From 1e4f4848567ae80c6c91e9b1777e443301ba20e5 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 16 Apr 2019 11:29:07 +0200
Subject: [PATCH] deeptools: add in2p3 config
---
src/nf_modules/deeptools/bam_to_bigwig.config | 28 +++++++++++++++++++
.../deeptools/compute_matrix.config | 15 ++++++++++
src/nf_modules/deeptools/plot_profile.config | 15 ++++++++++
3 files changed, 58 insertions(+)
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 452ca1c3..75f8575f 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -52,4 +52,32 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: index_bam {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sambamba/0.6.7/:/usr/bin:$PATH"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ memory = "10GB"
+ time = "24h"
+ }
+ }
+ process{
+ withName: bam_to_bigwig {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/deeptools/3.0.2/:/usr/bin:$PATH"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ memory = "10GB"
+ time = "24h"
+ }
+ }
+ }
}
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index 73309d65..f20b5a82 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -33,4 +33,19 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: compute_matrix {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/deeptools/3.0.2/:/usr/bin:$PATH"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ memory = "10GB"
+ time = "24h"
+ }
+ }
+ }
}
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index 9f3ce971..d31d37ab 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -33,4 +33,19 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: plot_profile {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/deeptools/3.0.2/:/usr/bin:$PATH"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ memory = "10GB"
+ time = "24h"
+ }
+ }
+ }
}
--
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