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" -- GitLab