Fix trim multiqc

CHANGELOG.md

@@ -28,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Fix channel i/o issue in StringTie workflow and add StringTie in github CI tests [#416](https://github.com/nf-core/rnafusion/pull/416)
 - Updated COSMIC database to fix 404 error while downloading fusionreport references [#420](https://github.com/nf-core/rnafusion/pull/420)
+- Update modules, and make sure MultiQC displays the QC results properly [#440](https://github.com/nf-core/rnafusion/pull/440)
 - Add 'when' condition to run collectinsertsize [#444](https://github.com/nf-core/rnafusion/pull/444)
 
 ### Removed

assets/multiqc_config.yml

@@ -4,9 +4,34 @@ report_comment: >
   <a href="https://nf-co.re/rnafusion/dev/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
-  software_versions:
+  nf-core-rnafusion-methods-description:
     order: -1000
-  nf-core-rnafusion-summary:
+  software_versions:
     order: -1001
+  nf-core-rnafusion-summary:
+    order: -1002
 
 export_plots: true
+
+# Run only these modules
+run_modules:
+  - custom_content
+  - fastqc
+  - fastp
+  - star
+  - samtools
+  - picard
+  - arriba
+
+module_order:
+  - fastp
+  - fastqc:
+      name: "FastQC (raw)"
+      info: "This section of the report shows FastQC results before adapter trimming."
+      path_filters:
+        - "*.zip"
+  - fastqc:
+      name: "FastQC (trimmed)"
+      info: "This section of the report shows FastQC results after adapter trimming."
+      path_filters:
+        - "*_trimmed*.zip"

conf/modules.config

@@ -68,12 +68,18 @@ process {
     withName: FASTQC {
         ext.args = '--quiet'
         ext.when         = { !params.skip_qc }
+        publishDir = [
+            path: { "${params.outdir}/fastqc" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
     }
 
-    withName: FASTQC_FOR_TRIM {
+    withName: FASTQC_FOR_FASTP {
         ext.args = '--quiet'
+        ext.prefix = { "${meta.id}_trimmed" }
         publishDir = [
-            path: { "${params.outdir}/fastqc_for_trim" },
+            path: { "${params.outdir}/fastqc_for_fastp" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]

modules.json

@@ -57,7 +57,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "214d575774c172062924ad3564b4f66655600730",
+                        "git_sha": "1537442a7be4a78efa3d1ff700a923c627bbda5d",
                         "installed_by": ["modules"]
                     },
                     "picard/collectinsertsizemetrics": {
@@ -77,7 +77,7 @@
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "5394565c5fe4c760e5b35977ec7607c62e81d1f8",
                         "installed_by": ["modules"]
                     },
                     "samtools/sort": {

subworkflows/local/fusioninspector_workflow.nf

@@ -19,6 +19,7 @@ workflow FUSIONINSPECTOR_WORKFLOW {
 
     main:
         ch_versions = Channel.empty()
+        ch_arriba_visualisation = Channel.empty()
         index ="${params.starfusion_ref}"
 
         ch_fusion_list = ( params.tools_cutoff > 1 ? fusion_list_filtered : fusion_list )
@@ -53,9 +54,11 @@ workflow FUSIONINSPECTOR_WORKFLOW {
             ch_bam_sorted_indexed_fusions = bam_sorted_indexed.join(FUSIONINSPECTOR.out.tsv)
             ARRIBA_VISUALISATION(ch_bam_sorted_indexed_fusions, ch_gtf, ch_arriba_ref_protein_domains, ch_arriba_ref_cytobands)
             ch_versions = ch_versions.mix(ARRIBA_VISUALISATION.out.versions)
+            ch_arriba_visualisation = ARRIBA_VISUALISATION.out.pdf
         }
 
     emit:
-        versions        = ch_versions.ifEmpty(null)
+        ch_arriba_visualisation
+        versions             = ch_versions.ifEmpty(null)
 }