From 3b593d46ecd6390fa9e484dcaa3cb9eda6d1d6d7 Mon Sep 17 00:00:00 2001
From: pierrespc <pierrespc@gmail.com>
Date: Mon, 20 Sep 2021 15:14:50 +0200
Subject: [PATCH] merged two pasteur config files for maestro

---
 .github/workflows/main.yml       |  3 +--
 README.md                        |  3 +--
 conf/maestro.config              | 26 ++++++++++++++++++++++++++
 conf/pasteurMaestroLong.config   | 26 --------------------------
 conf/pasteurMaestroNormal.config | 26 --------------------------
 docs/maestro.md                  | 10 ++++++++++
 docs/pasteurMaestroLong.md       |  8 --------
 docs/pasteurMaestroNormal.md     |  8 --------
 8 files changed, 38 insertions(+), 72 deletions(-)
 create mode 100644 conf/maestro.config
 delete mode 100644 conf/pasteurMaestroLong.config
 delete mode 100644 conf/pasteurMaestroNormal.config
 create mode 100644 docs/maestro.md
 delete mode 100644 docs/pasteurMaestroLong.md
 delete mode 100644 docs/pasteurMaestroNormal.md

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index b983f44..a8b6b91 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -47,13 +47,12 @@ jobs:
             - 'imperial_mb'
             - 'jax'
             - 'lugh'
+            - 'maestro'
             - 'mpcdf'
             - 'munin'
             - 'nu_genomics'
             - 'oist'
             - 'pasteur'
-            - 'pasteurNorm'
-            - 'pasteurLong'
             - 'phoenix'
             - 'prince'
             - 'sanger'
diff --git a/README.md b/README.md
index 2452442..e629e4a 100644
--- a/README.md
+++ b/README.md
@@ -116,13 +116,12 @@ Currently documentation is available for the following systems:
 * [ICR_DAVROS](docs/icr_davros.md)
 * [JAX](docs/jax.md)
 * [LUGH](docs/lugh.md)
+* [MAESTRO](docs/maestro.md)
 * [MPCDF](docs/mpcdf.md)
 * [MUNIN](docs/munin.md)
 * [NU_GENOMICS](docs/nu_genomics.md)
 * [OIST](docs/oist.md)
 * [PASTEUR](docs/pasteur.md)
-* [PASTEURNORM](docs/pasteurMaestroNormal.md)
-* [PASTEURLONG](docs/pasteurMaestroLong.md)
 * [PHOENIX](docs/phoenix.md)
 * [PRINCE](docs/prince.md)
 * [SANGER](docs/sanger.md)
diff --git a/conf/maestro.config b/conf/maestro.config
new file mode 100644
index 0000000..42ba030
--- /dev/null
+++ b/conf/maestro.config
@@ -0,0 +1,26 @@
+params {
+  config_profile_description = 'Institut Pasteur Maestro cluster profile'
+  config_profile_url = 'https://confluence.pasteur.fr/spaces/viewspace.action?key=FAQA'
+  config_profile_contact = 'Pierre Luisi (@pierrespc)'
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+  runOptions = '--home $HOME:/home/$USER --bind /pasteur'
+}
+
+process {
+  executor = 'slurm'
+  scratch = false
+  queue = 'common'
+  clusterOptions = {task.time < 24.h ? '--qos=normal' : '--qos=long'}
+}
+
+params {
+  igenomes_ignore = true
+  igenomesIgnore = true
+  max_memory = {task.time < 24.h ? 400.GB : 100.GB }
+  max_cpus = {task.time < 24.h ? 96 : 5 }
+  max_time = {task.time < 24.h ? 24.h : 8760.h }
+}
diff --git a/conf/pasteurMaestroLong.config b/conf/pasteurMaestroLong.config
deleted file mode 100644
index f2b8841..0000000
--- a/conf/pasteurMaestroLong.config
+++ /dev/null
@@ -1,26 +0,0 @@
-params {
-  config_profile_description = 'Institut Pasteur Maestro cluster profile'
-  config_profile_contact = 'Pierre Luisi (@pierrespc)'
-}
-
-singularity {
-  enabled = true
-  autoMounts = true
-  runOptions =  '--home $HOME:/home/$USER --bind /pasteur'
-}
-
-process {
-  executor = 'slurm'
-  scratch=false
-  queue = "common"
-  clusterOptions = "--qos=long"
-  
-}
-
-params {
-  igenomes_ignore = true
-  igenomesIgnore = true
-  max_memory = 100.GB
-  max_cpus = 5
-  max_time = 8760.h
-}
diff --git a/conf/pasteurMaestroNormal.config b/conf/pasteurMaestroNormal.config
deleted file mode 100644
index 049acd0..0000000
--- a/conf/pasteurMaestroNormal.config
+++ /dev/null
@@ -1,26 +0,0 @@
-params {
-  config_profile_description = 'Institut Pasteur Maestro cluster profile'
-  config_profile_contact = 'Pierre Luisi (@pierrespc)'
-}
-
-singularity {
-  enabled = true
-  autoMounts = true
-  runOptions =  '--home $HOME:/home/$USER --bind /pasteur'
-}
-
-process {
-  executor = 'slurm'
-  scratch=false
-  queue = "common"
-  clusterOptions = "--qos=normal"
-  
-}
-
-params {
-  igenomes_ignore = true
-  igenomesIgnore = true
-  max_memory = 400.GB
-  max_cpus = 96
-  max_time = 24.h
-}
diff --git a/docs/maestro.md b/docs/maestro.md
new file mode 100644
index 0000000..c931a05
--- /dev/null
+++ b/docs/maestro.md
@@ -0,0 +1,10 @@
+# nf-core/configs: Institut Pasteur Configuration on Maestro.
+
+If you are using TARS cluster, please refer to pasteur profile.
+
+This is an intent for configuration of nf-core in Maestro cluster on the normal or long qos depending on the ressources required
+
+I am not expert of nf-core so pelase refer to  docs/pasteur.md for installing and running nf-core 
+
+Run the pipeline with `-profile pasteur_maestro`
+
diff --git a/docs/pasteurMaestroLong.md b/docs/pasteurMaestroLong.md
deleted file mode 100644
index 22b1bce..0000000
--- a/docs/pasteurMaestroLong.md
+++ /dev/null
@@ -1,8 +0,0 @@
-# nf-core/configs: Institut Pasteur Configuration on Maestro
-
-This is an intent for configuration of nf-core in Maestro cluster on the long qos
-
-I am not expert of nf-core so pelase refer to  docs/pasteur.md for installing and running nf-core 
-
-Run the pipeline with `-profile pasteurLong`
-
diff --git a/docs/pasteurMaestroNormal.md b/docs/pasteurMaestroNormal.md
deleted file mode 100644
index 91d2f45..0000000
--- a/docs/pasteurMaestroNormal.md
+++ /dev/null
@@ -1,8 +0,0 @@
-# nf-core/configs: Institut Pasteur Configuration on Maestro
-
-This is an intent for configuration of nf-core in Maestro cluster on the normal qos
-
-I am not expert of nf-core so pelase refer to  docs/pasteur.md for installing and running nf-core 
-
-Run the pipeline with `-profile pasteurNorm`
-