Implementation of coveragePlot module

envs/env.yml

@@ -49,6 +49,8 @@ dependencies:
   - openssl=3.0.5=h166bdaf_2
   - pip=22.3=pyhd8ed1ab_0
   - python=3.9.13=h2660328_0_cpython
+  - pandas=2.1.1=py39hddac248_1
+  - biopython=1.81=py39h72bdee0_0
   - readline=8.1.2=h0f457ee_0
   - setuptools=65.5.0=pyhd8ed1ab_0
   - singularity=3.8.7=h8e8409e_0

vfnext/configs/containers.config

@@ -35,9 +35,6 @@ process {
     withName:alignConsensus2Ref {
         container = "$projectDir/containers/singularity_mafft.sif"
     }
-    withName:runIntraHostScript {
-        container = "$projectDir/containers/singularity_pythonScripts.sif"
-    }
     withName:runPangolin{
         container = "$projectDir/containers/pangolin_latest.sif"
     }
@@ -50,9 +47,6 @@ process {
     withName:fixWGS {
         container = "$projectDir/containers/singularity_pythonScripts.sif"
     }
-    withName:compileOutputs {
-        container = "$projectDir/containers/singularity_pythonScripts.sif"
-    }
     withName:runSnpEff{
         container = "$projectDir/containers/singularity_snpeff.sif"
     }
@@ -74,5 +68,7 @@ process {
     withName:runVfReport{
         container = "$projectDir/containers/vfreport.sif"
     }
-
+    withName:coveragePlot{
+        container = "$projectDir/containers/singularity_bamdash.sif"
+    }
 }

vfnext/containers/Singularity_bwa_v0717

@@ -46,7 +46,7 @@ Usage:
     apt update
     #for security fixe:
     #apt upgrade -y
-    apt install -y wget bzip2
+    apt install -y wget bzip2 procps
 
     #install conda
     cd /opt

vfnext/containers/Singularity_fastp_v0201

@@ -46,7 +46,7 @@ Usage:
     apt update
     #for security fixe:
     #apt upgrade -y
-    apt install -y wget bzip2
+    apt install -y wget bzip2 procps
 
     #install conda
     cd /opt

vfnext/containers/Singularity_nextclade

@@ -2,6 +2,7 @@ Bootstrap: docker
 From: continuumio/miniconda3:4.7.12
 
 %post
+conda install -c conda-forge procps-ng
 wget https://github.com/nextstrain/nextclade/releases/download/2.4.0/nextclade-x86_64-unknown-linux-gnu
 chmod 755 nextclade-x86_64-unknown-linux-gnu
 mv nextclade-x86_64-unknown-linux-gnu /usr/bin/nextclade
@@ -11,4 +12,3 @@ exec nextclade "$@"
 
 %startscript
 exec nextclade "$@"
-

vfnext/containers/Singularity_snpEff

@@ -6,6 +6,7 @@ conda install -c bioconda samtools=1.9 --force-reinstall
 conda install -c bioconda freebayes
 conda install -c bioconda snpeff=5.0
 conda install -c bioconda entrez-direct
+conda install -c conda-forge procps-ng
 
 %runscript
 cd /

vfnext/containers/Singularity_vfreport

@@ -8,7 +8,7 @@ DEBIAN_FRONTEND=noninteractive
 
 # Install OS dependencies
 apt-get update -qq -y && \
-apt install git -y 
+apt install git -y procps
 
 # Install Python dependencies
 pip install --upgrade pip

vfnext/containers/setupContainers.sh

@@ -53,9 +53,6 @@ echo "@ Building ivar_latest.sif..."
 singularity build --fakeroot --sandbox ivar_latest.sif Singularity_ivar
 echo "  > Done <"
 
-echo "@ Building singularity_pythonScripts.sif..."
-singularity build --fakeroot --sandbox singularity_pythonScripts.sif Singularity_pythonScripts
-
 echo "@ Building singularity_edirect.sif..."
 singularity build --fakeroot --sandbox singularity_edirect.sif Singularity_edirect
 
@@ -68,6 +65,9 @@ singularity build --fakeroot --sandbox singularity_samtools.sif docker://staphb/
 echo "@ Building vfreport.sif..."
 singularity build --fakeroot --sandbox vfreport.sif Singularity_vfreport
 
+echo "@ Building singularity_bamdash.sif..."
+singularity build --fakeroot --sandbox singularity_bamdash.sif Singularity_bamdash
+
 echo "@ Downloading snpeff database catalog..."
 singularity exec ./singularity_snpeff.sif snpEff databases > snpEff_DB.catalog
 

vfnext/main.nf

@@ -7,6 +7,7 @@ nextflow.enable.dsl = 2
 include { indexReferenceBWA } from './modules/bwaIndex.nf'
 include { runFastp } from './modules/runFastp.nf'
 include { align2ref } from './modules/align2ref.nf'
+include { coveragePlot } from './modules/coveragePlot.nf'
 include { runIvar } from './modules/runIvar.nf'
 include { runReadCounts } from './modules/runReadCounts.nf'
 include { alignConsensus2Ref } from './modules/alignConsensus2Ref.nf'
@@ -142,6 +143,10 @@ workflow {
      )
     | view(it -> log.warn("Excluding ${it[0]} bam files as input for Picard due to small size (< ${params.minBamSize} bytes)"))
 
+  //Rendering the depth coverage plot
+  coveragePlot(align2ref.out.regular_output,
+              ref_gcode)
+
   if ((params.writeMappedReads == true)){
     // write mapped reads
     getMappedReads(align2ref_Out_ch) 

vfnext/modules/compileOutput.nf

@@ -10,7 +10,7 @@ process compileOutputs{
     path("*")
   script:
     """
-    compileOutput.py -dD ${params.outDir} \
+    python $projectDir/bin/compileOutput.py -dD ${params.outDir} \
                             -oD ./ \
                             --depth ${params.depth} \
                             -virus_tag ${virus_tag}

vfnext/modules/coveragePlot.nf

@@ -0,0 +1,30 @@
+process coveragePlot {
+    publishDir "${params.outDir}/${sample_id}_results/", mode: "copy"
+
+    input:
+
+      tuple val(sample_id), path(bam_files), path(bai_files)
+      val(genome_code)
+    output:
+        path("*coveragePlot*")
+
+    script:
+
+    bam = bam_files[0].toString()
+    genomecode = genome_code.toString()
+    depth = params.depth
+    html = "${sample_id}_coveragePlot.html"
+    png = "${sample_id}_coveragePlot.png"
+    svg = "${sample_id}_coveragePlot.svg"
+
+    """
+    bamdash -b ${bam} -r ${genomecode} -c ${depth} -e svg
+    mv ${genomecode}_plot.svg ${svg}
+
+    bamdash -b ${bam} -r ${genomecode} -c ${depth} -e png
+    mv ${genomecode}_plot.png ${png}
+
+    bamdash -b ${bam} -r ${genomecode} -c ${depth}
+    mv ${genomecode}_plot.html ${html}
+    """
+}

vfnext/modules/runIntraHostScript.nf

@@ -10,7 +10,7 @@ process runIntraHostScript{
 
   script:
      """
-     python /intrahost_scriptv2.py \
+     python $projectDir/bin/intrahost_scriptv2.py \
             -in ${sample_id}.depth${params.depth}.fa.bc \
             -al ${sample_id}.depth${params.depth}.fa.algn \
             -dp ${params.minDpIntrahost} \

vfnext/modules/runSnpEff.nf

@@ -28,7 +28,6 @@ process runSnpEff{
     """
     freebayes -p 1 --reference-quality ${params.mapping_quality},${params.base_quality} \
             -f ${ref_fa} ${sorted_bam} > ${sample_id}.vcf
-    snpEff download -v ${genome_code}
     snpEff ann -Xmx4g \
             ${genome_code} ${sample_id}.vcf > ${sample_id}.ann.vcf
     # add sample id to htmls