Remove freyja boot

.github/workflows/test_profile.yml

@@ -24,7 +24,7 @@ jobs:
 
       - name: Run Cecret
         run: |
-          nextflow run . -profile docker,test -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 --vadr false --aci false --freyja false
+          nextflow run . -profile docker,test -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 --vadr false
 
           ls cecret*
 

.github/workflows/test_profile1.yml

@@ -24,7 +24,7 @@ jobs:
 
       - name: Run Cecret
         run: |
-          nextflow run . -profile docker,test1 -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 --vadr false --aci false --freyja false
+          nextflow run . -profile docker,test1 -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 --vadr false
 
           ls cecret*
 

.github/workflows/test_profile2.yml

@@ -24,7 +24,7 @@ jobs:
 
       - name: Run Cecret
         run: |
-          nextflow run . -profile docker,test2 -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 --vadr false --aci false --freyja false
+          nextflow run . -profile docker,test2 -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 --vadr false
 
           ls cecret*
 

.github/workflows/test_wastewater.yml

@@ -36,5 +36,7 @@ jobs:
 
           cat cecret*/cecret_results.txt
 
+          head cecret/freyja/aggregated-freyja.tsv
+
       - name: Clean
         run: rm -rf work .nextflow*

configs/cecret_config_template.config

@@ -196,7 +196,7 @@
 //params.kraken2_db = false
 
 //# For process samtools_ampliconstats and samtools_plot_ampliconstats
-//params.samtools_ampliconstats_options = ''
+//params.samtools_ampliconstats_options = '--max-amplicon-length 3000 --max-amplicons 3000'
 //params.samtools_ampliconstats = true
 //params.samtools_plot_ampliconstats_options = '-size 1200,900 -size2 1200,900 -size3 1200,900'
 //params.samtools_plot_ampliconstats = true
@@ -210,9 +210,8 @@
 //params.freyja_aggregate = true
 //params.freyja_variants_options = ''
 //params.freyja_demix_options = '--depthcutoff 100'
-//params.freyja_boot_options = '--nb 1000 --depthcutoff 100'
 //params.freyja_aggregate_options = ''
-//params.freyja_plot_options = '--mincov 100'
+//params.freyja_plot_options = ''
 //params.freyja_plot_filetype = 'png'
 
 //# For process nextclade

main.nf

@@ -52,6 +52,10 @@ params.bedtools_multicov_options            = false
 if (params.bedtools_multicov_options ) {
   println('WARNING : params.bedtools_multicov_options no longer does anything!')
 }
+params.freyja_boot_options                  = false
+if (params.freyja_boot_options  ) {
+  println('WARNING : params.freyja_boot_options no longer does anything!')
+}
 
 //# Starting the workflow --------------------------------------------------------------
 
@@ -179,9 +183,9 @@ params.nextclade_options                    = ''
 params.nextalign_options                    = '--include-reference'
 params.freyja_variants_options              = ''
 params.freyja_demix_options                 = "--depthcutoff ${params.minimum_depth}"
-params.freyja_boot_options                  = "--nb 1000 --depthcutoff ${params.minimum_depth}"
+
 params.freyja_aggregate_options             = ''
-params.freyja_plot_options                  = "--mincov ${params.minimum_depth}"
+params.freyja_plot_options                  = ""
 params.freyja_plot_filetype                 = 'png'
 
 //# Specifying some species-specific params

modules/freyja.nf

@@ -1,7 +1,7 @@
-process freyja {
+process freyja_variants {
   tag           "${sample}"
   label         "process_medium"
-  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   publishDir    "${params.outdir}", mode: 'copy'
   container     'quay.io/uphl/freyja:1.4.7-2023-10-31'
 
@@ -18,8 +18,8 @@ process freyja {
   tuple val(sample), file(bam), file(reference_genome)
 
   output:
-  path "freyja/${sample}_demix.tsv", optional: true, emit: freyja_demix
-  path "freyja/${sample}*",                          emit: files
+  tuple val(sample), file("freyja/${sample}_{depths,variants}.tsv"), optional: true, emit: variants
+  path "freyja/${sample}*",                                          optional: true, emit: files
   path "logs/${task.process}/${sample}.${workflow.sessionId}.log"
 
   shell:
@@ -36,17 +36,84 @@ process freyja {
       --depths freyja/!{sample}_depths.tsv \
       --ref !{reference_genome} \
       | tee -a $log
+  '''
+}
+
+process freyja_demix {
+  tag           "${sample}"
+  label         "process_medium"
+  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  publishDir    "${params.outdir}", mode: 'copy'
+  container     'quay.io/uphl/freyja:1.4.7-2023-10-31'
+
+  //#UPHLICA maxForks 10
+  //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
+  //#UPHLICA memory 60.GB
+  //#UPHLICA cpus 14
+  //#UPHLICA time '45m'
+
+  when:
+  params.freyja
+
+  input:
+  tuple val(sample), file(variants)
+
+  output:
+  path "freyja/${sample}_demix.tsv", optional: true, emit: demix
+  path "freyja/${sample}*",          optional: true, emit: files
+  path "logs/${task.process}/${sample}.${workflow.sessionId}.log"
+
+  shell:
+  '''
+    mkdir -p freyja logs/!{task.process}
+    log=logs/!{task.process}/!{sample}.!{workflow.sessionId}.log
+
+    date > $log
+    freyja --version >> $log
 
     freyja demix \
       !{params.freyja_demix_options} \
-      freyja/!{sample}_variants.tsv \
-      freyja/!{sample}_depths.tsv \
+      !{variants[1]} \
+      !{variants[0]} \
       --output freyja/!{sample}_demix.tsv \
       | tee -a $log
+  '''
+}
+
+process freyja_boot {
+  tag           "${sample}"
+  label         "process_medium"
+  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  publishDir    "${params.outdir}", mode: 'copy'
+  container     'quay.io/uphl/freyja:1.4.7-2023-10-31'
+
+  //#UPHLICA maxForks 10
+  //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
+  //#UPHLICA memory 60.GB
+  //#UPHLICA cpus 14
+  //#UPHLICA time '45m'
+
+  when:
+  params.freyja
+
+  input:
+  tuple val(sample), file(variants)
+
+  output:
+  path "freyja/${sample}*", emit: files
+  path "logs/${task.process}/${sample}.${workflow.sessionId}.log"
+
+  shell:
+  '''
+    mkdir -p freyja logs/!{task.process}
+    log=logs/!{task.process}/!{sample}.!{workflow.sessionId}.log
+
+    date > $log
+    freyja --version >> $log
 
     freyja boot !{params.freyja_boot_options} \
-      freyja/!{sample}_variants.tsv \
-      freyja/!{sample}_depths.tsv \
+      !{variants[1]} \
+      !{variants[0]} \
       --nt !{task.cpus} \
       --output_base freyja/!{sample}_boot.tsv \
       | tee -a $log
@@ -76,7 +143,7 @@ process freyja_aggregate {
   output:
   path "freyja/aggregated*",                                                   emit: files
   path "freyja/aggregated-freyja.tsv",                                         emit: aggregated_freyja_file
-  path "freyja/*mqc.png",                                                       emit: for_multiqc
+  path "freyja/*mqc.png",                                                      emit: for_multiqc
   path "freyja/*png"
   path "logs/${task.process}/${task.process}.${workflow.sessionId}.log"
 

nextflow.config

@@ -5,7 +5,7 @@ manifest {
   name              = 'Cecret'
   author            = 'Erin Young'
   homePage          = 'https://github.com/UPHL-BioNGS/Cecret'
-  version           = 'v3.8.20231031'
+  version           = 'v3.9.20231102'
   defaultBranch     = 'master'
   recurseSubmodules = false
   description       = 'Reference-based consensus creation'

nextflow_schema.json

@@ -119,12 +119,6 @@
             "hidden": true,
             "description": "Options for process"
         },
-        "freyja_boot_options": { 
-            "type": "string",
-            "hidden": true,
-            "default": "--nb 1000 --depthcutoff 100",
-            "description": "Options for process"
-        },
         "freyja_demix_options": { 
             "type": "string",
             "hidden": true,
@@ -144,7 +138,6 @@
         "freyja_plot_options": { 
             "type": "string",
             "hidden": true,
-            "default": "--mincov 100",
             "description": "Options for process"
         },
         "freyja_variants_options": { 

subworkflows/sarscov2.nf

@@ -1,4 +1,6 @@
-include { freyja; freyja_aggregate }     from '../modules/freyja'    addParams(params)
+include { freyja_aggregate }             from '../modules/freyja'    addParams(params)
+include { freyja_demix }                 from '../modules/freyja'    addParams(params)
+include { freyja_variants }              from '../modules/freyja'    addParams(params)
 include { pangolin }                     from '../modules/pangolin'  addParams(params)
 include { nextclade }                    from '../modules/nextclade' addParams(params)
 include { nextclade_dataset as dataset } from '../modules/nextclade' addParams(params)
@@ -26,8 +28,9 @@ workflow sarscov2 {
         }
 
         nextclade(ch_fastas.collect(), ch_dataset)
-        freyja(ch_bam.map{it -> tuple(it[0], it[1])}.combine(ch_reference_genome))
-        freyja_aggregate(freyja.out.freyja_demix.collect(), ch_freyja_script)
+        freyja_variants(ch_bam.map{it -> tuple(it[0], it[1])}.combine(ch_reference_genome))
+        freyja_demix(freyja_variants.out.variants)
+        freyja_aggregate(freyja_demix.out.demix.collect(), ch_freyja_script)
 
     emit:
         dataset     = ch_dataset