# The main entry point of your workflow.
# After configuring, running snakemake -n in a clone of this repository should successfully execute a dry-run of the workflow.

include: "rules/common.smk"
configfile: "config.yaml"


rule all:
    input:
        # The first rule should define the default target files
        # Subsequent target rules can be specified below. They should start with all_*.
        # SRA_fastq_for_download,
        # expand("Sample_Fastq/{sample}.fastq.gz", sample=SampleList),
        # "LongIntronWindowCounts/18858_cheRNA_L.bed.gz",
        # "LongIntronWindowCounts/19201_cheRNA_1.bed.gz",
        # "LongIntronWindowCounts/19138_cheRNA_1.bed.gz",
        # "Misc/GencodeHg38_all_introns.corrected.uniq.bed",
        # expand( "Alignments/SecondPassTest/{sample}/SJ.out.tab", sample=["18858_cytRNA_L", "18858_nucRNA_L", "18858_cheRNA_L"]),
        # config["Human_ref"]["genome_dir_hisat"] + "genome.1.ht2",
        # expand( "Alignments/SecondPass/{sample}/Unstranded.bw", sample=SampleList),
        # expand(config["gitinclude_output"] + "SJoutAnnotatedAndIntersected/{sample}.tab.gz", sample=SampleList),
        # expand(config["gitinclude_output"] +  "3ssCoverageBeds/{sample}.bed.gz", sample=SampleList),
        # expand("UnstrandedBigwigs/{sample}.bw", sample=SampleList),
        # expand("Junctions/{sample}.junctions.bed.gz", sample=SampleList),
        # expand("qualimap/{sample}/rnaseq_qc_results.txt", sample=SampleList),
        # expand("Alignments/SecondPass_PE/{sample}/Aligned.out.sorted.bam", sample=SampleList_PE),
        # "Misc/computeMatrix.gz",
        # "../../output/CountsPerBam.txt",
        "Misc/GencodeHg38_all_introns.downstream3ssWindows.bed",
        "Misc/GencodeHg38_all_introns.corrected.bed",
        # "Misc/computeMatrix.introns.gz",
        "Misc/Gm12878.chromHMM.hg19.bed.gz",
        # "leafcutter/leafcutter_perind.counts.gz"
        "../../data/Gm12878.chromHMM.hg38.bed.gz",
        # "Multiqc/multiqc_report.html",
        "../../output/VelosoTxnRates.xlsx",
        "MultiqcQuick/multiqc_report.html",
        "../../output/QuickAnalyses/IdxStats.tab",
        "../../output/QuickAnalyses/FeatureCounts.txt.gz",
        expand("QuickAnalyses/Bigwigs/{sample}.bw", sample=SampleList),
        # expand("../../output/LongIntronWindowCounts/{sample}.bed.gz", sample=YisSamples),
        # "../../output/GeneCounts.txt.gz"

include: "rules/other.smk"
include: "rules/DownloadAndMergeFastq.smk"
include: "rules/Align.smk"
include: "rules/QuickAlign.smk"
