/
16S-single.snakefile
50 lines (46 loc) · 1.31 KB
/
16S-single.snakefile
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# Single-end reads
include: "16S-common.snakefile"
rule single_denoise:
output:
table = "table.qza",
seqs = "rep-seqs.qza",
stats = "denoise-stats.qza"
input:
"filter.qza"
params:
trim_length = 150,
min_reads = 1,
jobs_to_start = 1
shell:
"qiime deblur denoise-16S"
" --i-demultiplexed-seqs {input}"
" --p-trim-length {params.trim_length}"
" --p-min-reads {params.min_reads}"
" --p-jobs-to-start {params.jobs_to_start}"
" --p-sample-stats"
" --o-table {output.table}"
" --o-representative-sequences {output.seqs}"
" --o-stats {output.stats}"
rule single_filter:
output:
filter = "filter.qza",
stats = "filter-stats.qza"
input:
"demux.qza"
shell:
"qiime quality-filter q-score"
" --i-demux {input}"
" --o-filtered-sequences {output.filter}"
" --o-filter-stats {output.stats}"
rule single_demultiplex:
output:
"demux.qza"
input:
fastq_files,
manifest = "manifest.csv"
shell:
"qiime tools import"
" --type 'SampleData[SequencesWithQuality]'"
" --input-path {input.manifest}"
" --input-format SingleEndFastqManifestPhred33"
" --output-path {output}"