Commit b2955080 authored by Blaise Li's avatar Blaise Li
Browse files

Added ressource used by snakemake wrapper.

parent cddd59c3
......@@ -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"
......
......@@ -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"
......
......@@ -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"
......
......@@ -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
......
......@@ -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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