Documentation: |
    A pipeline for executing a RNA-seq analysis on a model organism
    ----------------------------------------------------------------
    
    The pipeline includes the following stages:
    
        1. Merge Decompression and Concatenation (IF NEADED) of read files into single files per direction.
        2. FastQC_Merge Quality tests on the original reads using FastQC.
        3. MultiQC_pre_trim Quality report on the original reads using MultiQC.
        4. Trim_Galore  Reads trimming using Trim_Galore.
        5. FastQC_Trim_Galore Quality tests on reads after trimming using FastQC.
        6. RSEM_Genome indexing of the reference genome, mapping of the post trimming reads and count data creation.
        7. MultiQC_post_trim Quality report on the trimmed reads and mapping information using MultiQC.
    


Global_params:
    Default_wait:      10
    Qsub_opts:         -cwd
    Qsub_path:         /path/to/qsub/bin
    Qsub_q:            myqueue.q
    Executor:          Local
    conda:
        env: RNASeq
        path: null
Vars:
  Programs_path:
    FastQC: fastqc
    Multiqc: multiqc
    RSEM: rsem-calculate-expression
    RSEM_generate_data_matrix: rsem-generate-data-matrix
    RSEM_plot: rsem-plot-model
    RSEM_prepare_reference: rsem-prepare-reference
    Trim_Galore: trim_galore
    bowtie2: $CONDA_PREFIX/bin
    cutadapt: cutadapt
    star: $CONDA_PREFIX/bin
  Genome:
    gtf: /PATH2GTF/genome.gtf
    reference: /PATH2reference/genome.fa
  More_info:
    cpu_per_sample: '1'
    min_length: '25'
    min_quality: '25'
Step_params:
  Merge:
    module:   Import
    script_path:
  FastQC_Merge:
    base: Merge
    module: fastqc_html
    redirects:
      --threads: '{Vars.More_info.cpu_per_sample}'
    script_path: '{Vars.Programs_path.FastQC}'
  Trim_Galore:
    base: Merge
    cutadapt_path: '{Vars.Programs_path.cutadapt}'
    module: Trim_Galore
    redirects:
      --length: '{Vars.More_info.min_length}'
      -q: '{Vars.More_info.min_quality}'
    script_path: '{Vars.Programs_path.Trim_Galore}'
  FastQC_Trim_Galore:
    base: Trim_Galore
    module: fastqc_html
    redirects:
      --threads: '{Vars.More_info.cpu_per_sample}'
    script_path: '{Vars.Programs_path.FastQC}'
  RSEM_Genome:
    annotation: '{Vars.Genome.gtf}'
    base: Trim_Galore
    mapper: star
    mapper_path: '{Vars.Programs_path.star}'
    mode: genome
    module: RSEM
    plot_stat: null
    plot_stat_script_path: '{Vars.Programs_path.RSEM_plot}'
    redirects:
      --append-names: null
      --estimate-rspd: null
      --keep-intermediate-files: null
      --output-genome-bam: null
      -p: '{Vars.More_info.cpu_per_sample}'
    reference: '{Vars.Genome.reference}'
    rsem_generate_data_matrix_script_path: '{Vars.Programs_path.RSEM_generate_data_matrix}'
    rsem_prepare_reference_script_path: '{Vars.Programs_path.RSEM_prepare_reference}'
    script_path: '{Vars.Programs_path.RSEM}'
  MultiQC_pre_trim:
    base: FastQC_Merge
    module: Multiqc
    modules: fastqc,cutadapt,trimmomatic,bowtie2,bowtie1,star,htseq,prokka,samtools,quast
    redirects:
      --template: default
    script_path: '{Vars.Programs_path.Multiqc}'
  MultiQC_post_trim:
    base:
    - RSEM_Genome
    - FastQC_Trim_Galore
    module: Multiqc
    redirects:
      --template: default
    script_path: '{Vars.Programs_path.Multiqc}'
