remove host removal workflow

Author: aw-watson

workflows/Nextflow/main.nf

@@ -83,15 +83,6 @@ workflow {
         qcReport = FAQCS.out.qcReport
     }
 
-    //Host reads removal
-    hostRemovalReport = channel.empty()
-    if(params.modules.hostRemoval) {
-
-        HOSTREMOVAL(baseSettings.plus(params.hostRemoval).plus(params.faqcs),platform,paired,unpaired)
-        paired = HOSTREMOVAL.out.paired.ifEmpty(["${projectDir}/nf_assets/NO_FILE"])
-        unpaired = HOSTREMOVAL.out.unpaired.ifEmpty("${projectDir}/nf_assets/NO_FILE2")
-        hostRemovalReport = HOSTREMOVAL.out.hostRemovalReport
-    }
 
     //Assembly and validation alignment
     coverageTable = channel.empty()
@@ -178,7 +169,6 @@ workflow {
         counts.ifEmpty{file("DNE")},
         qcStats.ifEmpty{file("DNE1")},
         qcReport.ifEmpty{file("DNE2")},
-        hostRemovalReport.ifEmpty{file("DNE3")},
         rtaReports.ifEmpty{file("DNE4")}, 
         ctaReport.ifEmpty{file("DNE5")},
         contigStatsReport.ifEmpty{file("DNE6")},

workflows/Nextflow/modules/report/report.nf

@@ -26,7 +26,6 @@ process report {
     path fastqCount
     path qcStats
     path qcReport
-    path hostRemovalReport
     path readsTaxonomyReports
     path contigTaxonomyReport
     path contigStatsReport
@@ -62,7 +61,6 @@ process report {
 
 
     my \$qc_flag = (${settings['faqcs']})?"V":"";
-    my \$host_removal_flag = (${settings['hostRemoval']})?"V":"";
     my \$assembly_flag = (${settings["runAssembly"]})?"V":"";
     my \$annotation_flag = (${settings["annotation"]})?"V":"";
     my \$taxonomy_flag = (${settings["readsTaxonomyAssignment"]})?"V":"";
@@ -116,10 +114,6 @@ process report {
     }
 
 
-    if (-e "$hostRemovalReport"){
-        \$mergeFiles .= '$hostRemovalReport'.",";
-    }
-
     if (-e "$contigStatsReport"){
         \$mergeFiles .= '$contigStatsReport'.",";
     }
@@ -171,7 +165,6 @@ process report {
         push @conversions, "convert -strip -density 120 -flatten $qcReport[\$qc_boxplot_page] ./QC_quality_boxplot.png";
     }
 
-    push @conversions, "convert -strip -density 120 -flatten $hostRemovalReport ./HostRemovalStats.png" if (-e "$hostRemovalReport");
     push @conversions, "convert -strip -density 120 -flatten $contigStatsReport[0] ./Assembly_length.png" if (-e "$contigStatsReport");
     push @conversions, "convert -strip -density 120 -flatten $contigStatsReport[1] ./Assembly_GC_content.png" if (-e "$contigStatsReport");
     push @conversions, "convert -strip -density 120 -flatten $contigPlots[0] ./Assembly_CovDepth_vs_Len.png" if (-e "$contigPlots");
@@ -200,7 +193,6 @@ workflow REPORT {
     fastqCount
     qcStats
     qcReport
-    hostRemovalReport
     readsTaxonomyReports
     contigTaxonomyReport
     contigStatsReport
@@ -214,7 +206,6 @@ workflow REPORT {
         fastqCount,
         qcStats,
         qcReport,
-        hostRemovalReport,
         readsTaxonomyReports,
         contigTaxonomyReport,
         contigStatsReport,

workflows/Nextflow/nextflow.config

@@ -5,7 +5,6 @@ params {
     modules {
         sra2fastq = false
         faqcs = false
-        hostRemoval = false
         runAssembly = false
         annotation = false
         binning = false
@@ -22,7 +21,6 @@ params {
         sra2fastqOutDir = "EDGE_output/SRA"
         processProvidedContigsOutDir = "EDGE_output/ProcessedContigs"
         qcOutDir = "EDGE_output/ReadsQC"
-        hostRemovalOutDir = "EDGE_output/HostRemoval"
         assemblyOutDir = "EDGE_output/AssemblyBasedAnalysis"
         contigsTaxonomyOutDir = "EDGE_output/ContigTaxonomyAssignment"
         phageFinderOutDir = "EDGE_output/PhageFinder"
@@ -67,12 +65,6 @@ params {
 
     }
 
-    hostRemoval {
-        host = ["${projectDir}/nf_assets/NO_FILE3"]
-        similarity = 90
-        bwaMemOptions = null
-    }
-
     assembly {
         //assemblers: IDBA_UD, SPAdes, Unicycler, Megahit, LRASM
         assembler = "IDBA_UD"
@@ -267,9 +259,6 @@ process {
     withLabel: 'qc'{
         container= 'ghcr.io/lanl-bioinformatics/edge_run_faqcs:1.6.1'
     }
-    withLabel: 'hostRemoval' {
-        container= 'ghcr.io/lanl-bioinformatics/edge_host_removal:1.7.5'
-    }
     withLabel: 'assembly' {
         container = 'ghcr.io/lanl-bioinformatics/edge_run_assembly:1.7.0'
     }

workflows/Nextflow/templates/module_params.tmpl

@@ -28,11 +28,6 @@
         filtPhiX = <% if(typeof filtPhiX !== 'undefined') { %><%= filtPhiX %><% } else { %>false<%} %>
     }
 
-    hostRemoval {
-        host = ["${projectDir}/nf_assets/NO_FILE3"]
-        similarity = 90
-        bwaMemOptions = null
-    }
 
     assembly {
         //assemblers: IDBA_UD, SPAdes, Unicycler, Megahit, LRASM

workflows/Nextflow/templates/pipeline_config.tmpl

@@ -4,7 +4,6 @@ params {
     modules {
         sra2fastq = <% if(typeof source !== 'undefined' && source === 'sra') { %>true<% } else { %>false<%} %>
         faqcs = <%= runFaQCs %>
-        hostRemoval = false
         runAssembly = <%= assembly %>
         annotation = <%= annotation %>
         readsBinning = <%= binning %>
@@ -21,7 +20,6 @@ params {
         sra2fastqOutDir =  "<%= sraOutdir %>"
         processProvidedContigsOutDir = "<%= projOutdir %>"
         qcOutDir = "<%= projOutdir %>/ReadsQC"
-        hostRemovalOutDir = ""
         assemblyOutDir = "<%= projOutdir %>/Assembly"
         contigsTaxonomyOutDir = "<%= projOutdir %>/Taxonomy"
         phageFinderOutDir = ""