merge the master mask bed

docs/process/process_reference_genome.rst

@@ -34,7 +34,8 @@ ${reference_genome_gb_local.baseName}     gbff                        The locall
 
 **Shell script**::
 
-      gunzip -f ${reference_genome_local}
+      gunzip -f ${reference_genome_fna_local}
+      gunzip -f ${reference_genome_gb_local}
 
 ------------
 

docs/process/process_snippy.rst

@@ -135,3 +135,33 @@ ${params.snippy_variant_density}_${workflow.runName}.txt  bed)
 **Shell script**::
 
       sort -k1,1 -k2,2n ${snippy_subs_bed} | bedtools merge > ${params.snippy_variant_density}_${workflow.runName}.txt
+
+
+------------
+
+Snippy Merge Mask Bed
+------------------------------
+
+Sort and merge regions of high SNP density.
+
+========================================= =========================== ===========================
+Input                                     Type                        Description
+========================================= =========================== ===========================
+ch_bed_mask_master_merge                  bed                         Combined BED files of repeats, low-complexity and (optional) high-density SNP regions.
+========================================= =========================== ===========================
+
+========================================= =========================== ===========================
+Output                                    Type                        Description
+========================================= =========================== ===========================
+ch_bed_mask_snippy_multi                  bed                         Master masking BED file for process snippy_multi
+========================================= =========================== ===========================
+
+========================================================= =========================== ===========================
+Publish                                                   Type                        Description
+========================================================= =========================== ===========================
+master.bed                                                bed                         Master masking BED file.
+========================================================= =========================== ===========================
+
+**Shell script**::
+
+      cat ${bed_mask} | sort -k1,1 -k2,2n | bedtools merge > master.bed

nextflow.config

@@ -33,6 +33,7 @@ params{
   skip_snippy_detect_snp_high_density = false
   skip_reference_detect_repeats = false
   skip_reference_detect_low_complexity = false
+  skip_snippy_multi = false
 
   // Other to be sorted
   max_datasets = 100

pipeline.nf

@@ -324,7 +324,7 @@ if (!params.skip_reference_download){
     */
 
     // Other variables and config
-    tag "$reference_genome_local"
+    tag "$reference_genome_fna_local"
     publishDir "${params.outdir}/reference_genome", mode: 'copy'
 
     // IO and conditional behavior
@@ -620,49 +620,91 @@ if(!params.skip_snippy_detect_snp_high_density){
 
 }
 
-//------------------------------Multiple Alignment----------------------------//
-
+// --------------------------Merge Filtering BED Files------------------------//
 
-process snippy_multiple{
-/*
+process snippy_merge_mask_bed{
+  /*
 
   Input:
-  ch_():
+  ch_bed_mask_master_merge (bed): Combined BED files of repeats, low-complexity and (optional) high-density SNP regions.
 
   Output:
-  ch_ ():
+  ch_bed_mask_snippy_multi (bed): Master masking BED file for process snippy_multi
 
   Publish:
-
-*/
+  master.bed (bed): Master masking BED file.
+  */
   // Other variables and config
-  tag ""
-  publishDir
+  tag "bed_snippy_subs_density"
+  publishDir "${params.outdir}/snippy_filtering", mode: 'copy'
+  if (params.skip_snippy_detect_snp_high_density){
+  ch_bed_ref_detect_repeats
+      .mix(ch_bed_ref_low_complex)
+      .collectFile(name: "master_unmerged_skip_snp_density.bed")
+      .set{ch_bed_mask_master_merge}
+  }
 
+  else{
+    ch_bed_ref_detect_repeats
+        .mix(ch_bed_ref_low_complex, ch_snippy_subs_bed_density_multi)
+        .collectFile(name: "master_unmerged.bed")
+        .set{ch_bed_mask_master_merge}
+  }
   // IO and conditional behavior
   input:
-  file reference_genome_fna from ch_reference_genome_snippy_multi
-
+  file bed_mask from ch_bed_mask_master_merge
   output:
-
+  file "master.bed" into ch_bed_mask_snippy_multi
 
   // Shell script to execute
   script:
   """
-  # Store a list of all the Snippy output directories in a file
-  ls -d1 ${params.outdir}/snippy_pairwise/output${params.snippy_ctg_depth}X/* > allDir;
-  # Save the contents of that file as a variable
-  allDir=`cat allDir`;
-  # Perform multiple genome alignment (with custom filtering)
-  snippy-core \
-      --ref /mnt/c/Users/ktmea/Projects/Bacterial-Phylogenetics/reference/Yersinia_pestis_CO92_whole_genome.gb \
-      --prefix raw \
-      --mask ../mask/master.bed \
-      --mask-char N \
-      $allDir 2>&1 | tee snippy-raw.log
+  cat ${bed_mask} | sort -k1,1 -k2,2n | bedtools merge > master.bed
   """
 }
 
+
+//------------------------------Multiple Alignment----------------------------//
+
+if(!params.skip_snippy_multi){
+
+  process snippy_multi{
+  /*
+
+    Input:
+    ch_():
+
+    Output:
+    ch_ ():
+
+    Publish:
+
+  */
+    // Other variables and config
+    tag ""
+    echo true
+
+    // IO and conditional behavior
+    input:
+    file reference_genome_gb from ch_reference_genome_snippy_multi
+
+    output:
+
+
+    // Shell script to execute
+    script:
+    """
+    echo ${reference_genome_gb}
+    # Store a list of all the Snippy output directories in a file
+    ls -d1 ${params.outdir}/snippy_pairwise/output${params.snippy_ctg_depth}X/* > allDir;
+    # Save the contents of that file as a variable
+    allDir=`cat allDir`;
+    echo \$allDir;
+    """
+  }
+
+}
+
 // -------------------------------------------------------------------------- //
 //                           Visualization MultiQC                            //
 // -------------------------------------------------------------------------- //