Merge pull request #274 from UPHL-BioNGS/update-2023-12-26

Update 2023 12 26

README.md

@@ -1,5 +1,8 @@
 # Cecret
 
+UPDATE : THIS README IS (albiet slowly) GETTING TURNED INTO A WIKI. YOU CAN CHECK OUR PROGRESS HERE: https://github.com/UPHL-BioNGS/Cecret/wiki
+
+
 Named after the beautiful [Cecret lake](https://en.wikipedia.org/wiki/Cecret_Lake)
 
 Location: 40.570°N 111.622°W , Elevation: 9,875 feet (3,010 m), [Hiking level: easy](https://www.alltrails.com/trail/us/utah/cecret-lake-trail)

configs/cecret_config_template.config

@@ -225,7 +225,7 @@
 //params.freyja = true
 //params.freyja_aggregate = true
 //params.freyja_variants_options = ''
-//params.freyja_demix_options = '--depthcutoff 100'
+//params.freyja_demix_options = ''
 //params.freyja_aggregate_options = ''
 //params.freyja_plot_options = ''
 //params.freyja_plot_filetype = 'png'

main.nf

@@ -190,7 +190,7 @@ params.vadr_mdir                            = '/opt/vadr/vadr-models'
 params.nextclade_options                    = ''
 params.nextalign_options                    = '--include-reference'
 params.freyja_variants_options              = ''
-params.freyja_demix_options                 = "--depthcutoff ${params.minimum_depth}"
+params.freyja_demix_options                 = ""
 
 params.freyja_aggregate_options             = ''
 params.freyja_plot_options                  = ""

modules/bcftools.nf

@@ -18,8 +18,8 @@ process bcftools_variants {
   tuple val(sample), file(bam), file(reference_genome)
 
   output:
-  tuple val(sample), file(bam), file(reference_genome), file("bcftools_variants/${sample}.vcf"), emit: vcf
-  path "bcftools_variants/${sample}.vcf", emit: bcftools_variants_file
+  tuple val(sample), file("bcftools_variants/${sample}.vcf"), emit: vcf                   , optional: true
+  path "bcftools_variants/${sample}.vcf"                    , emit: bcftools_variants_file, optional: true
   path "logs/${task.process}/${sample}.${workflow.sessionId}.log"
 
   shell:

modules/freyja.nf

@@ -3,7 +3,7 @@ process freyja_variants {
   label         "process_medium"
   //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   publishDir    "${params.outdir}", mode: 'copy'
-  container     'quay.io/uphl/freyja:1.4.8-2023-12-19'
+  container     'quay.io/uphl/freyja:1.4.8-2023-12-26'
 
 
   //#UPHLICA maxForks 10
@@ -45,7 +45,7 @@ process freyja_demix {
   label         "process_medium"
   //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   publishDir    "${params.outdir}", mode: 'copy'
-  container     'quay.io/uphl/freyja:1.4.8-2023-12-19'
+  container     'quay.io/uphl/freyja:1.4.8-2023-12-26'
 
 
   //#UPHLICA maxForks 10
@@ -87,7 +87,7 @@ process freyja_boot {
   label         "process_medium"
   //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   publishDir    "${params.outdir}", mode: 'copy'
-  container     'quay.io/uphl/freyja:1.4.8-2023-12-19'
+  container     'quay.io/uphl/freyja:1.4.8-2023-12-26'
 
   //#UPHLICA maxForks 10
   //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
@@ -126,7 +126,7 @@ process freyja_aggregate {
   tag        "Aggregating results from freyja"
   label      "process_single"
   publishDir "${params.outdir}", mode: 'copy'
-  container  'quay.io/uphl/freyja:1.4.8-2023-12-19'
+  container  'quay.io/uphl/freyja:1.4.8-2023-12-26'
 
   //#UPHLICA maxForks 10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}

modules/heatcluster.nf

@@ -1,7 +1,7 @@
 process heatcluster {
   tag           "HeatCluster"
   publishDir    params.outdir, mode: 'copy'
-  container     'quay.io/uphl/heatcluster:1.0.2-2023-12-19'
+  container     'quay.io/uphl/heatcluster:1.0.2b-2023-12-26'
   maxForks      10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-medium'
@@ -16,7 +16,7 @@ process heatcluster {
   file(matrix)
 
   output:
-  path "heatcluster/heatcluster*"       , optional : true
+  path "heatcluster/*"                  , optional : true
   path "heatcluster/heatcluster_mqc.png", optional : true              , emit: for_multiqc
   path "logs/${task.process}/${task.process}.${workflow.sessionId}.log", emit: log_files
 
@@ -38,5 +38,6 @@ process heatcluster {
         | tee -a $log_file
 
     if [ -f "heatcluster/heatcluster.png" ] ; then cp heatcluster/heatcluster.png heatcluster/heatcluster_mqc.png ; fi
+    if [ -f "sorted_matrix.csv" ] ; then cp sorted_matrix.csv heatcluster/sorted_matrix.csv ; fi
   '''
 }

modules/igvreports.nf

@@ -2,7 +2,7 @@ process igv_reports {
   tag         "${sample}"
   label       "process_high"
   publishDir  path: "${params.outdir}", mode: 'copy'
-  container   'quay.io/biocontainers/igv-reports:1.9.1--pyh7cba7a3_0'
+  container   'quay.io/biocontainers/igv-reports:1.10.0--pyh7cba7a3_0'
 
   //#UPHLICA maxForks 10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
@@ -15,25 +15,25 @@ process igv_reports {
   params.igv_reports
 
   input:
-  tuple val(sample), file(bam), file(reference_genome), file(vcf)
+  tuple val(sample), file(vcf), file(bam), file(bai), file(reference_genome)
 
   output:
-    path "igv_reports/${sample}/igvjs_viewer.html"
+    path "igv_reports/${sample}_igvjs_viewer.html"
     path "logs/${task.process}/${sample}.${workflow.sessionId}.log"
 
   shell:
   '''
-    mkdir -p igv_reports/!{sample} logs/!{task.process}
+    mkdir -p igv_reports logs/!{task.process}
     log=logs/!{task.process}/!{sample}.!{workflow.sessionId}.log
 
     # time stamp + capturing tool versions
     date > $log
-    create_report -v >> $log
+    echo "igv-reports does not print version to screen" >> $log
 
     create_report !{params.igv_reports_options} \
         --fasta !{reference_genome} \
         --tracks !{vcf} !{bam} \
-        --output igv_reports/!{sample}/igvjs_viewer.html \
+        --output igv_reports/!{sample}_igvjs_viewer.html \
         !{vcf} \
         | tee -a $log
   '''

modules/ivar.nf

@@ -65,8 +65,8 @@ process ivar_variants {
   tuple val(sample), file(bam), file(reference_genome), file(gff_file)
 
   output:
-  path "ivar_variants/${sample}.variants.tsv",      emit: variant_tsv
-  path "ivar_variants/${sample}.ivar_variants.vcf", emit: ivar_variant_file
+  path "ivar_variants/${sample}.variants.tsv"     , emit: variant_tsv
+  path "ivar_variants/${sample}.ivar_variants.vcf", emit: vcf
   path "logs/${task.process}/${sample}.${workflow.sessionId}.log"
 
   shell:

nextflow.config

@@ -5,7 +5,7 @@ manifest {
   name              = 'Cecret'
   author            = 'Erin Young'
   homePage          = 'https://github.com/UPHL-BioNGS/Cecret'
-  version           = 'v3.10.20231219'
+  version           = 'v3.10.20231226'
   defaultBranch     = 'master'
   recurseSubmodules = false
   description       = 'Reference-based consensus creation'

nextflow_schema.json

@@ -122,7 +122,6 @@
         "freyja_demix_options": { 
             "type": "string",
             "hidden": true,
-            "default": "--depthcutoff 100",
             "description": "Options for process"
         },
         "freyja_plot_filetype": { 

subworkflows/qc.nf

@@ -47,7 +47,12 @@ workflow qc {
     samtools_ampliconstats(ch_trim_bam.map{ it -> tuple(it[0], it[1])}.combine(ch_primer_bed))
     samtools_plot_ampliconstats(samtools_ampliconstats.out.samtools_ampliconstats_files)
 
-    //igv_reports(bcftools_variants.out.vcf)
+    bcftools_variants.out.vcf
+      .join(ch_trim_bam, by: 0)
+      .combine(ch_reference_genome)
+      .set{ for_igv_reports }
+
+    igv_reports(for_igv_reports)
 
     samtools_coverage.out.samtools_coverage
       .collectFile(name: "samtools_coverage_summary.tsv",