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Commit 9b443175 authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
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add RG

parent 65593f21
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......@@ -205,7 +205,7 @@ if config["star_mapping"]["do"]:
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"
star_mapping_pass1_junctions = "02-Mapping/STAR/{REF}/{SAMPLE}_{REF}_init_SJ.out.tab"
star_mapping_pass1_read_groups = ""
final_output.extend(expand(star_mapping_pass1_junctions, SAMPLE=samples, REF=ref))
include: os.path.join(RULES, "star_mapping_pass1.rules")
......@@ -215,8 +215,8 @@ if config["star_mapping"]["do"]:
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"
star_mapping_pass2_read_groups = ""
star_mapping_pass2_junctions = "02-Mapping/STAR/{REF}/{SAMPLE}_{REF}_init_SJ.out.tab"
star_mapping_pass2_read_groups = "ID:{sample}"
star_mapping_pass2_sort = "02-Mapping/STAR/{REF}/{SAMPLE}_{REF}_Aligned.sortedByCoord.out.bam"
final_output.extend(expand(star_mapping_pass2_sort, SAMPLE=samples, REF=ref))
include: os.path.join(RULES, "star_mapping_pass2.rules")
......
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