Commit b550ff89 authored by peguerin's avatar peguerin
Browse files

format snakemake

parent 1a62992f

rules/step1.smk

+3 −4
Original line number Diff line number Diff line
@@ -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:

Snakefile

+1 −1

File changed.

Contains only whitespace changes.