diff --git a/Snakemake/1000RNASeq_chicken/ASE/rules/ASE_counter.smk b/Snakemake/1000RNASeq_chicken/ASE/rules/ASE_counter.smk index b239bb5d5621578990ca78f0c0a6a3d0552bfb6d..fc7ac09788aa96f50eec7fce8398cd8359541cfc 100644 --- a/Snakemake/1000RNASeq_chicken/ASE/rules/ASE_counter.smk +++ b/Snakemake/1000RNASeq_chicken/ASE/rules/ASE_counter.smk @@ -55,5 +55,5 @@ rule phASER: paired_option = lambda wildcards : '1' if len(table[table['sample_name'] == wildcards.sample]['forward_read']) == len(table[table['sample_name'] == wildcards.sample]['reverse_read'].dropna()) else '0' shell: """ - python2.7 phaser.py --vcf {input.vcf} --bam {input.bam} --sample {wildcards.sample} --threads {threads} --o 'Results/Counter/{wildcards.sample}_phASER --paired_end {params.paired_option} --baseq {params.baseQuality} --mapq {params.mappingQuality} + python2.7 phaser.py --vcf {input.vcf} --bam {input.bam} --sample {wildcards.sample} --threads {threads} --o Results/Counter/{wildcards.sample}_phASER --paired_end {params.paired_option} --baseq {params.baseQuality} --mapq {params.mappingQuality} """