SALMON TXIMPORT

This meta-wrapper includes the following steps:

Step	Tool	Reason
Indexation	Bash	Identify decoy sequences
Indexation	Salmon	Create decoy aware gentrome (genome + trancriptome) index
Quantification	Salmon	Quantify sequenced reads
Quantification	Tximport	Import counts and inferential replicates in R as a ready-to-use SummarizedExperiment object.

Example

This meta-wrapper can be used by integrating the following into your workflow:

rule salmon_decoy_sequences:
    input:
        transcriptome="resources/transcriptome.fasta",
        genome="resources/genome.fasta",
    output:
        gentrome=temp("resources/gentrome.fasta"),
        decoys=temp("resources/decoys.txt"),
    threads: 1
    log:
        "decoys.log",
    wrapper:
        "v2.1.1/bio/salmon/decoys"


rule salmon_index_gentrome:
    input:
        sequences="resources/gentrome.fasta",
        decoys="resources/decoys.txt",
    output:
        multiext(
            "salmon/transcriptome_index/",
            "complete_ref_lens.bin",
            "ctable.bin",
            "ctg_offsets.bin",
            "duplicate_clusters.tsv",
            "info.json",
            "mphf.bin",
            "pos.bin",
            "pre_indexing.log",
            "rank.bin",
            "refAccumLengths.bin",
            "ref_indexing.log",
            "reflengths.bin",
            "refseq.bin",
            "seq.bin",
            "versionInfo.json",
        ),
    cache: True
    log:
        "logs/salmon/transcriptome_index.log",
    threads: 2
    params:
        # optional parameters
        extra="",
    wrapper:
        "v2.1.1/bio/salmon/index"


rule salmon_quant_reads:
    input:
        r="reads/{sample}.fastq.gz",
        index=multiext(
            "salmon/transcriptome_index/",
            "complete_ref_lens.bin",
            "ctable.bin",
            "ctg_offsets.bin",
            "duplicate_clusters.tsv",
            "info.json",
            "mphf.bin",
            "pos.bin",
            "pre_indexing.log",
            "rank.bin",
            "refAccumLengths.bin",
            "ref_indexing.log",
            "reflengths.bin",
            "refseq.bin",
            "seq.bin",
            "versionInfo.json",
        ),
        gtf="resources/annotation.gtf",
    output:
        quant=temp("pseudo_mapping/{sample}/quant.sf"),
        quant_gene=temp("pseudo_mapping/{sample}/quant.genes.sf"),
        lib=temp("pseudo_mapping/{sample}/lib_format_counts.json"),
        aux_info=temp(directory("pseudo_mapping/{sample}/aux_info")),
        cmd_info=temp("pseudo_mapping/{sample}/cmd_info.json"),
        libparams=temp(directory("pseudo_mapping/{sample}/libParams")),
        logs=temp(directory("pseudo_mapping/{sample}/logs")),
    log:
        "logs/salmon/{sample}.log",
    params:
        # optional parameters
        libtype="A",
        extra="--numBootstraps 32",
    threads: 2
    wrapper:
        "v2.1.1/bio/salmon/quant"


rule tximport:
    input:
        quant=expand(
            "pseudo_mapping/{sample}/quant.sf", sample=["S1", "S2", "S3", "S4"]
        ),
        lib=expand(
            "pseudo_mapping/{sample}/lib_format_counts.json",
            sample=["S1", "S2", "S3", "S4"],
        ),
        aux_info=expand(
            "pseudo_mapping/{sample}/aux_info", sample=["S1", "S2", "S3", "S4"]
        ),
        cmd_info=expand(
            "pseudo_mapping/{sample}/cmd_info.json", sample=["S1", "S2", "S3", "S4"]
        ),
        libparams=expand(
            "pseudo_mapping/{sample}/libParams", sample=["S1", "S2", "S3", "S4"]
        ),
        logs=expand("pseudo_mapping/{sample}/logs", sample=["S1", "S2", "S3", "S4"]),
        tx_to_gene="resources/tx2gene.tsv",
    output:
        txi="tximport/SummarizedExperimentObject.RDS",
    params:
        extra="type='salmon'",
    log:
        "logs/tximport.log"
    wrapper:
        "v2.1.1/bio/tximport"

Note that input, output and log file paths can be chosen freely, as long as the dependencies between the rules remain as listed here. For additional parameters in each individual wrapper, please refer to their corresponding documentation (see links below).

When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Used wrappers

The following individual wrappers are used in this meta-wrapper:

• DECOYS
• SALMON_INDEX
• SALMON QUANT
• TXIMPORT

Please refer to each wrapper in above list for additional configuration parameters and information about the executed code.

Authors

• Thibault Dayris