Commit b550ff89 authored by peguerin's avatar peguerin

format snakemake

parent 1a62992f
......@@ -6,7 +6,7 @@ configfile: "config.yaml"
rule all:
input:
expand("{folder}{run}_R1.fastq.gz", run=config["fastqFiles"],folder=config["fastqFolderPath"]),
expand("{folder}{run}_R1.fastq.gz", run=config["fastqFiles"],folder=config["fastqFolderPath"]),
expand('assembled/{run}/{run}.fastq', run=config["fastqFiles"]),
expand('assembled/{run}/{run}.ali.fastq', run=config["fastqFiles"]),
expand('assembled/{run}/{run}.ali.assigned.fastq', run=config["fastqFiles"]),
......
......@@ -35,18 +35,17 @@ rule remove_unaligned:
rule assign_sequences:
input:
'assembled/{run}/{run}.ali.fastq',
lambda wildcards: config["barcodeFiles"][wildcards.run]
output:
assign='assembled/{run}/{run}.ali.assigned.fastq',
unid='assembled/{run}/{run}.unidentified.fastq'
singularity:
config["container"]
params:
barcodeFile=lambda wcs: config["barcodeFiles"][wcs.run]
log:
'log/assign_sequences/{run}.log'
params:
folderBarcodes=config['fastqFolderPath']
shell:
'''ngsfilter -t {params.folderBarcodes}{input[1]} -u {output.unid} {input[0]} --fasta-output > {output.assign} 2> {log}'''
'''ngsfilter -t {params.barcodeFile} -u {output.unid} {input[0]} --fasta-output > {output.assign} 2> {log}'''
### Split the input sequence file in a set of subfiles according to the values of attribute `sample`
rule split_sequences:
......
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