Commit 3d61dfba authored by Jan Hoeckesfeld's avatar Jan Hoeckesfeld
Browse files

indent fix

parent c7246bda
rule
spades:
input:
read1 = 'data/auxiliary/' + config['input_folder'] + '/{id}' + '.qc' + config['input_read_1_ending'],
read2 = 'data/auxiliary/' + config['input_folder'] + '/{id}' + '.qc' + config['input_read_2_ending']
output:
directory('data/auxiliary/' + config['input_folder'] + '/{id}/spades')
singularity:
'docker://pegi3s/spades:latest'
shell:
'spades.py -1 {input.read1} -2 {input.read2} -o {output} --phred-offset 33' + (
(' --trusted-contigs ' + 'data/input/' + config['reference_genome'] + '/' + config['genome_file_identifier']) if
config['reference_guided_assembly'] else '')
rule spades:
input:
read1 = 'data/auxiliary/' + config['input_folder'] + '/{id}' + '.qc' + config['input_read_1_ending'],
read2 = 'data/auxiliary/' + config['input_folder'] + '/{id}' + '.qc' + config['input_read_2_ending']
output:
directory('data/auxiliary/' + config['input_folder'] + '/{id}/spades')
singularity:
'docker://pegi3s/spades:latest'
shell:
'spades.py -1 {input.read1} -2 {input.read2} -o {output} --phred-offset 33' + (
(' --trusted-contigs ' + 'data/input/' + config['reference_genome'] + '/' + config['genome_file_identifier']) if
config['reference_guided_assembly'] else '')
rule
exactMatch:
input:
infolder = 'data/auxiliary/' + config['input_folder'] + '/{id}/spades'
output:
'data/output/' + config['input_folder'] + '/{id}/exactMatches.tsv'
params:
spaSeqs = 'data/auxiliary/spaSequences.fa',
scaffolds = 'data/auxiliary/' + config['input_folder'] + '/{id}/spades/scaffolds.fasta'
conda:
'../envs/biopythonworkbench.yaml'
script:
'../scripts/spaSequenceSearch.py'
rule exactMatch:
input:
infolder = 'data/auxiliary/' + config['input_folder'] + '/{id}/spades'
output:
'data/output/' + config['input_folder'] + '/{id}/exactMatches.tsv'
params:
spaSeqs = 'data/auxiliary/spaSequences.fa',
scaffolds = 'data/auxiliary/' + config['input_folder'] + '/{id}/spades/scaffolds.fasta'
conda:
'../envs/biopythonworkbench.yaml'
script:
'../scripts/spaSequenceSearch.py'
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