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Commit b78264f2 authored by christine.tranchant_ird.fr's avatar christine.tranchant_ird.fr
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modify cpu number by default

parent 267daf0a
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frangiPANe/snakefiles/bwa_mem.smk
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View file @ b78264f2
...@@ -14,7 +14,7 @@ rule bwa_mem: ...@@ -14,7 +14,7 @@ rule bwa_mem:
rg = f"@RG\\tID:{{sample_name}}\\tSM:{{sample_name}}\\tPL:Illumina", rg = f"@RG\\tID:{{sample_name}}\\tSM:{{sample_name}}\\tPL:Illumina",
other_options_bwaMem = frangipane_obj.get_config_value("PARAMS","bwa_mem"), other_options_bwaMem = frangipane_obj.get_config_value("PARAMS","bwa_mem"),
other_options_samtoolsSort = frangipane_obj.get_config_value("PARAMS","samtools_sort") other_options_samtoolsSort = frangipane_obj.get_config_value("PARAMS","samtools_sort")
threads: get_threads('bwa_mem', 1) threads: get_threads('bwa_mem', 2)
message: message:
f"""-------------------- f"""--------------------
-Running {{rule}} -Running {{rule}}
......
frangiPANe/snakefiles/samtools_view.smk
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View file @ b78264f2
...@@ -10,7 +10,7 @@ rule samtools_view: ...@@ -10,7 +10,7 @@ rule samtools_view:
output = f"{frangipane_obj.path_logs}/samtools_view/{{sample_name}}-{{ref_name}}.o" output = f"{frangipane_obj.path_logs}/samtools_view/{{sample_name}}-{{ref_name}}.o"
params: params:
other_options = frangipane_obj.get_config_value("PARAMS","samtools_view"), other_options = frangipane_obj.get_config_value("PARAMS","samtools_view"),
threads: get_threads('samtools_view', 1) threads: get_threads('samtools_view', 2)
message: message:
f"""-------------------- f"""--------------------
-Running {{rule}} -Running {{rule}}
......
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