nf-core/diann @ 0.0.0-6c4ed3a
Summary
Generic DIA-NN module for running any DIA-NN operation including in-silico library generation, preliminary analysis, empirical library assembly, individual analysis, and final quantification
Get started
Add the following snippet to your workflow script to include this module.
include { DIANN } from 'nf-core/diann'
License
MIT License
Name
|
DIANN |
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meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
ms_files
file
|
MS data file(s) in mzML or Bruker .d format (can be single file or list). Thermo RAW files are only supported on Linux with DIA-NN 2.0+; older versions require conversion to mzML or .d format first. For preliminary/assembly/individual analysis, these are actual file paths. For final quantification with --use-quant, this should be an empty list. *.{mzML,raw,d}
|
ms_file_names
string
|
MS file basenames (not paths) as strings (can be single name or list). Used for final quantification step with --use-quant where only filenames are needed. For other analysis steps, this should be an empty list. Example: ['sample1.mzML', 'sample2.mzML'] or [] |
fasta
file
|
FASTA database file for peptide searches. Use a placeholder file (e.g., 'NO_FASTA_FILE') if not needed for the specific analysis step. *.{fasta,fa}
|
library
file
|
Spectral library file in .speclib or .tsv format. Use a placeholder file (e.g., 'NO_LIB_FILE') if not needed for the specific analysis step. *.{speclib,tsv}
|
quant
directory
|
Directory containing .quant files from previous DIA-NN analysis. When provided, enables --use-quant mode to reuse cached quantification results, improving performance for empirical library assembly and final quantification. Pass empty list [] if not needed. Files are staged as 'quant/*' in the work directory. |
log
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.log.txt
file
|
DIA-NN log file containing run information and recommended settings *.log.txt
|
gg_matrix
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
${prefix}.gg_matrix.tsv
file
|
Gene group-level quantification matrix. Filename is determined by the prefix (task.ext.prefix or meta.id). *.gg_matrix.tsv
|
pg_matrix
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
${prefix}.pg_matrix.tsv
file
|
Protein group-level quantification matrix. Filename is determined by the prefix (task.ext.prefix or meta.id). *.pg_matrix.tsv
|
pr_matrix
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
${prefix}.pr_matrix.tsv
file
|
Precursor-level quantification matrix (peptides across runs). Filename is determined by the prefix (task.ext.prefix or meta.id). *.pr_matrix.tsv
|
diann_quant
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.quant
file
|
Quantification results in .quant format (intermediate output for empirical library assembly and final quantification) *.quant
|
main_report
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
${prefix}.tsv
file
|
Main DIA-NN report in TSV format containing peptide and protein quantification. Filename is determined by the prefix (task.ext.prefix or meta.id). *.tsv
|
report_stats
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
${prefix}.stats.tsv
file
|
Report statistics including identification and quantification metrics. Filename is determined by the prefix (task.ext.prefix or meta.id). *.stats.tsv
|
final_speclib
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
${prefix}.speclib
file
|
Empirical spectral library refined from experimental data. Produced by the library assembly step, which combines predicted library information with actual MS measurements to improve search accuracy. *.speclib
|
report_parquet
tuple
meta
map
|
|---|