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Commit 1520393d authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
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fix some issues

parent 1b971378
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......@@ -215,7 +215,7 @@ if config["star_mapping"]["do"]:
star_mapping_pass2_index = os.path.join(config["genome"]["genome_directory"],"{REF}/SAindex")
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}_init_SJ.out.tab"
star_mapping_pass2_junctions = "02-Mapping/STAR/{REF}/{SAMPLE}_{REF}_SJ.out.tab"
star_mapping_pass2_read_groups = ""
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))
......
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