rliterman@0: // Subworkflow to run RefChooser for list of queries
rliterman@0: 
rliterman@0: // Set directory structure
rliterman@0: output_directory = file(params.output_directory)
rliterman@0: log_directory = file(params.log_directory)
rliterman@0: mash_directory = file(params.mash_directory)
rliterman@0: 
rliterman@0: workflow {
rliterman@0:     main:
rliterman@0:     // Run RefChooser
rliterman@0:     reference_data = runRefChooser(query_data: query_data)
rliterman@0:     publish:
rliterman@0:     // Publish reference data
rliterman@0:     reference_data >> 'reference.fa'
rliterman@0: }
rliterman@0: 
rliterman@0: workflow runRefChooser{
rliterman@0:     take:
rliterman@0:     query_data
rliterman@0: 
rliterman@0:     emit:
rliterman@0:     reference_data
rliterman@0: 
rliterman@0:     main:
rliterman@0: 
rliterman@0:     // Make MASH sketches (1 CPU per query) and generate triangle (all CPUs)
rliterman@0:     mash_refs = query_data
rliterman@0:     .unique{it -> it[1]}
rliterman@0:     .map { [ it[0], it[1] ] }
rliterman@0:     | mashSketch 
rliterman@0:     | collect
rliterman@0:     | mashTriangle
rliterman@0:     | chooseRefs
rliterman@0:     | splitCsv | collect | flatten | collate(1) 
rliterman@0: 
rliterman@0:     reference_data = query_data
rliterman@0:     .map{it -> tuple(it[1].toString(),it[0])}
rliterman@0:     .join(mash_refs, by:0)
rliterman@0:     .map{tuple(it[1],it[0])}
rliterman@0:     .unique{it -> it[0]}.collect().flatten().collate(2)
rliterman@0: 
rliterman@0:     // Save reference data to file
rliterman@0:     reference_data
rliterman@0:     .collect{it -> it[0]}
rliterman@0:     | saveRefIDs
rliterman@0: }
rliterman@0: 
rliterman@0: process chooseRefs{
rliterman@0:     
rliterman@0:     executor = 'local'
rliterman@0:     cpus = 1
rliterman@0:     maxForks = 1
rliterman@0: 
rliterman@0:     input:
rliterman@0:     val(mash_triangle)
rliterman@0: 
rliterman@0:     output:
rliterman@0:     stdout
rliterman@0: 
rliterman@0:     script:
rliterman@0: 
rliterman@0:     ref_count = params.n_ref.toInteger()
rliterman@0:     ref_script = file("${projectDir}/bin/chooseRefs.py")
rliterman@0:     """
rliterman@0:     $params.load_python_module  
rliterman@0:     cd $mash_directory
rliterman@0: 
rliterman@0:     python $ref_script --ref_count $ref_count --mash_triangle_file $mash_triangle --trim_name "${params.trim_name}"
rliterman@0:     """
rliterman@0: }
rliterman@0: 
rliterman@0: process mashTriangle{
rliterman@0: 
rliterman@0:     input:
rliterman@0:     val(mash_sketches)
rliterman@0: 
rliterman@0:     output:
rliterman@0:     stdout
rliterman@0: 
rliterman@0:     script:
rliterman@0: 
rliterman@0:     sketch_file = file("${mash_directory}/Mash_Sketches.txt")
rliterman@0:     mash_triangle_file = file("${mash_directory}/Mash_Triangle")
rliterman@0: 
rliterman@0:     """
rliterman@0:     $params.load_mash_module
rliterman@0:     ls ${mash_directory}/*.msh > $sketch_file
rliterman@0:     mash triangle -p ${params.cores} -l $sketch_file > $mash_triangle_file
rliterman@0:     echo -n $mash_triangle_file
rliterman@0:     """
rliterman@0: }
rliterman@0: 
rliterman@0: process mashSketch{
rliterman@0:     cpus = 1
rliterman@0: 
rliterman@0:     input:
rliterman@0:     tuple val(query_name),val(query_fasta)
rliterman@0:     
rliterman@0:     output:
rliterman@0:     stdout
rliterman@0: 
rliterman@0:     script:
rliterman@0: 
rliterman@0:     mash_path = "${mash_directory}/${query_name}.msh"
rliterman@0:     """
rliterman@0:     $params.load_mash_module
rliterman@0:     mash sketch -s 10000 -p 1 -o $mash_path $query_fasta
rliterman@0:     echo -n "${mash_path}"
rliterman@0:     """
rliterman@0: }
rliterman@0: 
rliterman@0: process saveRefIDs{
rliterman@0:     executor = 'local'
rliterman@0:     cpus = 1
rliterman@0:     maxForks = 1
rliterman@0:     
rliterman@0:     input:
rliterman@0:     val(ref_ids)
rliterman@0: 
rliterman@0:     script:
rliterman@0:     ref_id_file = file(params.ref_id_file)
rliterman@0:     ref_id_file.append(ref_ids.join('\n') + '\n')        
rliterman@0:     """
rliterman@0:     """
rliterman@0: }