Merge pull request #408 from nf-core/collectinsertsizemetrics

add insertsizemetrics to QC workflow

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- Add picard CollectInserSizeMetrics to QC workflow [#408](https://github.com/nf-core/rnafusion/pull/408)
+
 ### Changed
 
 - Removed `--fusioninspector_filter` and `--fusionreport_filter` in favor of `--tools_cutoff` (default = 1, no filters applied) [#389](https://github.com/nf-core/rnafusion/pull/389)

README.md

@@ -66,7 +66,7 @@ In rnafusion the full-sized test includes reference building and fusion detectio
     - [FusionInspector](https://github.com/FusionInspector/FusionInspector)
     - [Arriba](https://github.com/suhrig/arriba) visualisation
     - QC for mapped reads ([`QualiMap: BAM QC`](https://kokonech.github.io/qualimap/HG00096.chr20_bamqc/qualimapReport.html))
-    - Collect metrics ([`picard CollectRnaSeqMetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360037057492-CollectRnaSeqMetrics-Picard-) and ([`picard MarkDuplicates`](https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-))
+    - Collect metrics ([`picard CollectRnaSeqMetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360037057492-CollectRnaSeqMetrics-Picard-), [`picard CollectInsertSizeMetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360037055772-CollectInsertSizeMetrics-Picard-) and ([`picard MarkDuplicates`](https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-))
 13. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 14. Compress bam files to cram with [samtools view](http://www.htslib.org/)
 

conf/modules.config

@@ -173,6 +173,10 @@ process {
         ext.when         = { !params.skip_qc && !params.fusioninspector_only && (params.starfusion || params.all) }
     }
 
+    withName: PICARD_COLLECTINSERTSIZEMETRICS {
+        ext.prefix       = { "${meta.id}_collectinsertsize"}
+    }
+
     withName: PIZZLY {
         ext.args = "-k 31 --align-score 2 --insert-size 400 --cache index.cache.txt"
         publishDir = [

docs/output.md

@@ -279,6 +279,7 @@ Picard CollectRnaMetrics and picard MarkDuplicates share the same output directo
 - `picard`
   - `<sample>.MarkDuplicates.metrics.txt` - metrics from MarkDuplicates
   - `<sample>_rna_metrics.txt` - metrics from CollectRnaMetrics
+  - `<sample>_insert_size_metrics.txt.txt` - metrics from CollectInsertSizeMetrics
   - `<sample>.bam` - BAM file with marked duplicates
 
 </details>

modules.json

@@ -55,6 +55,11 @@
                         "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
                         "installed_by": ["modules"]
                     },
+                    "picard/collectinsertsizemetrics": {
+                        "branch": "master",
+                        "git_sha": "240937a2a9c30298110753292be041188891f2cb",
+                        "installed_by": ["modules"]
+                    },
                     "picard/collectwgsmetrics": {
                         "branch": "master",
                         "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",

subworkflows/local/qc_workflow.nf

@@ -5,6 +5,8 @@
 include { QUALIMAP_RNASEQ }                            from '../../modules/nf-core/qualimap/rnaseq/main'
 include { PICARD_COLLECTRNASEQMETRICS }                from '../../modules/local/picard/collectrnaseqmetrics/main'
 include { PICARD_MARKDUPLICATES }                      from '../../modules/nf-core/picard/markduplicates/main'
+include { PICARD_COLLECTINSERTSIZEMETRICS }            from '../../modules/nf-core/picard/collectinsertsizemetrics/main'
+
 
 workflow QC_WORKFLOW {
     take:
@@ -31,12 +33,17 @@ workflow QC_WORKFLOW {
         ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions)
         ch_duplicate_metrics = Channel.empty().mix(PICARD_MARKDUPLICATES.out.metrics)
 
+        PICARD_COLLECTINSERTSIZEMETRICS(ch_bam_sorted)
+        ch_versions = ch_versions.mix(PICARD_COLLECTINSERTSIZEMETRICS.out.versions)
+        ch_insertsize_metrics = Channel.empty().mix(PICARD_COLLECTINSERTSIZEMETRICS.out.metrics)
+
 
     emit:
         versions            = ch_versions.ifEmpty(null)
         qualimap_qc         = ch_qualimap_qc
         rnaseq_metrics      = ch_rnaseq_metrics
         duplicate_metrics   = ch_duplicate_metrics
+        insertsize_metrics  = ch_insertsize_metrics
 
 }
 

tower.yml

@@ -18,7 +18,11 @@ reports:
   "**/picard/*.MarkDuplicates.metrics.txt":
     display: "Picard: Metrics from CollectRnaMetrics"
   "**/picard/*_rna_metrics.txt":
-    display: "Picard: Metrics from MarkDuplicates"
+    display: "GATK4: Metrics from MarkDuplicates"
+  "**/picard/*insert*size*metrics.txt":
+    display: "GATK4: Metrics from InsertSizeMetrics"
+  "**/picard/*pdf":
+    display: "GATK4: InsertSizeMetrics histogram"
   "**/pizzly/*.pizzly.txt":
     display: "Pizzly identified fusion TXT report"
   "**/qualimap/qualimapReport.html":

workflows/rnafusion.nf

@@ -290,6 +290,7 @@ workflow RNAFUSION {
     ch_multiqc_files = ch_multiqc_files.mix(STARFUSION_WORKFLOW.out.star_stats.collect{it[1]}.ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.rnaseq_metrics.collect{it[1]}.ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.duplicate_metrics.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.insertsize_metrics.collect{it[1]}.ifEmpty([]))