Snakefile

import pandas as pd
from models.basic import PipeLine
from models.constants import TASK_DESEQ, TASK_MULTI_QC

CONFIG_FILE = "config/config.yaml"

configfile: CONFIG_FILE

SAMPLES_DF = pd.read_csv(config['samples'])
BASE = config['base']
PIPELINE = PipeLine(CONFIG_FILE)


def get_final_outputs(wildcards):
    files = []
    for _, row in SAMPLES_DF.iterrows():
        srr = row["run"]
        paired = row["is_paired"]
        files.extend(PIPELINE.output_files(srr, paired))
    if TASK_DESEQ in PIPELINE.tasks:
        files.extend(PIPELINE.get_deseq2_outputs())
    # Always keep MultiQC at the top of the input list
    if TASK_MULTI_QC in PIPELINE.tasks:
        files.insert(0, f"{PIPELINE.base}/quality.html")
    return files


def get_fastq_files(wildcards):
    return PIPELINE.fastq(wildcards.SRR_ID)


"""
Important: Rule order is important. Be careful with which rule you use before.
"""

rule all:
    input: get_final_outputs
    threads: config["threads"]

# Include all other rules files
# This order is also important as some of the functions are reused in other
# files.
include: "rules/ncbi.smk"
include: "rules/sortmerna.smk"
include: "rules/fastqc.smk"
include: "rules/star.smk"
include: "rules/stringtie.smk"
include: "rules/salmon.smk"
include: "rules/kallisto.smk"
include: "rules/counts.smk"
include: "rules/deseq2.smk"
include: "rules/multiqc.smk"
include: "rules/trinity.smk"