100644
--- a/conf/cfc.config
+++ b/conf/cfc.config
@@ -13,6 +13,7 @@ singularity {
 process {
   beforeScript = 'module load devel/singularity/3.4.2'
   executor = 'slurm'
+  queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' }
 }
 
 weblog{
@@ -22,7 +23,7 @@ weblog{
 
 params {
   igenomes_base = '/nfsmounts/igenomes'
-  max_memory = 498.GB
-  max_cpus = 20
+  max_memory = 1999.GB
+  max_cpus = 128
   max_time = 140.h
 }

From 52842de88b0d64e2bdbfdf61a833b975879c2546 Mon Sep 17 00:00:00 2001
From: mseybold <matthias.seybold@uni-tuebingen.de>
Date: Fri, 6 Mar 2020 10:46:37 +0100
Subject: [PATCH 07/22] Update cfc.config

test failed, so added the the default queue
---
 conf/cfc.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/cfc.config b/conf/cfc.config
index 99917ba..d1a109a 100644
--- a/conf/cfc.config
+++ b/conf/cfc.config
@@ -13,7 +13,7 @@ singularity {
 process {
   beforeScript = 'module load devel/singularity/3.4.2'
   executor = 'slurm'
-  queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' }
+  queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' }
 }
 
 weblog{

From 2135996b13220dc76b4fe1b1196384307796c317 Mon Sep 17 00:00:00 2001
From: mseybold <matthias.seybold@uni-tuebingen.de>
Date: Fri, 6 Mar 2020 11:12:21 +0100
Subject: [PATCH 08/22] Update cfc.md

---
 docs/cfc.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/docs/cfc.md b/docs/cfc.md
index a7f6beb..acf93dd 100644
--- a/docs/cfc.md
+++ b/docs/cfc.md
@@ -10,8 +10,11 @@ Before running the pipeline you will need to load Nextflow and Singularity using
 ## Load Nextflow and Singularity environment modules
 module purge
 module load devel/java_jdk/1.8.0u121
-module load qbic/singularity_slurm/3.0.3
+module load devel/singularity/3.4.2
 ```
 
 >NB: You will need an account to use the HPC cluster CFC 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.
+New  HighMem nodes are available on the cfc, Partition/queue name is qbic, each node has 128Cores and 2TB of RAM.
+The old queue (Name compute) is set to default by slurm.
+Each process over 60GB of RAM or over 20cpus should run on those new nodes.

From 48400b8863b11dc2e70917fa3d586e56e5e41f6f Mon Sep 17 00:00:00 2001
From: mseybold <matthias.seybold@uni-tuebingen.de>
Date: Fri, 6 Mar 2020 11:14:27 +0100
Subject: [PATCH 09/22] Update RADME.md

fixed link to cfc.md
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 0e58b09..3b360a1 100644
--- a/README.md
+++ b/README.md
@@ -100,7 +100,7 @@ Currently documentation is available for the following systems:
 * [CCGA](docs/ccga.md)
 * [CCGA_DX](docs/ccga_dx.md)
 * [CCGA_MED](docs/ccga_med.md)
-* [CFC](docs/binac.md)
+* [CFC](docs/cfc.md)
 * [CRICK](docs/crick.md)
 * [CZBIOHUB_AWS](docs/czbiohub.md)
 * [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)

From f5364e45e7c007d9da5b24dcb50c5329b53b36ae Mon Sep 17 00:00:00 2001
From: Evan Floden <evanfloden@gmail.com>
Date: Fri, 6 Mar 2020 11:27:44 +0100
Subject: [PATCH 10/22] Update google.md or markdown linting

---
 docs/google.md | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/docs/google.md b/docs/google.md
index d3a65f5..0534a0b 100644
--- a/docs/google.md
+++ b/docs/google.md
@@ -2,33 +2,36 @@
 
 To be used with the `google` profile by specifying the `-profile google` when running nf-core pipelines.
 
-
 ![Google Cloud](images/google-cloud-logo.svg "https://cloud.google.com/life-sciences/docs/tutorials/nextflow")
 
-
 ## Quick Start
-```
+
+```bash
 GOOGLE_APPLICATION_CREDENTIALS=<your_key>.json
 NXF_MODE=google
 nextflow run nf-core/rnaseq -profile google,test --google_bucket <gs://your_bucket/work>
 ```
 
 ### Required Parameters
+
 #### `--google-bucket`
+
 The Google Cloud Storage bucket location to be used as a Nextflow work directory. Can also be specified with (`-w gs://your_bucket/work`).
 
 ### Optional Parameters
+
 #### `--google-zone`
+
 The Google zone where the computation is executed in Compute Engine VMs. Multiple zones can be provided separating them by a comma. Default (`europe-west2-c`).
 
 #### `--google-preemptible`
+
 Enables the usage of preemptible virtual machines with a retry error statergy for up to 5 retries. Default (`true`).
 
 #### `--google-debug`
+
 Copies the /google debug directory from the VM to the task bucket directory. Useful for debugging. Default (`false`).
 
-
 ## Cloud Life Sciences Setup
+
 Please refer to the [Google Cloud](https://cloud.google.com/life-sciences/docs/tutorials/nextflow) and [Nextflow](https://www.nextflow.io/docs/latest/google.html#cloud-life-sciences) documentation which describe how to setup the Google Cloud environment.
-
-

From ebae81ceb3a5a9d07d72d31b33867a369944d889 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <apeltzer@users.noreply.github.com>
Date: Fri, 6 Mar 2020 17:18:03 +0100
Subject: [PATCH 11/22] Update main.yml

Drop CCGA, as it was removed in an intermediate merge.
---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 5e9676d..36f9da1 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh']
+          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

From 6141e008a3f082bb048aa5f41743bcc4bc706270 Mon Sep 17 00:00:00 2001
From: Evan Floden <evanfloden@gmail.com>
Date: Mon, 9 Mar 2020 14:44:58 +0100
Subject: [PATCH 12/22] Update google.md

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

diff --git a/docs/google.md b/docs/google.md
index 0534a0b..9e8c521 100644
--- a/docs/google.md
+++ b/docs/google.md
@@ -9,7 +9,7 @@ To be used with the `google` profile by specifying the `-profile google` when ru
 ```bash
 GOOGLE_APPLICATION_CREDENTIALS=<your_key>.json
 NXF_MODE=google
-nextflow run nf-core/rnaseq -profile google,test --google_bucket <gs://your_bucket/work>
+nextflow run nf-core/rnaseq -profile test,google --google_bucket <gs://your_bucket/work>
 ```
 
 ### Required Parameters

From de914e56eed0a86d739f3f5fe74897858252aa69 Mon Sep 17 00:00:00 2001
From: marcel-keller <61977721+marcel-keller@users.noreply.github.com>
Date: Mon, 9 Mar 2020 16:08:01 +0200
Subject: [PATCH 13/22] Create ebc.config

---
 conf/ebc.config | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 conf/ebc.config

diff --git a/conf/ebc.config b/conf/ebc.config
new file mode 100644
index 0000000..ebcb775
--- /dev/null
+++ b/conf/ebc.config
@@ -0,0 +1,26 @@
+    //Profile config names for nf-core/configs
+    params {
+      config_profile_description = 'Generic Estonian Biocentre profile provided by nf-core/configs.'
+      config_profile_contact = 'Marcel Keller (@marcel-keller)'
+      config_profile_url = 'https://genomics.ut.ee/en/about-us/estonian-biocentre'
+    }
+
+    cleanup = true
+
+    conda {
+        cacheDir = '/ebc_data/nf-core/conda'
+
+    }
+    process {
+        executor = 'slurm'
+        conda = "$baseDir/environment.yml" 
+
+    }
+    executor {
+        queueSize = 16
+    }
+    params {
+      max_memory = 12.GB
+      max_cpus = 20
+      max_time = 120.h
+    }

From b8d020b78c54b162f5178f531fcc4dad9c69f5b5 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <apeltzer@users.noreply.github.com>
Date: Mon, 9 Mar 2020 15:12:49 +0100
Subject: [PATCH 14/22] Update cfc.md

---
 docs/cfc.md | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/docs/cfc.md b/docs/cfc.md
index acf93dd..f96a47d 100644
--- a/docs/cfc.md
+++ b/docs/cfc.md
@@ -15,6 +15,5 @@ module load devel/singularity/3.4.2
 
 >NB: You will need an account to use the HPC cluster CFC 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.
-New  HighMem nodes are available on the cfc, Partition/queue name is qbic, each node has 128Cores and 2TB of RAM.
-The old queue (Name compute) is set to default by slurm.
-Each process over 60GB of RAM or over 20cpus should run on those new nodes.
+
+The queues are set to be `qbic` or `compute` and will be chosen automatically for you depending on your job submission.

From 418f4b52b66125566aff9e985bc6ef9b30229875 Mon Sep 17 00:00:00 2001
From: marcel-keller <61977721+marcel-keller@users.noreply.github.com>
Date: Mon, 9 Mar 2020 16:23:16 +0200
Subject: [PATCH 15/22] Create ebc.md

---
 docs/ebc.md | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 docs/ebc.md

diff --git a/docs/ebc.md b/docs/ebc.md
new file mode 100644
index 0000000..f997f9a
--- /dev/null
+++ b/docs/ebc.md
@@ -0,0 +1,8 @@
+# nf-core/configs: EBC Configuration
+All nf-core pipelines have been successfully configured for use on the [Estonian Biocentre (EBC)](https://genomics.ut.ee/en/about-us/estonian-biocentre) cluster at the [High Performance Computing Center](https://hpc.ut.ee/en) of the the University of Tartu.
+To use, run the pipeline with `-profile ebc`. This will download and launch the [`ebc.config`](../conf/ebc.config) which has been pre-configured with a setup suitable for the EBC cluster. Using this profile, currently, a conda environment containing all of the required software will be downloaded and stored in a central location.
+
+The profile will put a maximum job limit of 12 GB, 20 CPUs and a maximum wall time of 120 hours.
+
+NB: You will need an account to use the HPC cluster on EBC cluster in order to run the pipeline. If in doubt contact IT.
+NB: Nextflow will need to submit the jobs via the SLURM scheduler to the HPC cluster and as such the commands above will have to be executed on one of the head nodes. If in doubt contact IT.

From f48a4cbfb8f4a3ad8845d2db7bf13759bb4c5888 Mon Sep 17 00:00:00 2001
From: marcel-keller <61977721+marcel-keller@users.noreply.github.com>
Date: Mon, 9 Mar 2020 16:25:19 +0200
Subject: [PATCH 16/22] Update main.yml

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

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 36f9da1..042dd26 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh']
+          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

From 88cfe1118738067c8d47ecb567e5d4e0b0184cc1 Mon Sep 17 00:00:00 2001
From: marcel-keller <61977721+marcel-keller@users.noreply.github.com>
Date: Mon, 9 Mar 2020 16:32:14 +0200
Subject: [PATCH 17/22] Update ebc.md

---
 docs/ebc.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/ebc.md b/docs/ebc.md
index f997f9a..45c9415 100644
--- a/docs/ebc.md
+++ b/docs/ebc.md
@@ -1,4 +1,5 @@
 # nf-core/configs: EBC Configuration
+
 All nf-core pipelines have been successfully configured for use on the [Estonian Biocentre (EBC)](https://genomics.ut.ee/en/about-us/estonian-biocentre) cluster at the [High Performance Computing Center](https://hpc.ut.ee/en) of the the University of Tartu.
 To use, run the pipeline with `-profile ebc`. This will download and launch the [`ebc.config`](../conf/ebc.config) which has been pre-configured with a setup suitable for the EBC cluster. Using this profile, currently, a conda environment containing all of the required software will be downloaded and stored in a central location.
 

From edc6a6aa87946ba943141298a7b262eb74aed754 Mon Sep 17 00:00:00 2001
From: marcel-keller <61977721+marcel-keller@users.noreply.github.com>
Date: Mon, 9 Mar 2020 16:35:45 +0200
Subject: [PATCH 18/22] Update nfcore_custom.config

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

diff --git a/nfcore_custom.config b/nfcore_custom.config
index d7f3ca4..848db80 100644
--- a/nfcore_custom.config
+++ b/nfcore_custom.config
@@ -22,6 +22,7 @@ profiles {
   czbiohub_aws_highpriority {
                  includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config";
                  includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config"}
+  ebc          { includeConfig "${params.custom_config_base}/conf/ebc.config" }
   genotoul     { includeConfig "${params.custom_config_base}/conf/genotoul.config" }
   google       { includeConfig "${params.custom_config_base}/conf/google.config" }
   denbi_qbic   { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" }

From 3b575195009b748cf632b4cd5294d32e3edc031a Mon Sep 17 00:00:00 2001
From: marcel-keller <61977721+marcel-keller@users.noreply.github.com>
Date: Mon, 9 Mar 2020 16:48:50 +0200
Subject: [PATCH 19/22] Update ebc.config

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

diff --git a/conf/ebc.config b/conf/ebc.config
index ebcb775..4b1332d 100644
--- a/conf/ebc.config
+++ b/conf/ebc.config
@@ -14,7 +14,7 @@
     process {
         executor = 'slurm'
         conda = "$baseDir/environment.yml" 
-
+        beforeScript = 'module load nextflow'
     }
     executor {
         queueSize = 16

From c00bbe982b7250898c9310e8bb9fbb6e774f1e13 Mon Sep 17 00:00:00 2001
From: marcel-keller <61977721+marcel-keller@users.noreply.github.com>
Date: Mon, 9 Mar 2020 16:51:38 +0200
Subject: [PATCH 20/22] Update ebc.config

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

diff --git a/conf/ebc.config b/conf/ebc.config
index 4b1332d..ea48f05 100644
--- a/conf/ebc.config
+++ b/conf/ebc.config
@@ -9,12 +9,12 @@
 
     conda {
         cacheDir = '/ebc_data/nf-core/conda'
-
     }
     process {
         executor = 'slurm'
         conda = "$baseDir/environment.yml" 
         beforeScript = 'module load nextflow'
+        queue = { task.time <= 24.h ? 'testing' : 'main' }
     }
     executor {
         queueSize = 16

From 8e3803e4d7dc8b95f15a084f4e9790bd8731fe5b Mon Sep 17 00:00:00 2001
From: marcel-keller <61977721+marcel-keller@users.noreply.github.com>
Date: Mon, 9 Mar 2020 16:57:45 +0200
Subject: [PATCH 21/22] Update ebc.config

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

diff --git a/conf/ebc.config b/conf/ebc.config
index ea48f05..4df0596 100644
--- a/conf/ebc.config
+++ b/conf/ebc.config
@@ -14,7 +14,6 @@
         executor = 'slurm'
         conda = "$baseDir/environment.yml" 
         beforeScript = 'module load nextflow'
-        queue = { task.time <= 24.h ? 'testing' : 'main' }
     }
     executor {
         queueSize = 16

From dcb478c904d35b3b49db20abc4a2ecdf990e3dc1 Mon Sep 17 00:00:00 2001
From: marcel-keller <61977721+marcel-keller@users.noreply.github.com>
Date: Mon, 9 Mar 2020 17:07:03 +0200
Subject: [PATCH 22/22] Update ebc.md

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

diff --git a/docs/ebc.md b/docs/ebc.md
index 45c9415..71f2622 100644
--- a/docs/ebc.md
+++ b/docs/ebc.md
@@ -3,6 +3,8 @@
 All nf-core pipelines have been successfully configured for use on the [Estonian Biocentre (EBC)](https://genomics.ut.ee/en/about-us/estonian-biocentre) cluster at the [High Performance Computing Center](https://hpc.ut.ee/en) of the the University of Tartu.
 To use, run the pipeline with `-profile ebc`. This will download and launch the [`ebc.config`](../conf/ebc.config) which has been pre-configured with a setup suitable for the EBC cluster. Using this profile, currently, a conda environment containing all of the required software will be downloaded and stored in a central location.
 
+> :warning: You must install your own [conda binary](conda.io) to run nf-core pipelines in a conda environment. Running with singularity will be added soon.
+
 The profile will put a maximum job limit of 12 GB, 20 CPUs and a maximum wall time of 120 hours.
 
 NB: You will need an account to use the HPC cluster on EBC cluster in order to run the pipeline. If in doubt contact IT.