update snakemake pipeline (4c8bd083) · Commits · Weipeng Mo / FLEP-seq

config.yml

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		# genome
		genome: /scem/work/mowp/db/Arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa
		genome: /data/Zhaijx/mowp/db/Arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa

		# mapping
		mm2thread: 36

		# sample
		sample: flep_seq_demo

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		@@ -102,7 +102,7 @@ rule merge_info:
		'Nanopore'
		shell:
		'''
		export PATH=/scem/work/mowp/anaconda3/envs/R/bin/:$PATH
		export PATH=/public/home/mowp/anaconda3/envs/R/bin:$PATH
		Rscript script/merge_read_info.R --type {params} --inreadinfo {input.read_info} --inadapter {input.adapter} --inpolya {input.polya} --out {output.read_info_result}
		'''

		@@ -121,7 +121,7 @@ rule splicing_kinetics:
		shell:
		'''
		python script/prepare_data_for_splice_kinetics.py --inreadinfo {input.read_info} --inbed {params.inbed} --out {output.splicing_data}
		export PATH=/scem/work/mowp/anaconda3/envs/R/bin/:$PATH
		export PATH=/public/home/mowp/anaconda3/envs/R/bin:$PATH
		Rscript script/plot_intron_splicing_kinetics.R --inrelpos {output.splicing_data} --inreadinfo {input.read_info} --inintron {params.select_intron} --out {output.splicing_kinetics} --pdf {output.figure}
		'''

		@@ -137,7 +137,7 @@ rule intron_retention_ratio:
		threads: 1
		shell:
		'''
		export PATH=/scem/work/mowp/anaconda3/envs/R/bin/:$PATH
		export PATH=/public/home/mowp/anaconda3/envs/R/bin:$PATH
		Rscript script/cal_polya_transcript_ir.R --inrelpos {input.splicing_data} --inreadinfo {input.read_info} --outrna {output.rna_ir} --outintron {output.intron_ir}
		'''