16S Snakemake workflow

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This is my Snakemake workflow for 16S amplicon sequencing runs. Using a Snakemake workflow helps increase reproducibility and access across different computers. These commands can also be broken out into separate bash scripts, but using a Snakemake work

Code Snippets

shell:
    """
    module purge all
    module load qiime2/2021.11

    qiime dada2 denoise-paired --verbose \
    --i-demultiplexed-seqs {input} \
    --p-trunc-len-f 240 --p-trunc-len-r 240 \
    --o-representative-sequences {output.seqs} \
    --o-table {output.table} \
    --o-denoising-stats {output.stats}

    """

SnakeMake QIIME2.0 From line 13 of rules/dada2.smk

shell:
    """
    module purge all
    module load qiime2/2021.11

    qiime tools import --input-path {input} \
    --input-format PairedEndFastqManifestPhred33 \
    --output-path {output} \
    --type SampleData[PairedEndSequencesWithQuality]
    """

SnakeMake QIIME2.0 From line 6 of rules/import.smk

shell:
    """
    module purge all
    module load qiime2/2021.11

    qiime demux summarize --i-data {input}  \
    --o-visualization {output}
    """

SnakeMake QIIME2.0 From line 22 of rules/import.smk

shell:
    """
    module purge all
    module load qiime2/2021.11

    qiime feature-table merge \
    --i-tables {input.round1} {input.round2} {input.round3} \
    --o-merged-table {output}

    """

SnakeMake QIIME2.0 From line 9 of rules/merge.smk

shell:
    """
    module purge all
    module load qiime2/2021.11

    qiime feature-table merge-seqs \
    --i-data {input.round1} {input.round2} {input.round3} \
    --o-merged-data {output}

    """

SnakeMake QIIME2.0 From line 28 of rules/merge.smk

shell:
    """
    module purge all
    module load qiime2/2021.11

    qiime metadata tabulate \
    --m-input-file {input.round1} \
    --o-visualization {output.round1}

    qiime metadata tabulate \
    --m-input-file {input.round2} \
    --o-visualization {output.round2}

    qiime metadata tabulate \
    --m-input-file {input.round3} \
    --o-visualization {output.round3}


    """

SnakeMake QIIME2.0 From line 10 of rules/metadata.smk

shell:
    """
    module purge all
    module load qiime2/2021.11

    qiime feature-classifier classify-sklearn \
    --i-classifier {params.classifier_path} \
    --i-reads {input} \
    --o-classification {output}
    """

SnakeMake QIIME2.0 From line 11 of rules/taxonomy.smk

shell:
    """
    module purge all
    module load qiime2/2021.11

    qiime phylogeny align-to-tree-mafft-fasttree \
    --i-sequences {input} \
    --o-alignment {output.alignment} \
    --o-masked-alignment {output.masked_alignment} \
    --o-tree {output.tree} --o-rooted-tree {output.rooted_tree}
    """

SnakeMake QIIME2.0 From line 12 of rules/tree.smk

shell:
    """
    module purge all
    module load qiime2/2021.11

    qiime cutadapt trim-paired --i-demultiplexed-sequences {input}  \
    --p-front-f GTGYCAGCMGCCGCGGTAA \
    --p-front-r CCGYCAATTYMTTTRAGTTT \
    --p-error-rate 0.1 \
    --p-overlap 3 \
    --o-trimmed-sequences {output}
    """

SnakeMake Cutadapt QIIME2.0 From line 6 of rules/trim.smk

shell:
    """
    module purge all
    module load qiime2/2021.11

    qiime demux summarize --i-data {input}  \
    --o-visualization {output}
    """