miRNA/Snakefile at master · solida-core/miRNA · GitHub

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import pandas as pd
report: "report/workflow.rst"
## USER FILES ##
samples = pd.read_csv(config["samples"], index_col="sample", sep="\t")
units = pd.read_csv(config["units"], index_col=["unit"], dtype=str, sep="\t")
reheader = pd.read_csv(config["reheader"],index_col="Client", dtype=str, sep="\t")
reheader = reheader[reheader["LIMS"].isin(samples.index.values)]
## ---------- ##


##### local rules #####
localrules: all, pre_rename_fastq_se, post_rename_fastq_se

rule all:
    input:
        "qc/multiqc.html",
        # expand("htseq/{sample.sample}.counts", sample=samples.reset_index().itertuples()),
        expand("reads/dedup/{sample.sample}.mirna_dedup.bam.bai", sample=samples.reset_index().itertuples()),
        expand("reads/counts/{sample.sample}.mirna.txt", sample=samples.reset_index().itertuples()),
        expand("delivery/counts/{Client.Client}_mirna_counts.tsv", Client=reheader.reset_index().itertuples()),


### rules inclusion
include_prefix="rules"
include:
    include_prefix + "/functions.py"
include:
    include_prefix + "/qc.smk"
include:
    include_prefix + "/umi_and_trimming.smk"
include:
    include_prefix + "/mapping.smk"
include:
    include_prefix + "/samtools.smk"
include:
    include_prefix + "/count_mirna.smk"
include:
    include_prefix + "/delivery.smk"