multiplesequencealign
nf-core/multiplesequencealign
Pipeline to run and benchmark multiple sequence alignment tools.
Key tools
Run it
nfclaw run multiplesequencealign --input samplesheet.csv --outdir results -profile dockernextflow run pipelines/multiplesequencealign/upstream -profile docker --input samplesheet.csv --outdir resultsnfclaw run multiplesequencealign --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
id | string | yes | matches ^\S+$ | |
fasta | string (file path) | no | matches ^\S+\.f(n|ast)?a$ | |
reference | string (file path) | no | matches ^\S+\.(f(n|ast)?a|ref)$ | |
optional_data | string | no | ||
template | string (file path) | no | matches ^\S+\.txt$ |
--input must match ^\S+\.(csv|tsv|yaml|yml|json)$.
For tabular CSV/TSV input, use this header (the columns the schema requires); fill each value per the table above and reference.md (no example value is invented here):
idAny of the optional columns above may be appended to the header when your data needs them: fasta, reference, optional_data, template.
From data files. --input may also be the data files — a directory (searched recursively), a quoted glob, or files (--input once per file) — from which nfclaw writes this samplesheet: id from file names; fasta, reference, optional_data, template from files matching their patterns, by sample name. Set other columns with --sheet-set COLUMN=VALUE. Preview it with --check; a run records it in <outdir>/provenance/ for replay.
Resources
Resource requests follow the pipeline's configs and selected profiles. nf-core's resource labels often assume a server — a single step can request far more memory than a workstation has, and retry rules can increase requests. If a run fails with Process requirement exceeds available memory (or CPUs), cap every request, and every retry, at what this machine actually has:
nfclaw run multiplesequencealign --input samplesheet.csv --outdir results -profile docker \ --limit-cpus 4 --limit-memory 15.GBnfclaw turns those into Nextflow's process.resourceLimits and passes them as a -c config — the mechanism nf-core prescribes for exactly this (docs). Set them to the machine's real capacity. --limit-time DURATION also caps how long any one task may run: a task that needs longer is stopped, and so is every retry, so set it only as a deliberate ceiling, never as a guess at how long the analysis takes. The generated config is kept in <outdir>/provenance/, so commands.sh replays the run under the same ceiling.
Nextflow engine
This release declares nextflowVersion = '!>=25.04.2'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run multiplesequencealign ... --nxf-ver 25.04.2--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Demo
nfclaw run multiplesequencealign --demo --outdir results # adds the upstream test profile (-profile test,docker)Samplesheet
A CSV with this header (the columns the schema requires). Fill each value per the constraints below; optional columns from the table may be appended.
id| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
id | string | required | matches ^\S+$ |
fasta | string (file path) | optional | matches ^\S+\.f(n|ast)?a$ |
reference | string (file path) | optional | matches ^\S+\.(f(n|ast)?a|ref)$ |
optional_data | string | optional | — |
template | string (file path) | optional | matches ^\S+\.txt$ |
Required parameters
--outdirstring (directory path)The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
Parameter explorer
51 parameters · 9 groupsEvery parameter from the pinned nextflow_schema.json. nfclaw checks explicit values before launch; complex rules use the pinned pipeline's runtime validation. Search, filter by group, and expand any parameter for its default, allowed values and constraints.
33 parameters · 18 hidden
Align options1
Build consensus alignment with M-COFFEE.
Eval options6
Extract total number of gaps and average number of gaps of the alignment.
Calculate the iRMSD of alignment.
Calculate the Sum of Pairs of alignment.
Calculate the Total Column Score of alignment.
Calculate the Transitive Consistency Score (TCS) of alignment.
Skip all of the evaluations computation on the msa.
Generic options1
Custom MultiQC yaml file containing HTML including a methods description.
Global options5
Produce uncompressed alignment files
Skip the conversion of pdb files to fasta.
Skip the preprocessing step for the input files.
Skip the validation of the input files.
Run on CPUs (default) or GPUs
Input Output options7
Email address for completion summary.
Path to the samplesheet file containing information about datasets to be aligned and evaluated (samplesheet).
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
Path to a folder containing all the optional data files to be used (e.g. structures).
Path to the input fasta file.
Suffix of the files given in the optional_data directory.
Input Tools options5
The aligner to be used.
Extra arguments for the aligner tool.
Extra arguments for the tree building tool.
Path to the file containing information about the tools to be deployed (toolsheet).
Tool to use for tree building.
Reports options4
Folder containing the main shiny app.
Skip the multiqc report generation.
Skip the shiny report generation.
Skip the visualization generation.
Stats options4
Calculate general statistics on input files.
Calculate the percentage similarity across the sequences in the input files.
Extract plddt from structure files. Only works if the files have been generated by AF2.
Skip all of the statistics computation on the fasta file.
Outputs
Results land in --outdir; the files and directory layout depend on the selected workflow, parameters and publication settings. Run metadata is normally placed in <outdir>/pipeline_info/ (execution report, software versions), when those outputs are enabled. The pinned tree includes MultiQC support; a report is produced only when its workflow step runs. --skip-multiqc true disables that report. nfclaw run also writes <outdir>/provenance/ with the exact params file and the run log, <outdir>/provenance/logs/run.log — the whole launch, whose last line states the outcome (Nextflow's own log is <outdir>/.nextflow.log); unless --no-provenance it adds a run manifest (pinned version, commit and exact command), input/output SHA-256 checksums, and a replayable commands.sh.
The exact output files and directory layout for this release are documented upstream: github.com/nf-core/multiplesequencealign/blob/1.1.1/docs/output.md
Check a run — in the foreground or the background — with nfclaw status <outdir>: success, still running, how it ended (with the error), or stopped without an outcome; exit 0 success, 3 running, 1 otherwise.