# kate: syntax python;
DATASETS = '1 2 3'.split()
rule mapmature_all:
input: '{ds}.bam'.format(ds=ds) for ds in DATASETS
rule gzip:
output: '{file}.gz'
input: '{file}'
shell: 'gzip < {input} > {output}'
rule cutadapt:
output: fastq=temp('{ds}.fastq')
input: '{ds}.txt'
shell:
'echo hello > {output.fastq}'
rule bwa_mature:
output: bam='{ds}.bam'
input: reads='{ds}.fastq.gz'
threads: 4
shell:
'echo starting with {threads} threads; sleep 10; touch {output.bam}'
works in 8.20.6