--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/subworkflows/snpdiffs/main.nf	Mon Dec 02 10:40:55 2024 -0500
@@ -0,0 +1,138 @@
+// Screening and SNP Pipeline processing
+output_directory = file(params.output_directory)
+log_directory = file(params.log_directory)
+screen_log_dir = file(params.screen_log_dir)
+snp_log_dir = file(params.snp_log_dir)
+snp_directory = file(params.snp_directory)
+
+if(params.tmp_dir == ""){
+    temp_dir = ""
+} else{
+    temp_dir = file(params.temp_dir)
+}
+ref_id_file = file(params.ref_id_file)
+
+ref_mode = params.ref_mode
+
+// Assess whether to rescue edge-filtered SNPs
+edge_rescue = "${params.rescue}" == "norescue" ? "norescue" : "rescue"
+
+// Set paths for output files 
+all_snpdiffs_list = file("${log_directory}/All_SNPDiffs.txt")
+snp_dirs_list = file("${log_directory}/SNP_Dirs.txt")
+screening_results_file = file("${output_directory}/Screening_Results.tsv")
+isolate_data_file = file("${output_directory}/Isolate_Data.tsv")
+snpdiffs_summary_file = file("${output_directory}/Raw_MUMmer_Summary.tsv")
+
+// Get QC thresholds
+min_cov = params.min_cov.toFloat()
+min_length = params.min_len.toInteger()
+min_iden = params.min_iden.toFloat()
+reference_edge = params.ref_edge.toInteger()
+query_edge = params.query_edge.toInteger()
+max_missing = params.max_missing.toFloat()
+n_ref = params.n_ref.toInteger()
+
+workflow {
+    main:
+    // Run SNP pipeline
+    runSNPPipeline(query_data: all_snpdiffs, reference_data: ref_id_file)
+}
+
+workflow runScreen {
+    
+    take:
+    all_snpdiffs
+
+    main:
+
+    all_snpdiffs
+    .unique{it -> it[2]} 
+    .collect() 
+    | screenSNPDiffs
+}
+
+process screenSNPDiffs{
+
+    input:
+    val(all_snpdiffs)
+
+    script:
+
+    screenDiffs = file("${projectDir}/bin/screenSNPDiffs.py")
+    """
+    $params.load_python_module
+    $params.load_bedtools_module
+    python $screenDiffs --snpdiffs_file "${all_snpdiffs_list}" --log_dir "${screen_log_dir}" --min_cov "${min_cov}" --min_len "${min_length}" --min_iden "${min_iden}" --ref_edge "${reference_edge}" --query_edge "${query_edge}" --density_windows "${params.dwin}" --max_snps "${params.wsnps}" --trim_name "${params.trim_name}" --output_file "${screening_results_file}" --ref_id "${ref_id_file}" --tmp_dir "${temp_dir}"
+    """
+} 
+
+workflow runSNPPipeline{
+    take:
+    all_snpdiffs
+    reference_data
+
+    main:
+    
+    query_snpdiffs = all_snpdiffs.map{tuple(it[0],it[2])}
+    ref_snpdiffs = all_snpdiffs.map{tuple(it[1],it[2])}
+
+    stacked_snpdiffs = query_snpdiffs.concat(ref_snpdiffs)
+    .collect().flatten().collate(2)
+
+    snp_dirs = stacked_snpdiffs
+    .combine(reference_data)
+    .filter{it -> it[0].toString() == it[2].toString()}
+    .map{it -> tuple(it[0],it[1])}
+    .groupTuple(by:0)
+    .map { ref, diff_files -> tuple( ref.toString(), diff_files.collect() ) }
+    | runSnpPipeline
+
+    //snp_dirs.collect() | compileResults
+}
+
+process compileResults{
+
+    executor = 'local'
+    cpus = 1
+    maxForks = 1
+    
+    input:
+    val(snp_directories)
+
+    script:
+
+    compile_script = file("${projectDir}/bin/compileSNPResults.py")
+    snp_dirs_list.write(snp_directories.join("\n")+ "\n")
+    """
+    $params.load_python_module
+    python $compile_script --snp_dirs_file "${snp_dirs_list}" --output_directory "${snp_directory}" --isolate_data_file "${isolate_data_file}" --mummer_data_file "${snpdiffs_summary_file}"
+    """
+}
+
+process runSnpPipeline{
+
+    input:
+    tuple val(reference_id),val(diff_files)
+
+    output:
+    stdout
+
+    script:
+
+    snp_script = file("${projectDir}/bin/runSNPPipeline.py")
+
+    // Set + create output directory
+    snp_dir = file("${snp_directory}/${reference_id}")
+    snp_dir.mkdirs()
+
+    // Write SNPDiffs list
+    out_snpdiffs = file("${snp_dir}/SNPDiffs.txt")
+    out_snpdiffs.write(diff_files.join("\n")+ "\n")
+    """
+    $params.load_python_module
+    $params.load_bedtools_module
+    python $snp_script --reference_id "${reference_id}" --output_directory "${snp_dir}" --snpdiffs_file "${out_snpdiffs}" --log_directory "${snp_log_dir}" --min_cov "${min_cov}" --min_len "${min_length}" --min_iden "${min_iden}" --ref_edge "${reference_edge}" --query_edge "${query_edge}" --density_windows "${params.dwin}" --max_snps "${params.wsnps}" --trim_name "${params.trim_name}" --max_missing "${max_missing}" --tmp_dir "${temp_dir}" --rescue "${edge_rescue}"
+    echo -n $snp_dir
+    """
+}
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