oarfish_snakemake_workflow/Snakefile at main · katsikora/oarfish_snakemake_workflow · GitHub

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import os
import yaml
#from snakemake.utils import glob_wildcards

##paths

##config
# 1. Load your initial static config into a temporary Python variable.
with open("configs/config.yaml", "r") as f:
    main_config = yaml.safe_load(f)
#2. Use the temporary variable to dynamically determine the path of the second config.
organism_config_path = os.path.join("organisms", f"{main_config['organism']}.yaml")
#3. Load the second config file into another temporary variable.
with open(organism_config_path, "r") as f:
    organism_config = yaml.safe_load(f)
# 4. Merge the second config into the first, using the temporary variables.
main_config.update(organism_config)
# 5. Assign the final, merged dictionary to the global `config` object.
config = main_config
#print("Full merged config:", config)
#define alleles
alleles=["h1","h2"]
fromBam=config["fromBam"]
#samples
# --- Read input path from config ---
# # Use the config variable to build the glob pattern
if fromBam:
    input_path = os.path.join(config['input_dir'], "{sample}.bam")
else:
    input_path = os.path.join(config['input_dir'], "{sample}_fastq.gz")
samples = glob_wildcards(input_path).sample
#
# # Print the extracted sample names to confirm it works
print("Found sample names:", samples)


##include rules
include: "snakefiles/make_index.smk"
if not fromBam:
    include: "snakefiles/oarfish.smk"

    if config["sampleSheet"]:
        include: "snakefiles/DE.smk"

    #define outputs
    req_files = ["index/spliced_index",
        expand("oarfish_output/{sample}.quant",sample=samples),
        expand("oarfish_output/{sample}.meta_info.json",sample=samples),
        expand("oarfish_output/{sample}.infreps.pq",sample=samples)]
    if config["sampleSheet"]:
        req_files.append(["edgeR_transcript_output/report.html","edgeR_gene_output/report.html"])
else:
    include: "snakefiles/make_allelic_reads.smk"
    include: "snakefiles/oarfish_allelic.smk"
    if config["sampleSheet"]:
        include: "snakefiles/DE_allelic.smk"

    #define outputs
    req_files = ["index/spliced_index",
        expand("oarfish_output/{sample}_{allele}.quant",sample=samples,allele=alleles),
        expand("oarfish_output/{sample}_{allele}.meta_info.json",sample=samples,allele=alleles),
        expand("oarfish_output/{sample}_{allele}.infreps.pq",sample=samples,allele=alleles)
    ]
    if config["sampleSheet"]:
        req_files.append(["edgeR_transcript_allele_output/report.html","edgeR_transcript_allele_condition_output/report.html"])
        req_files.append(["edgeR_gene_allele_output/report.html","edgeR_gene_allele_condition_output/report.html"])


rule all:
    input:
        req_files