From b295508037b9a40be1d917f1e503557186dcc93c Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Mon, 14 Oct 2019 12:00:53 +0200
Subject: [PATCH] Added ressource used by snakemake wrapper.

---
 CLIP/iCLIP.snakefile                  | 2 ++
 Degradome-seq/Degradome-seq.snakefile | 4 +++-
 PRO-seq/PRO-seq.snakefile             | 2 ++
 RNA_Seq_Cecere/RNA-seq.snakefile      | 1 +
 Ribo-seq/Ribo-seq.snakefile           | 2 ++
 5 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/CLIP/iCLIP.snakefile b/CLIP/iCLIP.snakefile
index e05d71b..3850f3e 100644
--- a/CLIP/iCLIP.snakefile
+++ b/CLIP/iCLIP.snakefile
@@ -469,6 +469,8 @@ rule sam2indexedbam:
         err = OPJ(log_dir, "{trimmer}", "sam2indexedbam", "{lib}_{rep}_{read_type}.err"),
     threads:
         4
+    resources:
+        mem_mb=4100
     wrapper:
         "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/sam2indexedbam"
 
diff --git a/Degradome-seq/Degradome-seq.snakefile b/Degradome-seq/Degradome-seq.snakefile
index ef159b9..d16a60e 100644
--- a/Degradome-seq/Degradome-seq.snakefile
+++ b/Degradome-seq/Degradome-seq.snakefile
@@ -144,7 +144,7 @@ rule trim_reads:
         trim3 = 4,
     shell:
         """
-        seqtk trimfq -b {params.trim3} {input.raw} | gzip > {output.trimmed} 
+        seqtk trimfq -b {params.trim3} {input.raw} | gzip > {output.trimmed}
         """
 
 
@@ -185,6 +185,8 @@ rule sam2indexedbam:
         err = OPJ(log_dir, "sam2indexedbam_{lib}_{rep}.err"),
     threads:
         8
+    resources:
+        mem_mb=4100
     wrapper:
         "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/sam2indexedbam"
 
diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile
index 0f3ffef..02c8c78 100644
--- a/PRO-seq/PRO-seq.snakefile
+++ b/PRO-seq/PRO-seq.snakefile
@@ -506,6 +506,8 @@ rule sam2indexedbam:
         err = OPJ(log_dir, "{trimmer}", "sam2indexedbam", "{lib}_{rep}_{type}.err"),
     threads:
         4
+    resources:
+        mem_mb=4100
     wrapper:
         "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/sam2indexedbam"
 
diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile
index f767ca2..9f32a1f 100644
--- a/RNA_Seq_Cecere/RNA-seq.snakefile
+++ b/RNA_Seq_Cecere/RNA-seq.snakefile
@@ -653,6 +653,7 @@ rule sam2indexedbam:
         log = OPJ(log_dir, "sam2indexedbam_{lib}_{rep}_{mapped_type}.log"),
         err = OPJ(log_dir, "sam2indexedbam_{lib}_{rep}_{mapped_type}.err"),
     resources:
+        mem_mb=4100,
         io=45
     threads:
         8
diff --git a/Ribo-seq/Ribo-seq.snakefile b/Ribo-seq/Ribo-seq.snakefile
index f9391b5..479db04 100644
--- a/Ribo-seq/Ribo-seq.snakefile
+++ b/Ribo-seq/Ribo-seq.snakefile
@@ -782,6 +782,8 @@ rule sam2indexedbam:
         err = OPJ(log_dir, "sam2indexedbam", "{lib}_{rep}_{read_type}.err"),
     threads:
         4
+    resources:
+        mem_mb=4100
     wrapper:
         "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/sam2indexedbam"
 
-- 
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