nf-core/diaproteomics
Automated quantitative analysis of DIA proteomics mass spectrometry measurements.
22.10.6.
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Define where the pipeline should find input data and save output data.
Input sample sheet (containing path and meta data of raw or mzML files)
stringUse this to specify a sample sheet table including your input raw or mzml files as well as their metainformation such as BatchID, MSstats_Condition and MSstats_BioReplicate (of note: the BioReplicate column is optional). For example:
| Sample | BatchID | MSstats_Condition | MSstats_BioReplicate | Spectra_Filepath |
| -----|:------------:| ----------:|----------:|------------------------------------------:|
| 1 | MelanomaStudy | Malignant | BioReplicate1 | data/Melanoma_DIA_standard_rep1.raw |
| 2 | MelanomaStudy | Malignant | BioReplicate1 | data/Melanoma_DIA_standard_rep2.raw |
| 3 | MelanomaStudy | Benign | BioReplicate2 | data/SkinTissue_DIA_standard_rep1.raw |
| 4 | MelanomaStudy | Benign | BioReplicate2 | data/SkinTissue_DIA_standard_rep2.raw |
| 5 | BreastCancerStudy | Malignant | BioReplicate1 | data/BreastCancer_DIA_standard_rep1.raw |
| 6 | BreastCancerStudy | Malignant | BioReplicate1 | data/BreastCancer_DIA_standard_rep2.raw |
| 7 | BreastCancerStudy | Benign | BioReplicate2 | data/BreastTissue_DIA_standard_rep1.raw |
| 8 | BreastCancerStudy | Benign | BioReplicate2 | data/BreastTissue_DIA_standard_rep2.raw |
Input sample sheet of spectral libraries (tsv, pqp, TraML)
stringUse this to specify a sample sheet table including your input spectral library files as well as their metainformation such as BatchID and MSstats_Condition. For example:
| Sample | BatchID | Library_Filepath |
| -----|:------------:|------------------------------------------:|
| 1 | MelanomaStudy | data/Melanoma_library.tsv |
| 2 | BreastCancerStudy | data/BraCa_library.tsv |
Path to internal retention time standard sample sheet (tsv, pqp, TraML)
stringUse this to specify a sample sheet table including your input internal retention time spectral library files as well as their metainformation such as BatchID and MSstats_Condition. For example:
| Sample | BatchID | irt_Filepath |
| -----|:------------:|------------------------------------------:|
| 1 | MelanomaStudy | data/Melanoma_irt_library.tsv |
| 2 | BreastCancerStudy | data/BraCa_irt_library.tsv |
The output directory where the results will be saved.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
Set this flag if the spectral library should be generated using EasyPQP from provided DDA data - identification search results and corresponding raw data.
booleanInput sample sheet to use for library generation eg. DDA raw data (mzML) and DDA identification data (pepXML, mzid, idXML)
stringUse this to specify a sample sheet table including your input DDA raw or mzml files as well as their corresponding peptide identification files and BatchID metainformation. For example:
| Sample | BatchID | Spectra_Filepath | Id_Filepath |
| -----|:------------:| ----------:|------------------------------------------:|
| 1 | MelanomaStudy | data/Melanoma_DDA_rep1.mzML | data/Melanoma_DDA_rep1.pepXML |
| 2 | MelanomaStudy | data/Melanoma_DDA_rep2.mzML | data/Melanoma_DDA_rep2.pepXML |
| 3 | BreastCancerStudy | data/BraCa_DDA_rep1.mzML | data/BraCa_DDA_rep1.pepXML |
| 4 | BreastCancerStudy | data/BraCa_DDA_rep2.mzML | data/BraCa_DDA_rep2.pepXML |
PSM fdr threshold to align peptide ids with reference run.
number0.01Minimum number of transitions for assay
integer4Maximum number of transitions for assay
integer6Method for generating decoys
stringSet this flag if using a spectral library that already includes decoy sequences and therefor skip assay and decoy generation.
booleanPath to unimod file needs to be provided
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/diaproteomics/unimod.xmlExample file:
https://raw.githubusercontent.com/nf-core/test-datasets/diaproteomics/unimod.xml
Set this flag if you only want to generate spectral libraries from DDA data
booleanSet this flag if pseudo internal retention time standards should be generated using EasyPQP from provided DDA data - identification search results and corresponding raw data.
booleanNumber of pseudo irts selected from dda identifications based on the best q-value
integer250Set this flag if pseudo irts should be selected from the 1st and 4th RT quantile only
booleanSet this flag if the libraries defined in the input or by generation should be merged according to the BatchID
booleanSet this flag if pairwise RT alignment should be applied to libraries when merging.
booleanMinimum number of peptides to compute RT alignment during pairwise merging of libraries
integer100Mass tolerance for transition extraction (ppm)
integer30Unit for mz window
stringppmMass tolerance for precursor transition extraction (ppm)
integer10Unit for mz window
stringppmRT window for transition extraction (seconds)
integer600Minimal random mean squared error for irt RT alignment
number0.95Number of bins defined for the RT Normalization
integer10Number of bins that have to be covered for the RT Normalization
integer8Method for irt RT alignment for example
stringForce the analysis of the OpenSwathWorkflow despite severe warnings
booleanWhether to use ms1 information for scoring and extraction
booleantrueMinimal distance to the upper edge of a Swath window to still consider a precursor, in Thomson
integerSet mode whether to work in memory or to store data as cache first
stringMachine learning classifier used for pyprophet target / decoy separation
stringMS Level of pyprophet FDR calculation
stringAbstraction level of pyrophet FDR calculation
stringThreshold for pyprophet FDR filtering on peakgroup abstraction level
number0.01Threshold for pyprophet FDR filtering on peptide abstraction level
number0.01Threshold for pyprophet FDR filtering on protein abstraction level
number0.01Start for pyprophet non-parametric pi0 estimation
number0.1End for pyprophet non-parametric pi0 estimation
number0.5Steps for pyprophet non-parametric pi0 estimation
number0.05DIAlignR global alignment FDR threshold: After the chromatogram alignment all peaks should still satisfy the global alignment FDR threshold.
number0.01DIAlignR analyte FDR threshold: Before the chromatogram alignment only peaks satisfying this threshold will be matched across runs.
number0.01DIAlignR unalignment FDR threshold: XICs below this threshold will be considered valid without any alignment.
number0.01DIAlignR alignment FDR threshold: After the chromatogram alignment aligned peaks should satisfy this threshold.
number0.05DIAlignR query FDR threshold: During the chromatogram alignment only peaks satisfying this maximum FDR threshold will be considered as potential matches.
number0.05DIAlignR XICfilter parameter
stringWhether DIAlignR should be executed using multithreading (may cause errors)
booleantrueSet this flag if statistical normalization and visualizations should be generated using MSstats
booleantrueSet this flag if output plots should be generated.
booleantrue- BarChartProtein/Peptide Counts
- Pie Chart: Peptide Charge distribution
- Density Scatter: Library vs run RT deviations for all identifications
- Heatmap: Peptide quantities across MS runs
- Pyprophet score plots
In addition MSstats will run and export comparative protein statistics plots such as Volcano plots if protein level is specified.
Optional mzTab export (Warning: the mzTab format is not yet well supported for DIA)
booleanLess common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Boolean whether to validate parameters against the schema at runtime
booleantrueEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$This works exactly as with --email, except emails are only sent if the workflow is not successful.
Send plain-text email instead of HTML.
booleanSet to receive plain-text e-mails instead of HTML formatted.
Do not use coloured log outputs.
booleanSet to disable colourful command line output and live life in monochrome.
Directory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoShow all params when using --help
booleanSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^[\d\.]+\s*.(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^[\d\.]+\.*(s|m|h|d)$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterProvide git commit id for custom Institutional configs hosted at nf-core/configs. This was implemented for reproducibility purposes. Default: master.
## Download and use config file with following git commit id
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96
Base directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell nextflow where to find them with the custom_config_base option. For example:
## Download and unzip the config files
cd /path/to/my/configs
wget https://github.com/nf-core/configs/archive/master.zip
unzip master.zip
## Run the pipeline
cd /path/to/my/data
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
Note that the nf-core/tools helper package has a
downloadcommand to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.
Institutional configs hostname.
stringInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
string