diff --git a/CLIP/iCLIP.snakefile b/CLIP/iCLIP.snakefile index e05d71b33d24086e79043419772784aeaf77a25b..3850f3ea54a032e0bea13dff4428e40484ff4a72 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 ef159b9a71528445b054d5933e4e23f774fc9c90..d16a60ebc46d34f93552e0a9ac5fd192f8771b51 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 0f3ffef1e86e02933c818ca8b05e13988582d285..02c8c784c0e940bf13e70c518f5012e999cb4bbc 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 f767ca2c3f0f1d3b917085f09c7a807397864db8..9f32a1f9f7e53cd6d2d8426d96c56b7e04de4d0b 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 f9391b595ba202d88373dc1fb3b46e432570b4ab..479db0451c1d993732aadb9bed9956c2b68ca019 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"