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Merge pull request #286 from nf-core/multiqc-optimisations

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MultiQC Optimisations
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James A. Fellows Yates 2023-04-21 22:44:36 +02:00 committed by GitHub
commit b299a25bc7
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3 changed files with 8 additions and 3 deletions
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1
CHANGELOG.md
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@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#270](https://github.com/nf-core/taxprofiler/pull/270/files) Fixed warning for host removal index parameter, and improved index checks (♥ to @prototaxites for reporting, fix by @jfy133) - [#270](https://github.com/nf-core/taxprofiler/pull/270/files) Fixed warning for host removal index parameter, and improved index checks (♥ to @prototaxites for reporting, fix by @jfy133)
- [#274](https://github.com/nf-core/taxprofiler/pull/274/files) Substituted the samtools/bam2fq module with samtools/fastq module (fix by @sofstam) - [#274](https://github.com/nf-core/taxprofiler/pull/274/files) Substituted the samtools/bam2fq module with samtools/fastq module (fix by @sofstam)
- [#275](https://github.com/nf-core/taxprofiler/pull/275/files) Replaced function used for error reporting to more Nextflow friendly method (fix by @jfy133) - [#275](https://github.com/nf-core/taxprofiler/pull/275/files) Replaced function used for error reporting to more Nextflow friendly method (fix by @jfy133)
- [#286](https://github.com/nf-core/taxprofiler/pull/286/files) Runtime optimisation of MultiQC step via improved log file processing (fix by @Midnighter & @jfy133)
### `Dependencies` ### `Dependencies`

3
assets/multiqc_config.yml
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@ -37,8 +37,7 @@ run_modules:
sp: sp:
diamond: diamond:
contents: "diamond v" fn_re: ".*.diamond.log$"
num_lines: 10
fastqc/data: fastqc/data:
fn_re: ".*(fastqc|falco)_data.txt$" fn_re: ".*(fastqc|falco)_data.txt$"
fastqc/zip: fastqc/zip:

7
workflows/taxprofiler.nf
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@ -273,7 +273,12 @@ workflow TAXPROFILER {
ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
if ( params.preprocessing_qc_tool == 'falco' ) { if ( params.preprocessing_qc_tool == 'falco' ) {
ch_multiqc_files = ch_multiqc_files.mix(FALCO.out.txt.collect{it[1]}.ifEmpty([])) // only mix in files acutally used by MultiQC
ch_multiqc_files = ch_multiqc_files.mix(FALCO.out.txt
.map { meta, reports -> reports }
.flatten()
.filter { path -> path.name.endsWith('_data.txt')}
.ifEmpty([]))
} else { } else {
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
} }