reportho
nf-core/reportho
A pipeline for ortholog fetching and analysis
Key tools
Run it
nfclaw run reportho --input samplesheet.csv --outdir results -profile dockernextflow run pipelines/reportho/upstream -profile docker --input samplesheet.csv --outdir resultsnfclaw run reportho --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
id | string | no | matches ^\S+$ | |
query | string | no | matches ^\S+$ | |
fasta | string (file path) | no | matches ^\S+\.fa(sta)?$ |
--input must match ^\S+\.csv$.
The samplesheet is a CSV with this header; fill each value per the table above and reference.md (no example value is invented here):
id,query,fastaFrom 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 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 reportho --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 = '!>=25.04.0'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run reportho ... --nxf-ver 25.04.0--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Demo
nfclaw run reportho --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.
id,query,fasta| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
id | string | optional | matches ^\S+$ |
query | string | optional | matches ^\S+$ |
fasta | string (file path) | optional | matches ^\S+\.fa(sta)?$ |
Required parameters
--inputstring (file path)Path to comma-separated file containing information about the samples in the experiment.
Constraint · matches ^\S+\.csv$
--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 · 6 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
Downstream options1
Skip report generation.
Generic options4
Display the help message.
Display the full detailed help message.
Custom MultiQC yaml file containing HTML including a methods description.
Display hidden parameters in the help message (only works when --help or --help_full are provided).
Input Output options5
Email address for completion summary.
Path to comma-separated file containing information about the samples in the experiment.
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.
Output intermediate files, including specific prediction lists.
Ortholog options21
Path to the EggNOG ID map.
Path to the EggNOG database.
Use local databases for the analysis.
Minimum sequence coverage in Diamond
Minimum sequence identity in Diamond
Minimum score for the ortholog search.
Run the pipeline in offline mode. Overrides all online database flags.
Path to the Ensembl-OMA ID map.
Path to the OMA database.
Path to the RefSeq-OMA ID map.
Path to the Uniprot-OMA ID map.
Path to the OrthoInspector database.
The version of the OrthoInspector database to use.
Path to the PANTHER database.
Use EggNOG for the ortholog search.
Skip merging IDs based on sequence.
Skip using OMA for the ortholog search.
Skip using OrthoInspector for the ortholog search.
Skip using PANTHER for the ortholog search.
Use all ortholog search methods. Will mix online and local methods if needed. Overrides all individual database flags.
Use centroid strategy for the ortholog search. Overrides min_score.
Process Skipping options2
Skip MultiQC.
Skip the ortholog plots.
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/reportho/blob/1.1.0/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.