Commit aaf097a4 authored by Blaise Li's avatar Blaise Li
Browse files

Using more processors to map and index.

Hopefully this will be more efficient on pisa.
parent 2c544b0a
......@@ -233,7 +233,7 @@ rule trim_and_dedup:
process_type = "iCLIP",
trim5 = 8,
trim3 = 4,
threads: 4 # Actually, to avoid too much IO
threads: 8 # Actually, to avoid too much IO
message:
"Trimming adaptor from raw data using {wildcards.trimmer}, deduplicating reads, and removing 5' and 3' random n-mers for {wildcards.lib}_{wildcards.rep}."
benchmark:
......@@ -470,7 +470,7 @@ rule sam2indexedbam:
log = OPJ(log_dir, "{trimmer}", "sam2indexedbam", "{lib}_{rep}_{read_type}.log"),
err = OPJ(log_dir, "{trimmer}", "sam2indexedbam", "{lib}_{rep}_{read_type}.err"),
threads:
4
8
resources:
mem_mb=4100
wrapper:
......
......@@ -168,7 +168,7 @@ rule map_on_genome:
resources:
io=5
threads:
4
8
wrapper:
f"file://{wrappers_dir}/map_on_genome"
......
......@@ -392,7 +392,7 @@ rule trim_and_dedup:
process_type = "PRO-seq",
trim5 = lambda wildcards : lib2UMI[wildcards.lib][0],
trim3 = lambda wildcards : lib2UMI[wildcards.lib][1],
threads: 4 # Actually, to avoid too much IO
threads: 8 # Actually, to avoid too much IO
message:
"Trimming adaptor from raw data using {wildcards.trimmer}, deduplicating reads, and removing 5' and 3' random n-mers for {wildcards.lib}_{wildcards.rep}."
benchmark:
......@@ -429,7 +429,7 @@ rule trim_only:
process_type = "PRO-seq",
trim5 = lambda wildcards : lib2UMI[wildcards.lib][0],
trim3 = lambda wildcards : lib2UMI[wildcards.lib][1],
threads: 4 # Actually, to avoid too much IO
threads: 8 # Actually, to avoid too much IO
message:
"Trimming adaptor from raw data using {wildcards.trimmer} and removing 5' and 3' random n-mers for {wildcards.lib}_{wildcards.rep}."
benchmark:
......@@ -481,6 +481,8 @@ rule map_on_genome:
log:
log = OPJ(log_dir, "{trimmer}", "map_{type}_on_genome", "{lib}_{rep}.log"),
err = OPJ(log_dir, "{trimmer}", "map_{type}_on_genome", "{lib}_{rep}.err"),
threads:
8
# shell:
# """
# genome_dir="${{HOME}}/Genomes"
......@@ -506,7 +508,7 @@ rule sam2indexedbam:
log = OPJ(log_dir, "{trimmer}", "sam2indexedbam", "{lib}_{rep}_{type}.log"),
err = OPJ(log_dir, "{trimmer}", "sam2indexedbam", "{lib}_{rep}_{type}.err"),
threads:
4
8
resources:
mem_mb=4100
wrapper:
......
......@@ -567,7 +567,7 @@ rule map_on_genome:
resources:
io=5
threads:
4
8
#shell:
# mapping_command(aligner)
wrapper:
......@@ -620,7 +620,7 @@ rule remap_on_genome:
resources:
io=5
threads:
4
8
#shell:
# mapping_command(aligner)
wrapper:
......
......@@ -755,7 +755,7 @@ rule map_on_genome:
log = OPJ(log_dir, "map_on_genome", "{lib}_{rep}_{read_type}.log"),
err = OPJ(log_dir, "map_on_genome", "{lib}_{rep}_{read_type}.err")
threads:
4
8
wrapper:
f"file://{wrappers_dir}/map_on_genome"
......@@ -787,7 +787,7 @@ rule sam2indexedbam:
log = OPJ(log_dir, "sam2indexedbam", "{lib}_{rep}_{read_type}.log"),
err = OPJ(log_dir, "sam2indexedbam", "{lib}_{rep}_{read_type}.err"),
threads:
4
8
resources:
mem_mb=4100
wrapper:
......
......@@ -1014,7 +1014,7 @@ rule map_on_genome:
log = OPJ(log_dir, "map_on_genome", "{lib}_{rep}_%s.log" % size_selected),
err = OPJ(log_dir, "map_on_genome", "{lib}_{rep}_%s.err" % size_selected)
threads:
4
8
resources:
mem_mb=700
wrapper:
......@@ -1067,7 +1067,7 @@ rule remap_on_genome:
log = OPJ(log_dir, "remap_on_genome", "{lib}_{rep}_{read_type}.log"),
err = OPJ(log_dir, "remap_on_genome", "{lib}_{rep}_{read_type}.err")
threads:
4
8
resources:
mem_mb=700
wrapper:
......@@ -1102,7 +1102,7 @@ rule sam2indexedbam:
log = OPJ(log_dir, "sam2indexedbam", "{lib}_{rep}_{read_type}.log"),
err = OPJ(log_dir, "sam2indexedbam", "{lib}_{rep}_{read_type}.err"),
threads:
4
8
resources:
mem_mb=4100
wrapper:
......
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