// sets global params
params.output_folder = "./output" 
params.input_folder = 'input_folder'

// Q1 - This is a really rigid way of reading paired end read files
// See the section below for a Question 1 about how to do this more elegantly
fastq_pair_ch = Channel.fromFilePairs(params.input_folder + '/*_R{1,2}.fq', flat:true)


process align {

    /* Process 1:
     * Paired-end read fastq files are aligned to IMGT TCRs and flat files
     * are exported containing v,j gene usage and cdr3a and cdr3nuc
     * and many other fields
     * 
     * Inputs : 
     * 
     * Returns :
     */

  
    // Q2 - See Below for Question 2

	container 'milaboratory/mixcr:3-imgt'
	
	publishDir params.output_folder

	input:
    set pair_name, file(fastq1), file(fastq2) from fastq_pair_ch

    output:  
    file "${pair_name}.result.txt" into align_result_channel

    """
    mixcr align ${fastq1} ${fastq2} test2.vdjca --species hsa
    mixcr assemble test2.vdjca output.clns
    mixcr exportClones output.clns output.clns.txt
    mixcr exportAlignments test2.vdjca ${pair_name}.result.txt
    """

}

process cut_fields{

    /* Process 2
     * Cuts MiXCR exported alignments at tabs returns field 3,5,21,30
     * 3: v gene
     * 5: j gene 
     * 21: cdr3_nucleotide
     * 30 : cdr3_amino_acid
     * 
     * Inputs :
     * 
     * Returns :
     */

    container 'milaboratory/mixcr:3-imgt'
    
    publishDir params.output_folder

    input:
    set file(res) from align_result_channel

    output:
    file "${res}.v_j_cdr3_n_cdr3_aa.txt" into final_results

    """
    more "${res}" | cut -d'\t' -f3,5,21,30 > ${res}.v_j_cdr3_n_cdr3_aa.txt
    """
}

params.manifest = "manifest.txt"  
params.output_folder = "./output" 


fastq_ch = Channel.from(file(params.manifest).readLines())
                  .map {it -> file(it)}

process meta {
    /* 
     * publishDir params.output_folder
     */

    input:
    file input_fastq from fastq_ch
    
    output:
    file "${input_fastq}.meta.tsv" into result

    """
    python /Users/kmayerbl/gitrepo/nf-example/meta.py ${input_fastq} > ${input_fastq}.meta.tsv
    """
}

process remove_r {
    publishDir params.output_folder

    input:
    file uppercase_fastq from result
    
    output:
    file "${uppercase_fastq}.remove_r.tsv" 

    """
    python /Users/kmayerbl/gitrepo/nf-example/remove_r.py ${uppercase_fastq} > "${uppercase_fastq}.remove_r.tsv" 
    """    

}