shell:
	"""
	set +u; module load bioinfo/obitools-v1.2.11; set -u
	obidistribute -n {params.nfiles} -p {params.R1}  {input.R1}
	obidistribute -n {params.nfiles} -p {params.R2} {input.R2}
	"""

shell:
	"""
	set +u; module load bioinfo/obitools-v1.2.11; set -u
	illuminapairedend -r {input.R2} {input.R1} > {output}
	"""

	shell:
		"""
		cat {input} > {output}
  		"""

shell:
	"""
	set +u; module load bioinfo/obitools-v1.2.11; set -u
	obiannotate -S ali:'"good" if score>{params.minscore} else "bad"' {input} | obisplit -t ali -p {params.prefix} 2> {log}
	"""

shell:
	"""
	set +u; module load bioinfo/obitools-v1.2.11; set -u
	obiannotate --without-progress-bar --sanger -S 'Avgqphred:-int(math.log10(sum(sequence.quality)/len(sequence))*10)' {input} | ngsfilter --fasta-output -t {params.ngs} -u {output.unassigned} > {output.demultiplexed} 2> {log}
	"""

shell:
	"""
	cat {input} > {output} 2> {log}
	"""

shell:
	"""
	set +u; module load bioinfo/obitools-v1.2.11; set -u
	obiannotate -S start:"hash(str(sequence))%{params.nfiles}" {input} | obisplit -t start -p {params.tmp}
	"""

shell:
	"""
	set +u; module load bioinfo/obitools-v1.2.11; set -u
	obiuniq -m sample {input} > {output}
	"""

shell:
	"""
	cat {input} > {output} 2> {log}
	"""

shell:
	"""
	set +u; module load bioinfo/obitools-v1.2.11; set -u
	obiannotate --length -S 'GC_content:len(str(sequence).replace("a","").replace("t",""))*100/len(sequence)' {input} | obigrep -l {params.minlength} -s '^[acgt]+$' -p 'count>{params.mincount}' > {output} 2> {log}
	"""

shell:
	"""
	set +u; module load bioinfo/obitools-v1.2.11; set -u
	obiselect -c cluster -n 1 --merge sample -M -f count {input} > {output} 2> {log}
	"""

shell:
	"""
	set +u; module load bioinfo/obitools-v1.2.11; set -u
	obitab -n NA -d -o {input} > {output} 2> {log}
	"""