Merge pull request #11 from WEHI-ResearchComputing/mosdepth

Add mosdepth coverage to multiqc report

Docker/Dockerfile

@@ -33,6 +33,6 @@ RUN conda update --all -c conda-forge --override-channels && \
     bwa=0.7.17 \
     samtools=1.16.1 \
     fastqc=0.11.8-0 \
-    multiqc=1.12.0 \
     mosdepth=0.3.8 \
+    multiqc=1.12.0 \
     && conda clean -ay

config/modules.config

@@ -49,6 +49,11 @@ process {
         memory = { 4.GB * task.attempt }
         time = '12h'
     }
+    withLabel: Mosdepth {
+        cpus = 5
+        memory = { 4.GB * task.attempt }
+        time = '2h'
+    }
     withLabel: Multiqc {
         cpus = 2
         memory = { 1.GB * task.attempt }

config/multiqc_config.yaml

@@ -1,4 +1,15 @@
 extra_fn_clean_exts:
   - "_R1"
 export_plots: true
-
+remove_sections:
+  - fastqc_per_sequence_gc_content
+  - fastqc_adapter_content
+  - fastqc_per_base_sequence_content
+  - mosdepth-coverage-dist-cov
+mosdepth_config:
+  general_stats_coverage:
+    - 10
+    - 30
+  exclude_contigs:
+    - "*_API_*"
+    -  "*_M*"

config/nextflow_sh.config

@@ -47,6 +47,8 @@ profiles {
             withLabel:Fastqc {
                 module='fastqc/0.11.8'
             }
+            withLabel:Mosdepth {
+            }
             withLabel:Multiqc {
                 module ='MultiQC/1.10.1'
             }
@@ -70,6 +72,9 @@ profiles {
             withLabel:Fastqc {
                 conda= "envs/fastqc.yaml"
             }
+            withLabel:Mosdepth {
+                conda= "envs/mosdepth.yaml"
+            }
             withLabel:Multiqc {
                 conda ='envs/multiqc.yaml'
             }

main.nf

@@ -28,6 +28,7 @@ include { RPlotFull } from './modules/stvariant.nf'
 include { RPlotROI } from './modules/stvariant.nf'
 
 include{ FastQC } from './modules/qc.nf'
+include{ MosDepth } from './modules/qc.nf'
 include{ MultiQC } from './modules/qc.nf'
 
 process foo {
@@ -129,7 +130,12 @@ workflow {
 
     merged_ch=Merge(parent_ch) // Emits tuple val(parentId),path(parentId.bam)
     //----------------QC tools------------------------------------------
-    MultiQC(FastQC(bam_ch.bamnodup.map{row->row[1]}.unique({it.baseName}).collect()).zip.collect().ifEmpty([]))  
+    //MultiQC integrates files from fastqc and mosdepth, found in input dir, into single report
+    fastqc_ch=FastQC(bam_ch.bamnodup.map{row->row[1]}.unique({it.baseName}).collect())
+
+    mosdepth_ch=MosDepth(bam_ch.bamnodup.join(bam_ch.bai)) // join bams with their index based on groupId
+
+    MultiQC( fastqc_ch.zip.mix(mosdepth_ch).collect().ifEmpty([]) )  
     //----------------BCF tools----------------------------------------
     //BCF Input Channel Emits parentId,groupId,ref,bamlist,bams,parentbams
     input_ch.map{row -> tuple(row[0],row[4],row[5])}

modules/qc.nf

@@ -17,6 +17,24 @@ process FastQC {
     """
 }
 
+process MosDepth {
+    label 'Mosdepth'
+    tag "${groupId}"
+    publishDir "${params.outdir}/QC", mode: 'copy'
+    cache true
+    input:
+    tuple  val(sampleId), path(bam), path(bai)
+
+    output:
+    path("*.global.dist.txt"), emit: txt
+
+
+    script:
+    """
+    mosdepth -t ${task.cpus} --no-per-base --mapq 10 ${bam.baseName} ${bam} 
+    """
+}
+
 process MultiQC {
     label 'Multiqc'
     cache true

nextflow.config

@@ -35,7 +35,7 @@ profiles {
         docker.enabled          = false
         singularity.pullTimeout = "3h"
         process {
-            withLabel: 'BWAAlign|Samtools|Bcftools|Fastqc|Multiqc|RGridss|Rfilter|IndexDedup' {
+            withLabel: 'BWAAlign|Samtools|Bcftools|Fastqc|Mosdepth|Multiqc|RGridss|Rfilter|IndexDedup' {
                 container = "ghcr.io/wehi-researchcomputing/nf-malaria-variant-analysis:latest"
             }
         }
@@ -45,7 +45,7 @@ profiles {
         apptainer.enabled     = false
         singularity.enabled   = false
         process {
-            withLabel: 'BWAAlign|Samtools|Bcftools|Fastqc|Multiqc|RGridss|Rfilter|IndexDedup' {
+            withLabel: 'BWAAlign|Samtools|Bcftools|Fastqc|Mosdepth|Multiqc|RGridss|Rfilter|IndexDedup' {
                 container = "ghcr.io/wehi-researchcomputing/nf-malaria-variant-analysis:latest"
             }
         }