--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/subworkflows/alignData/main.nf	Mon Dec 02 10:40:55 2024 -0500
@@ -0,0 +1,129 @@
+// Subworkflow to run MUMmer for query/referece comparisons
+
+// Set path variables
+output_directory = file(params.output_directory)
+mummer_directory = file(params.mummer_directory)
+mummer_log_directory = file(params.mummer_log_directory)
+snpdiffs_directory = file(params.snpdiffs_directory)
+log_directory = file(params.log_directory)
+
+if(params.tmp_dir == ""){
+    temp_dir = ""
+} else{
+    temp_dir = file(params.temp_dir)
+}
+
+ref_mode = params.ref_mode
+ref_id_file = file(params.ref_id_file)
+
+// Set path to accessory scripts/files
+all_snpdiffs_list = file("${log_directory}/All_SNPDiffs.txt")
+isolate_data_file = file("${output_directory}/Isolate_Data.tsv")
+snpdiffs_summary_file = file("${output_directory}/Raw_MUMmer_Summary.tsv")
+mummerScript = file("$projectDir/bin/compileMUMmer.py")
+
+workflow {
+    main:
+    // Align genomes
+    snpdiffs = alignGenomes(to_align: read_data, snpdiffs_data: snpdiffs_data)
+    publish:
+    // Publish snpdiffs
+    snpdiffs >> 'snpdiffs.tsv'
+}
+
+workflow alignGenomes{
+    take:
+    to_align
+    snpdiffs_data
+
+    emit:
+    return_snpdiffs
+
+    main:
+    
+    // Align anything that needs aligning
+    sample_pairwise = to_align
+    .filter{"${it[0]}" != "${it[2]}"} // Don't map things to themselves
+    | runMUMmer 
+    | splitCsv
+    
+    log_hold = sample_pairwise
+    .concat(snpdiffs_data)
+    .unique{it -> it[2]}
+    .collect{it -> it[2]}
+
+    snpdiff_files = saveMUMmerLog(log_hold)
+    .collect().flatten().collate(1)
+
+    return_snpdiffs = sample_pairwise
+    .concat(snpdiffs_data)
+    .map { it -> tuple([it[0], it[1]].sort().join(',').toString(),it[0], it[1], it[2]) }
+    .unique{it -> it[0]}
+    .map{it->tuple(it[3],it[1],it[2])}
+    .join(snpdiff_files,by:0)
+    .map{it->tuple(it[1],it[2],it[0])}
+}
+
+process runMUMmer{
+
+    cpus = 1
+    memory '4 GB'
+
+    input:
+    tuple val(query_name),val(query_fasta),val(ref_name),val(ref_fasta)
+
+    output:
+    stdout
+    
+    script:
+
+    report_id = "${query_name}__vs__${ref_name}"
+    mummer_log = file("${mummer_log_directory}/${report_id}.log")
+
+    // Ensure MUmmer directories exist
+    if(!mummer_directory.isDirectory()){
+        error "$mummer_directory does not exist..."
+    } else{
+        """
+        $params.load_mummer_module
+        $params.load_python_module
+        $params.load_bedtools_module
+        $params.load_bbtools_module
+
+        cd ${mummer_directory}
+        dnadiff -p ${report_id} ${ref_fasta} ${query_fasta}
+        
+        rm -rf ${mummer_directory}/${report_id}.mdelta
+        rm -rf ${mummer_directory}/${report_id}.mcoords
+        rm -rf ${mummer_directory}/${report_id}.1delta
+        rm -rf ${mummer_directory}/${report_id}.delta
+        rm -rf ${mummer_directory}/${report_id}.qdiff
+        rm -rf ${mummer_directory}/${report_id}.rdiff
+        rm -rf ${mummer_directory}/${report_id}.unref
+        rm -rf ${mummer_directory}/${report_id}.unqry
+
+        python ${mummerScript} --query "${query_name}" --query_fasta "${query_fasta}" --reference "${ref_name}" --reference_fasta "${ref_fasta}" --mummer_dir "${mummer_directory}" --snpdiffs_dir "${snpdiffs_directory}" --temp_dir "${temp_dir}" --log_file "${mummer_log}"
+        """
+    }
+}
+
+process saveMUMmerLog{
+
+    executor = 'local'
+    cpus = 1
+    maxForks = 1
+
+    input:
+    val(snpdiffs_paths)
+
+    output:
+    val(snpdiffs_paths)
+
+    script:
+    saveSNPDiffs = file("$projectDir/bin/saveSNPDiffs.py")
+    all_snpdiffs_list.write(snpdiffs_paths.join('\n') + '\n')
+    """
+    $params.load_python_module
+    python $saveSNPDiffs --snpdiffs_file "${all_snpdiffs_list}" --summary_file "${snpdiffs_summary_file}" --isolate_file "${isolate_data_file}" --trim_name "${params.trim_name}" --ref_id_file "${ref_id_file}"
+    """
+}
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