From 26bf56f75361cac6515c5635c63d593532c8d722 Mon Sep 17 00:00:00 2001
From: Katherine Eaton <ktmeaton@gmail.com>
Date: Thu, 26 Mar 2020 16:28:09 -0400
Subject: [PATCH] snippy pairwise docs

---
 pipeline0.nf | 87 ++++++++++++++++++++++++++++++++++++++++++++++------
 1 file changed, 78 insertions(+), 9 deletions(-)

diff --git a/pipeline0.nf b/pipeline0.nf
index def5bc48f..0e39977de 100644
--- a/pipeline0.nf
+++ b/pipeline0.nf
@@ -402,18 +402,18 @@ if (!params.skip_reference_detect_low_complexity){
 
   process reference_detect_low_complexity{
     /*
-     Detect low complexity regions with dustmasker.
-     Convert the identified regions file to a bed format.
+    Detect low complexity regions with dustmasker.
+    Convert the identified regions file to a bed format.
 
-     Input:
-     ch_reference_genome_low_complexity (fasta): The reference genome fasta from the process reference_download.
+    Input:
+    ch_reference_genome_low_complexity (fasta): The reference genome fasta from the process reference_download.
 
-     Output:
-     ch_bed_ref_low_complexity (bed): A bed file containing regions of low-complexity regions.
+    Output:
+    ch_bed_ref_low_complexity (bed): A bed file containing regions of low-complexity regions.
 
-     Publish:
-     ${reference_genome_fna.baseName}.dustmasker.intervals (intervals) Interval file containing regions of low-complexity.
-     ${reference_genome_fna.baseName}.dustmasker.bed (bed) Bed file created from intervals and adjusted for 0-base system.
+    Publish:
+    ${reference_genome_fna.baseName}.dustmasker.intervals (intervals) Interval file containing regions of low-complexity.
+    ${reference_genome_fna.baseName}.dustmasker.bed (bed) Bed file created from intervals and adjusted for 0-base system.
     */
     // Other variables and config
     tag "$reference_genome_fna"
@@ -438,3 +438,72 @@ if (!params.skip_reference_detect_low_complexity){
   }
 
 }
+
+// -------------------------------------------------------------------------- //
+//                                  Snippy Pipeline                           //
+// -------------------------------------------------------------------------- //
+
+// --------------------------------Pairwise Alignment-------------------------//
+
+if(!params.skip_snippy_pairwise){
+
+  process snippy_pairwise{
+    /*
+    Pairwise align contigs to reference genome with snippy.
+
+    Input:
+    ch_assembly_fna_snippy_pairwise (fasta): The genomic assembly from process assembly_download.
+    ch_reference_genome_snippy_pairwise (fasta): The reference genome from process reference_download.
+
+    Output:
+    ch_snippy_snps_variant_summary (text): Table of summarized SNP counts for process variant_summary.
+    ch_snippy_subs_vcf_detect_density (text): VCF of substitutions for process pairwise_detect_snp_high_density.
+
+    Publish:
+    ${assembly_fna.baseName}_snippy.summary.txt (text): Table of summarized SNP counts.
+    ${assembly_fna.baseName}_snippy.subs.vcf (text): VCF of substitutions.
+    ${assembly_fna.baseName}_snippy.\* (text): All default snippy pipeline output.
+    */
+    // Other variables and config
+    tag "$assembly_fna"
+    publishDir "${params.outdir}/snippy_pairwise", mode: 'copy'
+    echo true
+
+    // IO and conditional behavior
+    input:
+    file assembly_fna from ch_assembly_fna_snippy_pairwise
+    file reference_genome_fna from ch_reference_genome_snippy_pairwise
+    output:
+    file "output${params.snippy_ctg_depth}X/*/*"
+    file "output${params.snippy_ctg_depth}X/*/*_snippy.summary.txt" into ch_snippy_snps_variant_summary
+    file "output${params.snippy_ctg_depth}X/*/*_snippy.subs.vcf" into ch_snippy_subs_vcf_detect_density
+
+    // Shell script to execute
+    script:
+    """
+    snippy \
+      --prefix ${assembly_fna.baseName}_snippy \
+      --cpus ${params.snippy_cpus} \
+      --reference ${reference_genome_fna} \
+      --outdir output${params.snippy_ctg_depth}X/${assembly_fna.baseName} \
+      --ctgs ${assembly_fna} \
+      --mapqual ${params.snippy_map_qual} \
+      --mincov ${params.snippy_ctg_depth} \
+      --minfrac ${params.snippy_min_frac} \
+      --basequal ${params.snippy_base_qual} \
+      --report;
+
+    snippy_snps_in=output${params.snippy_ctg_depth}X/${assembly_fna.baseName}/${assembly_fna.baseName}_snippy.txt
+    snippy_snps_txt=output${params.snippy_ctg_depth}X/${assembly_fna.baseName}/${assembly_fna.baseName}_snippy.summary.txt
+
+    COMPLEX=`awk 'BEGIN{count=0}{if (\$1 == "Variant-COMPLEX"){count=\$2}}END{print count}' \$snippy_snps_in;`
+    DEL=`awk 'BEGIN{count=0}{if (\$1 == "Variant-DEL"){count=\$2}}END{print count}' \$snippy_snps_in;`
+    INS=`awk 'BEGIN{count=0}{if (\$1 == "Variant-INS"){count=\$2}}END{print count}' \$snippy_snps_in;`
+    MNP=`awk 'BEGIN{count=0}{if (\$1 == "Variant-MNP"){count=\$2}}END{print count}' \$snippy_snps_in;`
+    SNP=`awk 'BEGIN{count=0}{if (\$1 == "Variant-SNP"){count=\$2}}END{print count}' \$snippy_snps_in;`
+    TOTAL=`awk 'BEGIN{count=0}{if (\$1 == "VariantTotal"){count=\$2}}END{print count}' \$snippy_snps_in;`
+    echo -e output${params.snippy_ctg_depth}X/${assembly_fna.baseName}"\\t"\$COMPLEX"\\t"\$DEL"\\t"\$INS"\\t"\$MNP"\\t"\$SNP"\\t"\$TOTAL >> \$snippy_snps_txt
+    """
+  }
+
+}