Update snakefile (2c0b8f98) · Commits · Weipeng Mo / FLEP_seq_pipeline

config.yml

0 → 100644

+5 −0

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		sample_name: 20210728_atx1_seedling_part
		genome: /scem/work/mowp/db/Arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa
		mm2thread: 36
		fast5_dir: guppy_out/workspace
		sequencing_summary: sequencing_summary.txt

+5 −4

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		'''
		@Author : windz
		@Date : 2020-05-08 09:51:48
		Author : windz
		Date : 2020-05-08 09:51:48
		LastEditTime : 2020-12-07 09:51:37
		@Description : A pipline for calling polya tail length
		Description : A pipline for calling polya tail length

		You can run like this:
		snakemake -j 8 -p -c 'bsub -J {rulename} -n {threads} -o log/%J.stdout -e log/%J.stderr'
		@@ -16,6 +16,7 @@ if not os.path.exists('log'):

		configfile: 'config.yml'
		SAMPLE_NAME=config['sample_name']
		genome_data=config['genome']


		rule all:
		@@ -43,7 +44,7 @@ rule mapping_to_genome:
		output:
		bam='aligned_data/{sample_name}.sorted.bam'
		params:
		genome='/scem/work/mowp/db/Arabidopsis_thaliana/dna/genome.fasta'
		genome=genome_data
		threads: 32
		shell:
		'''