Examples 
¶
Ready-to-run examples for popular Nextflow pipelines with nf-lamin artifact tracking. Source files are in the examples/ directory. All examples follow the best-practice config pattern.
nf-core/rnaseq¶
nf-core/rnaseq is a bioinformatics pipeline for bulk RNA-seq analysis. It produces gene count matrices, alignment files, QC reports, and more.
Running¶
export NXF_VER=25.10.4
nextflow run nf-core/rnaseq \
-r 3.23.0 \
-profile docker,test \
-c examples/rnaseq/nextflow.config \
--outdir output/rnaseq/
The test profile runs on publicly available test data (chr22 subset).
Configuration¶
The examples/rnaseq/nextflow.config tracks the following:
Input artifacts: samplesheet (via include_paths), FASTQ reads, reference FASTA, GTF/GFF annotation files.
Output artifacts (enabled): MultiQC report, merged gene count matrices (counts, TPM, lengths, scaled), merged transcript quantification files, SummarizedExperiment RDS files, transcript-to-gene mapping.
Output artifacts (disabled, opt-in): per-sample Salmon quant files, BAM files, BAM indexes, BigWig coverage tracks, DESeq2 QC outputs, featureCounts tables, FastQC reports/zips, MultiQC raw data, trimming reports, pipeline info.
plugins {
id '[email protected]'
}
lamin {
instance = "laminlabs/lamindata"
api_key = secrets.LAMIN_API_KEY
input_artifacts {
enabled = true
rules {
samplesheet { include_paths = { params.input }; kind = 'dataset'; order = 1 }
fastq_reads { pattern = '.*\\.fastq(\\.gz)?$'; kind = 'dataset'; order = 2 }
reference_fasta { pattern = '.*\\.(fasta|fa)(\\.gz)?$'; kind = 'dataset'; order = 3 }
annotation { pattern = '.*\\.(gtf|gff|gff3)(\\.gz)?$'; kind = 'dataset'; order = 4 }
}
}
output_artifacts {
enabled = true
key = [relativize: params.outdir]
exclude_pattern = '.*'
rules {
// Enabled by default
multiqc_report { type = 'include'; pattern = '.*multiqc_report\\.html$'; kind = 'report' }
gene_counts { type = 'include'; pattern = '.*salmon\\.merged\\.gene_(counts|tpm|counts_length_scaled|counts_scaled|lengths)\\.tsv$'; kind = 'dataset' }
summarized_experiment { type = 'include'; pattern = '.*\\.SummarizedExperiment\\.rds$'; kind = 'dataset' }
// Disabled (set enabled = true to include)
bam_files { type = 'include'; enabled = false; pattern = '.*\\.bam$'; kind = 'dataset' }
bigwig_files { type = 'include'; enabled = false; pattern = '.*\\.bigWig$'; kind = 'dataset' }
// ... see full config for all rules
}
}
}
nf-core/scrnaseq¶
nf-core/scrnaseq is a bioinformatics pipeline for single-cell RNA-seq analysis. It supports multiple aligners (STARSolo, Cellranger, Kallisto, Alevin) and produces count matrices in multiple formats.
Running¶
export NXF_VER=25.10.4
nextflow run nf-core/scrnaseq \
-r 4.1.0 \
-profile docker,test \
-c examples/scrnaseq/nextflow.config \
--outdir output/scrnaseq/
The test profile runs on a small chr19 mouse dataset with STARSolo.
Configuration¶
The examples/scrnaseq/nextflow.config tracks the following:
Input artifacts: samplesheet (via include_paths), FASTQ reads, reference FASTA, GTF annotation files.
Output artifacts (enabled): MultiQC report, combined filtered/raw h5ad count matrices, per-sample filtered/raw h5ad count matrices.
Output artifacts (disabled, opt-in): RDS conversions (Seurat/SingleCellExperiment), BAM files, STARSolo filtered/raw mtx matrices, STARSolo summary statistics, FastQC reports/zips, MultiQC raw data, pipeline info.
plugins {
id '[email protected]'
}
lamin {
instance = "laminlabs/lamindata"
api_key = secrets.LAMIN_API_KEY
input_artifacts {
enabled = true
rules {
samplesheet { include_paths = { params.input }; kind = 'dataset'; order = 1 }
fastq_reads { pattern = '.*\\.fastq(\\.gz)?$'; kind = 'dataset'; order = 2 }
reference_fasta { pattern = '.*\\.(fasta|fa)(\\.gz)?$'; kind = 'dataset'; order = 3 }
annotation { pattern = '.*\\.(gtf|gff|gff3)(\\.gz)?$'; kind = 'dataset'; order = 4 }
}
}
output_artifacts {
enabled = true
key = [relativize: params.outdir]
exclude_pattern = '.*'
rules {
// Enabled by default
multiqc_report { type = 'include'; pattern = '.*multiqc_report\\.html$'; kind = 'report' }
combined_filtered_h5ad { type = 'include'; pattern = '.*/mtx_conversions/combined_filtered_matrix\\.h5ad$'; kind = 'dataset' }
combined_raw_h5ad { type = 'include'; pattern = '.*/mtx_conversions/combined_raw_matrix\\.h5ad$'; kind = 'dataset' }
sample_filtered_h5ad { type = 'include'; pattern = '.*/mtx_conversions/.+/.+_filtered_matrix\\.h5ad$'; kind = 'dataset' }
// Disabled (set enabled = true to include)
rds_conversions { type = 'include'; enabled = false; pattern = '.*/mtx_conversions/.*\\.rds$'; kind = 'dataset' }
bam_files { type = 'include'; enabled = false; pattern = '.*\\.bam$'; kind = 'dataset' }
// ... see full config for all rules
}
}
}
bigbio/quantms¶
bigbio/quantms is a proteomics pipeline for data-dependent acquisition (DDA) quantitative mass spectrometry. It produces mzTab results, MSstats tables, and QC reports.
Running¶
export NXF_VER=25.10.4
nextflow \
-trace ai.lamin \
run bigbio/quantms \
-r 1.7.0 \
-profile docker,test_lfq \
-c examples/quantms/nextflow.config \
--outdir output/quantms/
The test_lfq profile runs a label-free quantification workflow on publicly available test data.
Configuration¶
The examples/quantms/nextflow.config tracks the following:
Input artifacts: SDRF experimental design files, protein database FASTA files.
Output artifacts (enabled): mzTab identification/quantification results, MSstats input table, MSstats comparison results, Triqler input table, pMultiQC report.
Output artifacts (disabled, opt-in): ConsensusXML intermediate files, spectra statistics (parquet), pMultiQC raw data and plots, pipeline info.
plugins {
id '[email protected]'
}
lamin {
instance = "laminlabs/lamindata"
api_key = secrets.LAMIN_API_KEY
input_artifacts {
enabled = true
rules {
sdrf { pattern = '.*\\.sdrf\\.tsv$'; kind = 'dataset' }
fasta { pattern = '.*\\.(fasta|fa)(\\.gz)?$'; kind = 'dataset' }
}
}
output_artifacts {
enabled = true
key = [relativize: params.outdir]
exclude_pattern = '.*'
rules {
// Enabled by default
mztab { type = 'include'; pattern = '.*\\.mzTab$'; kind = 'dataset' }
msstats_in { type = 'include'; pattern = '.*msstats_in\\.csv$'; kind = 'dataset' }
multiqc_report { type = 'include'; pattern = '.*/pmultiqc/multiqc_report\\.html$'; kind = 'report' }
// Disabled (set enabled = true to include)
consensusxml { type = 'include'; enabled = false; pattern = '.*\\.consensusXML$'; kind = 'dataset' }
spectra_statistics { type = 'include'; enabled = false; pattern = '.*/mzml_statistics/.*\\.parquet$'; kind = 'dataset' }
// ... see full config for all rules
}
}
}