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Run FastQC and restore its citation text #76

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4895569
Run FastQC and restore its citation text
vinisalazar Aug 5, 2026
a7f6ab2
Swap FastQC for the fastq_shortreads_preprocess_qc subworkflow
vinisalazar Aug 5, 2026
21dfd94
Merge branch 'dev' into feat/run-fastqc
vinisalazar Aug 5, 2026
6613458
Drop the orphaned run-merging schema group and param
vinisalazar Aug 5, 2026
b46d2aa
Test FastQC output and document database version compatibility
vinisalazar Aug 5, 2026
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7 changes: 2 additions & 5 deletions subworkflows/local/utils_nfcore_funcprofiler_pipeline/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -182,8 +182,7 @@ def validateInputSamplesheet(input) {
// Generate methods description for MultiQC
//
def toolCitationText() {
// pending fastq_shortreads_preprocess_qc implementation
def text_qc = ""
def text_qc = ["Read quality was assessed with FastQC (Andrews 2010)."].join(' ').trim()

def text_humann = [
"Functional profiling was performed with",
Expand Down Expand Up @@ -221,9 +220,7 @@ def toolCitationText() {
}

def toolBibliographyText() {
//
//def text_qc = [!params.skip_preprocessing_qc ? "<li>Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available at: <a href=\"http://www.bioinformatics.babraham.ac.uk/projects/fastqc/\">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/</a></li>" : ""].join(' ').trim()
def text_qc = "" // pending implementation of fastq_shortreads_preprocess_qc subworkflow
def text_qc = [!params.skip_preprocessing_qc ? "<li>Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available at: <a href=\"http://www.bioinformatics.babraham.ac.uk/projects/fastqc/\">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/</a></li>" : ""].join(' ').trim()

def text_humann = [
params.run_humann_v3 || params.run_humann_v4 ? "<li>Beghini, F., McIver, L. J., Blanco-M\u00edguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Thomas, A. M., Manghi, P., Valles-Colomer, M., Weingart, G., Zhang, Y., Zolfo, M., Huttenhower, C., Franzosa, E. A., & Segata, N. (2021). Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife, 10, e65088. <a href=\"https://doi.org/10.7554/eLife.65088\">10.7554/eLife.65088</a></li>" : "",
Expand Down
8 changes: 8 additions & 0 deletions workflows/funcprofiler.nf
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Expand Up @@ -3,6 +3,7 @@
IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { FASTQC } from '../modules/nf-core/fastqc/main'
include { MULTIQC } from '../modules/nf-core/multiqc/main'
include { paramsSummaryMap } from 'plugin/nf-schema'
include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline'
Expand Down Expand Up @@ -61,6 +62,13 @@ workflow FUNCPROFILER {
samplesheet
)

if (!params.skip_preprocessing_qc) {
FASTQC(
DATAPREP.out.reads
)
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.map { _meta, zip -> zip })
}

DBPREP(
databases
)
Expand Down
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