Merge pull request #680 from nf-core/dev

Release v2.4.0

Author: ramprasadn

.nf-core.yml

@@ -18,4 +18,4 @@ template:
   name: raredisease
   org: nf-core
   outdir: .
-  version: 2.3.0
+  version: 2.4.0

CHANGELOG.md

@@ -3,6 +3,28 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 2.4.0 - Vitalstatistix [2025-02-24]
+
+### `Added`
+
+- Add markduplicates metrics to multiqc [#679](https://github.com/nf-core/raredisease/pull/679)
+
+### `Changed`
+
+### `Fixed`
+
+### Parameters
+
+| Old parameter | New parameter |
+| ------------- | ------------- |
+|               |               |
+
+### Tool updates
+
+| Tool | Old version | New version |
+| ---- | ----------- | ----------- |
+|      |             |             |
+
 ## 2.3.0 - Getafix [2025-02-13]
 
 ### `Added`

assets/multiqc_config.yml

@@ -2,11 +2,11 @@ custom_logo: "nf-core-raredisease_logo_light.png"
 custom_logo_url: https://github.com/nf-core/raredisease/
 custom_logo_title: "nf-core/raredisease"
 
-report_comment: >
+report_comment: >2
 
-  This report has been generated by the <a href="https://github.com/nf-core/raredisease/releases/tag/2.3.0"
+  This report has been generated by the <a href="https://github.com/nf-core/raredisease/releases/tag/2.4.0"
   target="_blank">nf-core/raredisease</a> analysis pipeline. For information about
-  how to interpret these results, please see the <a href="https://nf-co.re/raredisease/2.3.0/docs/output"
+  how to interpret these results, please see the <a href="https://nf-co.re/raredisease/2.4.0/docs/output"
   target="_blank">documentation</a>.
 
 report_section_order:

nextflow.config

@@ -436,7 +436,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=24.04.2'
-    version         = '2.3.0'
+    version         = '2.4.0'
     doi             = '10.5281/zenodo.7995798'
 }
 

ro-crate-metadata.json

@@ -37,6 +37,7 @@ workflow ALIGN {
         ch_bwamem2_bam        = Channel.empty()
         ch_bwamem2_bai        = Channel.empty()
         ch_fastp_json         = Channel.empty()
+        ch_markdup_metrics    = Channel.empty()
         ch_mt_bam_bai         = Channel.empty()
         ch_mt_marked_bam      = Channel.empty()
         ch_mt_marked_bai      = Channel.empty()
@@ -66,9 +67,10 @@ workflow ALIGN {
                 val_platform,
                 val_sort_threads
             )
-            ch_bwamem2_bam = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bam
-            ch_bwamem2_bai = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bai
-            ch_versions    = ch_versions.mix(ALIGN_BWA_BWAMEM2_BWAMEME.out.versions)
+            ch_bwamem2_bam     = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bam
+            ch_bwamem2_bai     = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bai
+            ch_markdup_metrics = ALIGN_BWA_BWAMEM2_BWAMEME.out.metrics
+            ch_versions        = ch_versions.mix(ALIGN_BWA_BWAMEM2_BWAMEME.out.versions)
         } else if (params.aligner.equals("sentieon")) {
             ALIGN_SENTIEON (                        // Triggered when params.aligner is set as sentieon
                 ch_reads,
@@ -77,8 +79,8 @@ workflow ALIGN {
                 ch_genome_bwaindex,
                 val_platform
             )
-            ch_sentieon_bam = ALIGN_SENTIEON.out.marked_bam
-            ch_sentieon_bai = ALIGN_SENTIEON.out.marked_bai
+            ch_sentieon_bam    = ALIGN_SENTIEON.out.marked_bam
+            ch_sentieon_bai    = ALIGN_SENTIEON.out.marked_bai
             ch_versions     = ch_versions.mix(ALIGN_SENTIEON.out.versions)
         }
 
@@ -137,6 +139,7 @@ workflow ALIGN {
         genome_marked_bam  = ch_genome_marked_bam  // channel: [ val(meta), path(bam) ]
         genome_marked_bai  = ch_genome_marked_bai  // channel: [ val(meta), path(bai) ]
         genome_bam_bai     = ch_genome_bam_bai     // channel: [ val(meta), path(bam), path(bai) ]
+        markdup_metrics    = ch_markdup_metrics    // channel: [ val(meta), path(txt) ]
         mt_marked_bam      = ch_mt_marked_bam      // channel: [ val(meta), path(bam) ]
         mt_marked_bai      = ch_mt_marked_bai      // channel: [ val(meta), path(bai) ]
         mt_bam_bai         = ch_mt_bam_bai         // channel: [ val(meta), path(bam), path(bai) ]

subworkflows/local/align.nf

@@ -913,6 +913,7 @@ workflow RAREDISEASE {
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(CALL_SNV.out.mt_txt.map{it[1]}.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.fastp_json.map{it[1]}.collect().ifEmpty([]))
+    ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.markdup_metrics.map{it[1]}.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.sex_check.map{it[1]}.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics.map{it[1]}.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics.map{it[1]}.collect().ifEmpty([]))