Commit 4fefc9e3 authored by peguerin's avatar peguerin
Browse files

debug rules

parent 85b68b5a
......@@ -3,15 +3,15 @@ rule assign_sequences:
input:
'01-assembly/{run}/{run}.ali.fastq',
output:
assign='01-assembly/{run}/{run}.ali.assigned.fastq',
unid='01-assembly/{run}/{run}.unidentified.fastq'
assign='03-assign_sequences/{run}.ali.assigned.fastq',
unid='03-assign_sequences/{run}.unidentified.fastq'
singularity:
config["container"]
params:
barcodeFile=lambda wcs: config["barcodeFiles"][wcs.run],
barcodeFolder=config['fastqFolderPath']
log:
'99-log/assign_sequences/{run}.log'
'../99-log/01-assembly/03-assign_sequences/{run}.log'
shell:
'''ngsfilter -t {params.barcodeFolder}{params.barcodeFile} -u {output.unid} {input} --fasta-output > {output.assign} 2> {log}'''
......@@ -19,12 +19,12 @@ rule assign_sequences:
### Split the input sequence file in a set of subfiles according to the values of attribute `sample`
rule split_sequences:
input:
'01-assembly/{run}/{run}.ali.assigned.fastq'
'03-assign_sequences/{run}.ali.assigned.fastq'
params:
'02-demultiplex/02-01-raw/{run}_sample_'
'02-demultiplex/01-raw/{run}_sample_'
singularity:
config["container"]
log:
'99-log/split_sequences/{run}.log'
'../99-log/01-assembly/04-split_sequences/{run}.log'
shell:
'''obisplit -p "{params}" -t sample --fasta {input} 2> {log}'''
......@@ -14,7 +14,7 @@ rule all:
expand('../99-log/01-assembly/02-remove_unaligned/{run}.log',run=config["fastqFiles"]),
expand('../99-log/01-assembly/01-illuminapairedend/{run}.log',run=config["fastqFiles"]),
expand('../99-log/01-assembly/03-assign_sequences/{run}.log',run=config["fastqFiles"]),
expand('../99-log/01-assembly/04-split_sequences/{run}.log',run=config["fastqFiles"]),
expand('../99-log/01-assembly/04-split_sequences/{run}.log',run=config["fastqFiles"])
include: "../00-rules/assembly.smk"
include: "../00-rules/demultiplex.smk"
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