Merge pull request #413 from nf-core/update-multiqc-freyja

Update multiqc & add freyja to MQC

Author: Joon-Klaps

CHANGELOG.md

@@ -20,7 +20,8 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [[PR #387](https://github.com/nf-core/viralrecon/pull/387)] - Software closes gracefully when encountering an error
 - [[PR #395](https://github.com/nf-core/viralrecon/pull/395)] - Remove minia from default assemblers because it is unreliable
 - [[PR #393](https://github.com/nf-core/viralrecon/pull/393)] - Changed primer set to params
-- [[PR [#405](https://github.com/nf-core/viralrecon/issues/405)]] - Including parameter `depthcutoff` to freyja demix and boot
+- [[PR #405](https://github.com/nf-core/viralrecon/pull/412)] - Including parameter `depthcutoff` to freyja demix and boot
+- [[PR #413](https://github.com/nf-core/viralrecon/pull/413)] - Update multiqc module & include freyja in report
 
 ### Parameters
 
@@ -44,6 +45,7 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
 | `freyja`   |             | 1.3.12      |
+| `multiqc`  | 1.14        | 1.19        |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present.
 >

assets/multiqc_config_illumina.yml

@@ -20,6 +20,7 @@ run_modules:
   - quast
   - pangolin
   - cutadapt
+  - freyja
 
 module_order:
   - fastqc:
@@ -62,6 +63,11 @@ module_order:
       info: "This section of the report shows Pangolin lineage analysis results for the called variants."
       path_filters:
         - "./variants/*.pangolin.csv"
+  - freyja:
+      name: "VARIANTS: Freyja"
+      info: "This section of the report shows relative lineage abundances from mixed SARS-CoV-2 samples from Freyja demix."
+      path_filters:
+        - "./freyja_demix/*.tsv"
   - bcftools:
       name: "VARIANTS: BCFTools"
       info: "This section of the report shows BCFTools stats results for the called variants."

assets/multiqc_config_nanopore.yml

@@ -16,6 +16,7 @@ run_modules:
   - snpeff
   - quast
   - pangolin
+  - freyja
 
 module_order:
   - pangolin:
@@ -26,6 +27,9 @@ module_order:
       path_filters:
         - "./samtools_stats/*"
   - mosdepth
+  - freyja:
+    path_filters:
+      - "./freyja_demix/*.tsv"
   - bcftools:
       path_filters:
         - "./bcftools_stats/*.txt"

conf/modules_illumina.config

@@ -226,6 +226,7 @@ if (!params.skip_variants) {
                 publishDir = [
                     path: { "${params.outdir}/variants/freyja/" },
                     mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
                 ]
             }
         }

conf/modules_nanopore.config

@@ -266,6 +266,7 @@ if (!params.skip_freyja) {
             publishDir = [
                 path: { "${params.outdir}/${params.artic_minion_caller}/freyja/" },
                 mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             ]
         }
     }

docs/images/freyja_screenshot.png

@@ -266,6 +266,8 @@ Phylogenetic Assignment of Named Global Outbreak LINeages ([Pangolin](https://gi
 
 [Freyja](https://github.com/andersen-lab/Freyja) is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference). The method uses lineage-determining mutational "barcodes" derived from the [UShER](https://usher-wiki.readthedocs.io/en/latest/#) global phylogenetic tree as a basis set to solve the constrained (unit sum, non-negative) de-mixing problem.
 
+<p align="center"><img src="images/freyja_screenshot.png" alt="Freyja screenshot"></p>
+
 ### Nanopore: ASCIIGenome
 
 <details markdown="1">
@@ -641,6 +643,8 @@ iVar outputs a tsv format which is not compatible with downstream analysis such
 
 [Freyja](https://github.com/andersen-lab/Freyja) is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference). The method uses lineage-determining mutational "barcodes" derived from the [UShER](https://usher-wiki.readthedocs.io/en/latest/#) global phylogenetic tree as a basis set to solve the constrained (unit sum, non-negative) de-mixing problem.
 
+<p align="center"><img src="images/freyja_screenshot.png" alt="Freyja screenshot"></p>
+
 ### ASCIIGenome
 
 <details markdown="1">

docs/output.md

@@ -1,10 +1,10 @@
 process MULTIQC {
     label 'process_medium'
 
-    conda "bioconda::multiqc=1.14"
+    conda "bioconda::multiqc=1.19"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.19--pyhdfd78af_0' }"
 
     input:
     path 'multiqc_config.yaml'
@@ -32,6 +32,7 @@ process MULTIQC {
     path ('assembly_spades/*')
     path ('assembly_unicycler/*')
     path ('assembly_minia/*')
+    path ('freyja_demix/*')
 
     output:
     path "*multiqc_report.html"     , emit: report

modules/local/multiqc_illumina.nf

@@ -1,10 +1,10 @@
 process MULTIQC {
     label 'process_medium'
 
-    conda "bioconda::multiqc=1.14"
+    conda "bioconda::multiqc=1.19"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.19--pyhdfd78af_0' }"
 
     input:
     path 'multiqc_config.yaml'
@@ -25,6 +25,7 @@ process MULTIQC {
     path ('snpeff/*')
     path pangolin_lineage
     path nextclade_clade
+    path ('freyja_demix/*')
 
     output:
     path "*multiqc_report.html", emit: report

modules/local/multiqc_nanopore.nf

@@ -477,6 +477,7 @@ workflow ILLUMINA {
     //
     // SUBWORKFLOW: Determine variants with Freyja
     //
+    ch_freyja_multiqc = Channel.empty()
     if (!params.skip_variants && !params.skip_freyja) {
         BAM_VARIANT_DEMIX_BOOT_FREYJA(
             ch_bam,
@@ -486,7 +487,8 @@ workflow ILLUMINA {
             params.freyja_barcodes,
             params.freyja_lineages,
         )
-        ch_versions= ch_versions.mix(BAM_VARIANT_DEMIX_BOOT_FREYJA.out.versions)
+        ch_versions       = ch_versions.mix(BAM_VARIANT_DEMIX_BOOT_FREYJA.out.versions)
+        ch_freyja_multiqc = BAM_VARIANT_DEMIX_BOOT_FREYJA.out.demix
     }
 
     //
@@ -670,7 +672,8 @@ workflow ILLUMINA {
             ch_cutadapt_multiqc.collect{it[1]}.ifEmpty([]),
             ch_spades_quast_multiqc.collect{it[1]}.ifEmpty([]),
             ch_unicycler_quast_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_minia_quast_multiqc.collect{it[1]}.ifEmpty([])
+            ch_minia_quast_multiqc.collect{it[1]}.ifEmpty([]),
+            ch_freyja_multiqc.collect{it[1]}.ifEmpty([]),
         )
         multiqc_report = MULTIQC.out.report.toList()
     }

workflows/illumina.nf

@@ -444,6 +444,7 @@ workflow NANOPORE {
     //
     // SUBWORKFLOW: Determine variants with Freyja
     //
+    ch_freyja_multiqc = Channel.empty()
     if (!params.skip_freyja) {
         BAM_VARIANT_DEMIX_BOOT_FREYJA(
             ARTIC_MINION.out.bam_primertrimmed,
@@ -453,7 +454,8 @@ workflow NANOPORE {
             params.freyja_barcodes,
             params.freyja_lineages,
         )
-        ch_versions= ch_versions.mix(BAM_VARIANT_DEMIX_BOOT_FREYJA.out.versions)
+        ch_versions       = ch_versions.mix(BAM_VARIANT_DEMIX_BOOT_FREYJA.out.versions)
+        ch_freyja_multiqc = BAM_VARIANT_DEMIX_BOOT_FREYJA.out.demix
     }
 
     //
@@ -564,7 +566,8 @@ workflow NANOPORE {
             ch_quast_multiqc.collect{it[1]}.ifEmpty([]),
             ch_snpeff_multiqc.collect{it[1]}.ifEmpty([]),
             ch_pangolin_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_nextclade_multiqc.collectFile(name: 'nextclade_clade_mqc.tsv').ifEmpty([])
+            ch_nextclade_multiqc.collectFile(name: 'nextclade_clade_mqc.tsv').ifEmpty([]),
+            ch_freyja_multiqc.collect{it[1]}.ifEmpty([]),
         )
         multiqc_report = MULTIQC.out.report.toList()
     }