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Commit 65593f21 authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
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fix some issues with star

parent 1520393d
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......@@ -196,13 +196,13 @@ if config["star_mapping"]["do"]:
star_index_log = "02-Mapping/STAR/logs/STAR_{REF}_indexing.log"
include: os.path.join(RULES, "star_index.rules")
#else:
# star_index_output_dir = os.path.join(config["genome"]["genome_directory"],"{REF}")
# star_index_output_done = os.path.join(config["genome"]["genome_directory"],"{REF}/SAindex" )
else:
star_index_output_dir = os.path.join(config["genome"]["genome_directory"],"{REF}")
star_index_output_done = os.path.join(config["genome"]["genome_directory"],"{REF}/SAindex" )
#first pass mapping
star_mapping_pass1_input = adapters_output
star_mapping_pass1_index = star_index_output_done
star_mapping_pass1_index = star_index_output_dir
star_mapping_pass1_logs = "02-Mapping/STAR/logs/{SAMPLE}_{REF}_init.out"
star_mapping_pass1_output_prefix = "02-Mapping/STAR/{REF}/{SAMPLE}_{REF}_init_"
star_mapping_pass1_junctions = "02-Mapping/STAR/{REF}/{SAMPLE}_{REF}_SJ.out.tab"
......@@ -212,7 +212,7 @@ if config["star_mapping"]["do"]:
#Second pass mapping
star_mapping_pass2_input = adapters_output
star_mapping_pass2_index = os.path.join(config["genome"]["genome_directory"],"{REF}/SAindex")
star_mapping_pass2_index = star_index_output_dir
star_mapping_pass2_logs = "02-Mapping/STAR/logs/{SAMPLE}_{REF}.out"
star_mapping_pass2_output_prefix = "02-Mapping/STAR/{REF}/{SAMPLE}_{REF}"
star_mapping_pass2_junctions = "02-Mapping/STAR/{REF}/{SAMPLE}_{REF}_SJ.out.tab"
......
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