Merge pull request #394 from nf-core/multiqc

Multiqc

CHANGELOG.md

@@ -23,6 +23,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Removed
 
+- Removed trimmed fastqc report from multiqc [#394](https://github.com/nf-core/rnafusion/pull/394)
+
 ## v2.3.0 = [2022/04/24]
 
 ### Added

subworkflows/local/trim_workflow.nf

@@ -10,7 +10,6 @@ workflow TRIM_WORKFLOW {
 
     main:
         ch_versions = Channel.empty()
-        ch_reports = Channel.empty()
 
         if (params.trim) {
 
@@ -21,7 +20,6 @@ workflow TRIM_WORKFLOW {
 
             ch_reads_all = reads
             ch_reads_fusioncatcher = REFORMAT.out.reads_out
-            ch_reports = FASTQC_FOR_TRIM.out.zip.collect{it[1]}.ifEmpty([])
         }
         else if (params.fastp_trim) {
             FASTP(reads, params.adapter_fasta, false, false)
@@ -32,11 +30,7 @@ workflow TRIM_WORKFLOW {
 
             ch_reads_all = FASTP.out.reads
             ch_reads_fusioncatcher = ch_reads_all
-            ch_reports = ch_reports.mix(
-                FASTQC_FOR_FASTP.out.zip.collect{it[1]}.ifEmpty([]),
-                FASTP.out.json.collect{meta, json -> json},
-                FASTP.out.html.collect{meta, html -> html}
-            )
+
         }
         else {
             ch_reads_all = reads
@@ -46,7 +40,6 @@ workflow TRIM_WORKFLOW {
     emit:
         ch_reads_all
         ch_reads_fusioncatcher
-        ch_reports
         versions      = ch_versions.ifEmpty(null)
     }
 

workflows/rnafusion.nf

@@ -288,7 +288,6 @@ 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(TRIM_WORKFLOW.out.ch_reports.ifEmpty([]))