covarplot fix, min depth parameter inclusion

replikation · Aug 3, 2021 · 3939285 · 3939285
1 parent 2bddebb
commit 3939285
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Showing 6 changed files with 30 additions and 11 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -24,6 +24,7 @@ params {
     reference_for_qc = ''
     seq_threshold = '0.90'
     n_threshold = '0.05'
+    min_depth = '20'
 
     // settings
     buildDB = false

diff --git a/poreCov.nf b/poreCov.nf
@@ -428,6 +428,7 @@ ${c_yellow}Parameters - nCov genome reconstruction${c_reset}
     --rapid         use rapid-barcoding-kit [default: ${params.rapid}]
     --minLength     min length filter raw reads [default: 350 (primer-scheme: V1-3); 500 (primer-scheme: V1200)]
     --maxLength     max length filter raw reads [default: 700 (primer-scheme: V1-3); 1500 (primer-scheme: V1200)]
+    --min_depth     nucleotides below min depth will be masked to "N" [default ${params.min_depth}]
     --medaka_model  medaka model for the artic workflow [default: ${params.medaka_model}]
 
 ${c_yellow}Parameters - Genome quality control${c_reset}
@@ -517,7 +518,7 @@ def rki() {
     RKI output for german DESH upload:
     \033[2mOutput stored at:    $params.output/$params.rkidir  
     Min Identity to NC_045512.2: $params.seq_threshold [--seq_threshold]
-    Min Coverage:        20 [ no parameter]
+    Min Depth:        $params.min_depth [--min_depth]
     Proportion cutoff N: $params.n_threshold [--n_threshold]\u001B[0m
     \u001B[1;30m______________________________________\033[0m
     """.stripIndent()

diff --git a/workflows/process/artic.nf b/workflows/process/artic.nf
@@ -10,12 +10,24 @@ process artic_medaka {
         tuple val(name), path("*.consensus.fasta"), emit: fasta
         tuple val(name), path("${name}_mapped_*.primertrimmed.sorted.bam"), path("${name}_mapped_*.primertrimmed.sorted.bam.bai"), emit: reference_bam
         tuple val(name), path("SNP_${name}.pass.vcf"), emit: vcf
-        //tuple val(name), path("${name}.pass.vcf.gz"), path("${name}.coverage_mask.txt.nCoV-2019_1.depths"), path("${name}.coverage_mask.txt.nCoV-2019_2.depths"), emit: covarplot
-        tuple val(name), path("${name}.pass.vcf.gz"), emit: covarplot
+        tuple val(name), path("${name}.pass.vcf.gz"), path("${name}.coverage_mask.txt.nCoV-2019_1.depths"), path("${name}.coverage_mask.txt.nCoV-2019_2.depths"), emit: covarplot
     script:   
         """
-        artic minion --medaka --medaka-model ${params.medaka_model} --normalise 500 --threads ${task.cpus} --scheme-directory ${external_scheme} \
-            --read-file ${reads} nCoV-2019/${params.primerV} ${name}
+        artic minion    --medaka \
+                        --medaka-model ${params.medaka_model} \
+                        --min-depth ${params.min_depth} \
+                        --normalise 500 \
+                        --threads ${task.cpus} \
+                        --scheme-directory ${external_scheme} \
+                        --read-file ${reads} \
+                        nCoV-2019/${params.primerV} ${name}
+
+        # generate depth files
+        artic_make_depth_mask --depth ${params.min_depth} \
+            --store-rg-depths ${external_scheme}/nCoV-2019/${params.primerV}/nCoV-2019.reference.fasta \
+            ${name}.primertrimmed.rg.sorted.bam \
+            ${name}.coverage_mask.txt
+
         zcat ${name}.pass.vcf.gz > SNP_${name}.pass.vcf
 
         sed -i "1s/.*/>${name}/" *.consensus.fasta
@@ -60,6 +72,12 @@ process artic_nanopolish {
             --sequencing-summary sequencing_summary*.txt \
             nCoV-2019/${params.primerV} ${name}
 
+        # generate depth files
+        artic_make_depth_mask --depth ${params.min_depth} \
+            --store-rg-depths ${external_scheme}/nCoV-2019/${params.primerV}/nCoV-2019.reference.fasta \
+            ${name}.primertrimmed.rg.sorted.bam \
+            ${name}.coverage_mask.txt
+
         zcat ${name}.pass.vcf.gz > SNP_${name}.pass.vcf
 
         sed -i "1s/.*/>${name}/" *.consensus.fasta

diff --git a/workflows/process/covarplot.nf b/workflows/process/covarplot.nf
@@ -2,15 +2,14 @@ process covarplot {
     label "covarplot"
     publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy'
     input:
-        //tuple val(name), path(vcf), path(depth1), path(depth2), path(primer_bed)
-        tuple val(name), path(vcf), path(primer_bed)
+        tuple val(name), path(vcf), path(depth1), path(depth2), path(primer_bed)
     output:
         tuple val(name), path("${name}_amplicon_coverage*.png")
     script:
         """
-        covarplot.py -v ${vcf} -b ${primer_bed}/nCoV-2019/${params.primerV}/nCoV-2019.scheme.bed -s .
+        covarplot.py -v ${vcf} -d1 ${depth1} -d2 ${depth2} -b ${primer_bed}/nCoV-2019/${params.primerV}/nCoV-2019.scheme.bed -s .
         mv ${name}.CoVarPlot.png ${name}_amplicon_coverage.png
-        covarplot.py -v ${vcf} -b ${primer_bed}/nCoV-2019/${params.primerV}/nCoV-2019.scheme.bed -s . --log
+        covarplot.py -v ${vcf} -d1 ${depth1} -d2 ${depth2} -b ${primer_bed}/nCoV-2019/${params.primerV}/nCoV-2019.scheme.bed -s . --log
         mv ${name}.CoVarPlot.png ${name}_amplicon_coverage_log.png
         """
     stub:

diff --git a/workflows/process/filter_fastq_by_length.nf b/workflows/process/filter_fastq_by_length.nf
@@ -1,6 +1,6 @@
 process filter_fastq_by_length {
         label 'ubuntu'
-        publishDir "${params.output}/${params.readsdir}/2.filtered_reads/", mode: 'copy', pattern: "${name}_filtered.fastq.gz"
+        publishDir "${params.output}/${params.readsdir}/filtered_reads/", mode: 'copy', pattern: "${name}_filtered.fastq.gz"
     input:
         tuple val(name), path(reads) 
     output:

diff --git a/workflows/process/kraken2.nf b/workflows/process/kraken2.nf
@@ -1,6 +1,6 @@
 process kraken2 {
         label 'kraken2'
-        publishDir "${params.output}/${params.readqcdir}/1.read_classification", mode: 'copy'
+        publishDir "${params.output}/${params.readqcdir}/${name}/tax_read_classification", mode: 'copy'
     input:
         tuple val(name), path(reads)
         path(database)