added basecounts to report

phac-nml · Dec 6, 2023 · 811de08 · 811de08
1 parent cea26f1
commit 811de08
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Showing 5 changed files with 43 additions and 18 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -80,7 +80,7 @@ process {
     //    errorStrategy = 'terminate'
     //    publishDir = [
     //        mode: params.publish_dir_mode,
-    //        path: "${params.outdir}/read_quality/raw_reads",
+    //        path: "${params.outdir}/ReadQuality/raw_reads",
     //        pattern: "*.json"
     //    ]
     //}
@@ -134,7 +134,7 @@ process {
         publishDir = [
             [
                 mode: params.publish_dir_mode,
-                path: "${params.outdir}/read_quality/RawReadData",
+                path: "${params.outdir}/ReadQuality/RawReadData",
                 pattern: "*.json"
             ],
         ]
@@ -151,7 +151,7 @@ process {
         ext.args = '--quiet'
         publishDir = [
             [
-                path: "${params.outdir}/read_quality/fastqc",
+                path: "${params.outdir}/ReadQuality/fastqc",
                 mode: params.publish_dir_mode,
                 pattern: "*{${params.fastqc.html_ext},${params.fastqc.zip_ext}}",
             ]
@@ -165,7 +165,7 @@ process {
         // scratch = false
         publishDir = [
             [
-                path: "${params.outdir}/read_quality/sub_sampled_reads",
+                path: "${params.outdir}/ReadQuality/SubSampledReads",
                 mode: params.publish_dir_mode,
                 pattern: "*${params.seqtk.reads_ext}"
             ]
@@ -179,7 +179,7 @@ withName: SEQTK_SIZE {
         // scratch = false
         publishDir = [
             [
-                path: "${params.outdir}/Assembly/quality/BaseCounts",
+                path: "${params.outdir}/ReadQuality/SubSampledReads/BaseCounts",
                 mode: params.publish_dir_mode,
                 pattern: "*.txt"
             ]
@@ -292,7 +292,7 @@ withName: SEQTK_SIZE {
         stageInMode = params.stage_in_mode
             publishDir = [
                 [
-                    path: "${params.outdir}/read_quality/mash_sketch",
+                    path: "${params.outdir}/ReadQuality/mash_sketch",
                     mode: params.publish_dir_mode,
                     pattern: "*${params.mash.sketch_ext}"
                 ]
@@ -386,15 +386,15 @@ withName: SEQTK_SIZE {
         errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
         maxForks = 20
         maxErrors = 3
-        //dir_out =  process.toString().contains("QC_READS") ? "read_quality/${params.mash.output_dir}/mash" : "taxon_determination/mash"
+        //dir_out =  process.toString().contains("QC_READS") ? "ReadQuality/${params.mash.output_dir}/mash" : "taxon_determination/mash"
         ext.args = "-w"
         //container = params.mash.container
         ext.containers = params.mash
         // scratch = false
         stageInMode = params.stage_in_mode
         publishDir = [
             [
-                path: "${params.outdir}/read_quality/${params.mash.output_dir}/mash",
+                path: "${params.outdir}/ReadQuality/${params.mash.output_dir}/mash",
                 mode: params.publish_dir_mode,
                 pattern: "*${params.mash.output_reads_ext}"
             ],
@@ -422,7 +422,7 @@ withName: SEQTK_SIZE {
         stageInMode = params.stage_in_mode
         publishDir = [
             [
-                path: { "${params.outdir}/read_quality/${params.r_contaminants.output_dir}"},
+                path: { "${params.outdir}/ReadQuality/${params.r_contaminants.output_dir}"},
                 mode: params.publish_dir_mode,
                 pattern: "*.gz" // specifying this outside of config as yet to handle singletons TODO decide on singleton usage
             ]
@@ -545,12 +545,12 @@ withName: SEQTK_SIZE {
         // scratch = false
         publishDir = [
                 [
-                    path: { "${params.outdir}/read_quality/fastp/trimmed_reads"},
+                    path: { "${params.outdir}/ReadQuality/fastp/trimmed_reads"},
                     mode: params.publish_dir_mode,
                     pattern: "*${params.fastp.fastq_ext}"
                 ],
                 [
-                    path: { "${params.outdir}/read_quality/fastp/reports"},
+                    path: { "${params.outdir}/ReadQuality/fastp/reports"},
                     mode: params.publish_dir_mode,
                     pattern: "*{${params.fastp.json_ext},${params.fastp.html_ext}}"
                 ]
@@ -566,7 +566,7 @@ withName: SEQTK_SIZE {
         stageInMode = params.stage_in_mode
         publishDir = [
             [
-                path: { "${params.outdir}/read_quality/chopper/trimmed_reads"},
+                path: { "${params.outdir}/ReadQuality/chopper/trimmed_reads"},
                 mode: params.publish_dir_mode,
                 pattern: "*${params.chopper.fastq_ext}"
             ]
@@ -691,17 +691,17 @@ withName: SEQTK_SIZE {
         ext.containers = params.kat
         publishDir = [
             [
-                path: { "${params.outdir}/read_quality/kat/hist/histogram" },
+                path: { "${params.outdir}/ReadQuality/kat/hist/histogram" },
                 mode: params.publish_dir_mode,
                 pattern: "*${params.kat.hist_ext}"
             ],
             [
-                path: { "${params.outdir}/read_quality/kat/hist/json" },
+                path: { "${params.outdir}/ReadQuality/kat/hist/json" },
                 mode: params.publish_dir_mode,
                 pattern: "*${params.kat.json_ext}"
             ],
             [
-                path: { "${params.outdir}/read_quality/kat/hist/png" },
+                path: { "${params.outdir}/ReadQuality/kat/hist/png" },
                 mode: params.publish_dir_mode,
                 pattern: "*${params.kat.png_ext}"
             ]

diff --git a/nextflow.config b/nextflow.config
@@ -175,7 +175,7 @@ params {
     seqtk_size {
         singularity = 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3'
         docker = 'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3'
-        report_tag = "SeqtkSize"
+        report_tag = "SeqtkBaseCount"
     }
 
     // FASTP options
@@ -290,6 +290,11 @@ params {
     //    sample_header = "Assembly"
     //}
 
+    //quast_genome_size{
+    //    genome_size_field = "Total length (>= 1000 bp)"
+    //    report_tag = "QuastGenomeSize"
+    //}
+
 
     checkm {
         // TODO add to trouble shooting if checkm fails and provides EOF errors, to try changing the container

diff --git a/subworkflows/local/assemble_reads.nf b/subworkflows/local/assemble_reads.nf
@@ -1,6 +1,7 @@
 // Workflow for assembling reads
 // TODO add in read sub-sampling to reduce errors
 
+include { SEQTK_SIZE } from "../../modules/local/seqtk_size.nf"
 include { SPADES_ASSEMBLE } from "../../modules/local/spades_assemble.nf"
 include { FLYE_ASSEMBLE } from "../../modules/local/flye_assemble.nf"
 include { MINIMAP2_INDEX } from "../../modules/local/minimap2_index.nf"
@@ -16,6 +17,16 @@ workflow ASSEMBLE_READS{
     main:
     versions = Channel.empty()
     final_contigs = Channel.empty()
+    reports = Channel.empty()
+
+    // no report channel here?
+    base_counts = SEQTK_SIZE(sample_data)
+    reports = reports.mix(base_counts.map{
+        meta, file_bc -> tuple(meta, extract_base_count(file_bc));
+    })
+
+    versions = versions.mix(base_counts.versions)
+
 
     def platform_comp = params.platform.replaceAll("\\s", "").toString() // strip whitespace from entries
     if(platform_comp == params.opt_platforms.illumina){
@@ -52,7 +63,6 @@ workflow ASSEMBLE_READS{
         minimap2_idx = MINIMAP2_INDEX(ch_assembled.contigs)
         //TODO Move mapping to its own workflow
         versions = versions.mix(minimap2_idx.versions)
-        //TODO no idea if I am doing this right, get input in the future
         ch_mapping_data = sample_data.join(minimap2_idx.index)
         //Decided to leave Racon out of the polishing work flow but to wrap this in statement in a optional value in the future
         output_paf = Channel.value(true)
@@ -70,4 +80,14 @@ workflow ASSEMBLE_READS{
     graphs = ch_assembled.graphs
     final_contigs = final_contigs
     versions = versions
+    reports = reports
+}
+
+
+def extract_base_count(meta, data){
+    def base_count_pos = 1;
+    def rows = data.splitCSV(header: false, sep: '\t') // get first line split as second val is the base count
+    def base_count = rows[base_count_pos];
+    def base_long = base_count.toLong();
+    return base_long
 }
diff --git a/subworkflows/local/qc_assemblies.nf b/subworkflows/local/qc_assemblies.nf
@@ -1,7 +1,6 @@
 // Run annotate and apply QC metrics
 include { QUAST } from "../../modules/local/quast_assembly.nf"
 include { CHECKM_LINEAGEWF } from "../../modules/local/checkm_lineagewf.nf"
-
 include { MLST } from "../../modules/local/mlst.nf"
 
 workflow QC_ASSEMBLIES {

diff --git a/workflows/CleanAssemble.nf b/workflows/CleanAssemble.nf
@@ -120,6 +120,7 @@ workflow CLEAN_ASSEMBLE_READS {
 
         // Isolate workflow
         ch_assembled_reads = ASSEMBLE_READS(ch_trimmed_reads)
+        ch_reports = ch_reports.mix(ch_assembled_reads.reports)
         ch_versions = ch_versions.mix(ch_assembled_reads.versions)
 
         if(!params.skip_polishing){