Global_params:
    # Executor:   Local
    Default_wait:           10
    Qsub_opts:              -V -cwd
    Qsub_path:              /path/to/qsub/bin
    Qsub_q:                 myqueue.q
    module_path:            ../neatseq_flow_modules
    job_limit:          /path/to/job_limit

Documentation: |
    A pipeline for basic preparation of fastq reads
    ----------------------------------------------------------------
    
    The pipeline includes the following stages:
    1. Preparation and QA:
        a. Merging the reads into a single file per sample.
        b. QC with fastqc
        c. Trimming with trimmomatic or TrimGalore  (Notice the 'SKIP' directive in trimmo instance!)
        d. QC on trimmed reads with fastqc
        e. Report with multiQC

Vars:
    paths:
        trimmo:             /path/to/trimmomatic-0.32.jar
        trimmo_dir:         /path/to/trimmo_dir
        fastqc:             /path/to/fastqc
        trimgal:            /path/to/TrimGalore  
        multiqc:            /path/to/multiQC
        cutadapt:           /path/to/cutadapt  
        fastq_screen:       /path/to/fastq_screen
        fastq_screen_conf:  /path/to/fastq_screen.conf
        bowtie2:            /path/to/bowtie2
    databases:
        human:              /path/to/human/bowtie2_ind
        mouse:              /path/to/mouse/bowtie2_ind
        phix:               /path/to/phiX/bowtie2_ind    

Step_params:
# ---------------------------------- 1. Merge, QC  and trimming
    merge1:
        module:   Import
        script_path:
        intermediate:
        tag:            basic
        
    merge_advanced:
        module:   Import
        src:
            - Forward
            - Reverse
            - Single
            - Nucleotide
        trg:
            - ..guess..
            - fastq.R
            - fastq.S
            - ..guess..
        script_path:    
            - gzip -cd
            - ..guess..
            - ..guess..
            - ..import..
        scope:
            - sample
            - sample
            - sample
            - project
        ext:
            - fastq
            - ..guess..
            - fq
            - ..guess..
        intermediate:
        tag:            basic

    fastq_screen_alt1:
        module:         fastq_screen
        base:           merge1
        script_path:        {Vars.paths.fastq_screen}
        qsub_params:
            -pe:        shared 10
        redirects:
            --conf:     {Vars.paths.fastq_screen_conf}
            --filter:   200
            --tag:
            --force: 
            --threads:  10
        export:

    fastq_screen_alt2:
        module:         fastq_screen
        base:           merge1
        script_path:        {Vars.paths.fastq_screen}
        qsub_params:
            -pe:        shared 10
        aligner:
            bowtie2:    {Vars.paths.bowtie2}
        genomes:
            Human:      {Vars.databases.human} 
            Mouse:      {Vars.databases.mouse} 
            PhiX:       {Vars.databases.phix}  
        redirects:
            --filter:   200
            --tag:
            --force: 
            --threads:  10
        # conda:
            # path:   JKJLJLJL
            # env:    

    fqc_merge1:
        module:         fastqc_html
        base:           merge1
        script_path:    {Vars.paths.fastqc}
        qsub_params:
            -pe:        shared 15
        redirects:
            --threads:  15
    
    # subset_samples_cat1:
        # module:         subet_samples
        # base:           merge1
        # script_path:
        # category:       Category2
        # levels:         A
        
    trim1:
        module:             trimmo
        base:               merge1   #subset_samples_cat1
        script_path:        'java -jar {Vars.paths.trimmo}'
        # SKIP:
        spec_dir:           {Vars.paths.trimmo_dir}
        todo:               ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
        redirects:
            -threads:       20
        # sample_list:
            # category:       Category1
            # levels:         A
        intermediate:
            
    trim_gal: 
        module:         Trim_Galore
        base:           merge1
        script_path:    {Vars.paths.trimgal}
        tag:            trim_galore_tag    
        cutadapt_path:  {Vars.paths.cutadapt}
        redirects:
            --length:   50
            --quality:  20 # Parameters for running Trim Galore
            --max_n:    1
            --trim-n:
            --yoohoo:
            # --paired:
            # --retain_unpaired:
    fqc_trimgal:
        module:         fastqc_html
        base:           trim_gal
        script_path:    {Vars.paths.fastqc}
        # exclude_sample_list:    [Sample1, Sample2]
        qsub_params:
            -pe:        shared 15
        redirects:
            --threads:  15
    MultQC_merge:
        module:         Multiqc
        base:           fqc_merge1
        script_path:    {Vars.paths.multiqc}        
        redirects:
            --interactive:
    MultQC_trimgal:
        module:         Multiqc
        base:           fqc_trimgal
        script_path:    {Vars.paths.multiqc}        
        tag:
        SKIP:   #False
        redirects:
            --interactive:
        # stop_and_show: