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- rule hisat2_align:
- input:
- rU: lambda wildcards: ('-U '+ read_files[wildcards.reads]['unpaired']) if wildcards.read_type=='trimmed' else '',
- r1: lambda wildcards: '-1 '+ read_files[wildcards.reads]['R1'],
- r2: lambda wildcards: '-2 '+ read_files[wildcards.reads]['R2']
- output:
- 'aligned.sam'
- params:
- idx: 'index_prefix',
- extra: ''
- shell:
- 'hisat2 {params.extra} -x {params.idx} {input.rU} {input.r1} {input.r2}'
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