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Multiqc #394

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Sep 11, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
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9 changes: 1 addition & 8 deletions subworkflows/local/trim_workflow.nf
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@ workflow TRIM_WORKFLOW {

main:
ch_versions = Channel.empty()
ch_reports = Channel.empty()

if (params.trim) {

Expand All @@ -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)
Expand All @@ -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
Expand All @@ -46,7 +40,6 @@ workflow TRIM_WORKFLOW {
emit:
ch_reads_all
ch_reads_fusioncatcher
ch_reports
versions = ch_versions.ifEmpty(null)
}

1 change: 0 additions & 1 deletion workflows/rnafusion.nf
Original file line number Diff line number Diff line change
Expand Up @@ -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([]))



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