config.yaml

references:
    basepath: "path_to_references_data"
    provider: "reference_provider"
    release: "reference_release"

genome_fasta: "_genome_fasta"

mirna_ref: "../data/ref/miRNA/miRBase_main_mature.fasta"
mirna_ref_precursors: "../data/ref/miRNA/miRBase_main_precursors.fasta"
mirna_other: "../data/ref/miRNA/miRBase_other_mature.fasta"
htseq_gff: "../data/ref/mirbase/file.gff3"


rules:
    trim_galore_se:
        params: "--small_rna --dont_gzip"
    multiqc:
        arguments: "--force "
    mirdeep2_alignment:
        params: "-e -h -j -l 18 -m -v"
    mirdeep2_identification:
        params: "-t hsa -P -b 0 -v"
    fastq_screen:
        params: "../data/fastq_screen.config"
    bowtie_mapping:
        params: "-v 2 -m 10 -a"
        basename: "ucsc_hg19 " ## to edit
    mir_trace:
        params: "-s hsa"
    htseq:
        params: "-f bam -r pos -t miRNA -i Name"

### common codes: Homo sapiens= hsa; Mus musculus=mmu; Rattus norvegicus=rno

wrappers:
    fastqc: "fastqc_wrapper"
    trim_galore_se: "trim_galore_se_wrapper"

samples: samples.tsv
units: units.tsv
reheader: reheader.tsv
internal_sid: "LIMS"