circdna
nf-core/circdna
Pipeline for the identification of circular DNAs
Key tools
Run it
nfclaw run circdna --input samplesheet.csv --outdir results --input-format <input_format> --circle-identifier <circle_identifier> -profile dockernextflow run pipelines/circdna/upstream -profile docker --input samplesheet.csv --outdir results --input_format <input_format> --circle_identifier <circle_identifier>nfclaw run circdna --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
sample | string | yes | matches ^\S+$ | |
fastq_1 | string | yes | matches ^\S+\.f(ast)?q\.gz$ | |
fastq_2 | string | no |
--input must match ^\S+\.csv$.
The samplesheet is a CSV with this header (the columns the schema requires); fill each value per the table above and reference.md (no example value is invented here):
sample,fastq_1Any of the optional columns above may be appended to the header when your data needs them: fastq_2.
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: sample from file names; fastq_1/fastq_2 from FastQ files (mates paired by _R1/_R2, or by _1/_2 when their read names show they are mates). Set other columns with --sheet-set COLUMN=VALUE. Preview it with --check; a run records it in <outdir>/provenance/ for replay.
Reference genome
No reference genome is set by default: supply your own reference. A genome name alone does not specify where reference files come from. Confirm the selected reference's paths and source in the pinned upstream/nextflow.config and upstream/conf/ before running. To supply your own reference, use e.g. --fasta; the reference_genome_options group in reference.md lists every reference option. Set --igenomes-ignore true to disable the lookup entirely.
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 circdna --input samplesheet.csv --outdir results --input-format <input_format> --circle-identifier <circle_identifier> -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 = '!>=23.04.0'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run circdna ... --nxf-ver 23.04.0--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Nextflow 23.04.0 predates process.resourceLimits (24.04.0), so --limit-* cannot be combined with this pin — nfclaw refuses it rather than run without the ceiling; cap resources with the release's own --max-cpus, --max-memory, --max-time instead.
Demo
nfclaw run circdna --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.
sample,fastq_1| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
sample | string | required | matches ^\S+$ |
fastq_1 | string | required | matches ^\S+\.f(ast)?q\.gz$ |
fastq_2 | string | optional | — |
Required parameters
--inputstring (file path)Path to comma-separated file containing information about the samples in the experiment.
Constraint · matches ^\S+\.csv$
--input-formatstringSpecify input format. Default *FASTQ*. Options 'FASTQ' or 'BAM'.
--outdirstring (directory path)The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
--circle-identifierstringSpecifies the circular DNA identification algorithm to use - available 'circle_map_realign', 'circle_map_repeats', 'circle_finder', 'circexplorer2', and 'ampliconarchitect'. Multiple circle_identifier's can be specified with a comma-separated string. E.g. --circle_identifier 'circle_map_realign,unicycler'.
Parameter explorer
58 parameters · 12 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.
34 parameters · 24 hidden
Amplicon Architect options5
Copy Number Threshold for seeds to be considered by AmpliconArchitect.
Absolute path to the downloaded AA data repository. See AmpliconArchitect.
Path to cnn file inside the AmpliconArchitect Data Repository of the respective reference genome. By default it uses the 'aa_data_repo' and the 'reference_build' input to construct the file path.
Path to the directory containing the mosek license file 'mosek.lic'.
When running AmpliconArchitect, specify reference build ['GRCh37', 'GRCh38', 'mm10']. This is *mandatory* to match fasta and AA reference build!
Circdna Identifier options1
Specifies the circular DNA identification algorithm to use - available 'circle_map_realign', 'circle_map_repeats', 'circle_finder', 'circexplorer2', and 'ampliconarchitect'. Multiple circle_identifier's can be specified with a comma-separated string. E.g. --circle_identifier 'circle_map_realign,unicycler'.
Circle Finder options1
Store bed files created during Circle_finder run.
Circle Map options1
Store bam file with read candidates for circle-map circular dna calling.
Generic options1
Custom MultiQC yaml file containing HTML including a methods description.
Input Output options7
Specify if bam file is sorted [false, true]. If false or not specified, bam file will be sorted!
Email address for completion summary.
Path to comma-separated file containing information about the samples in the experiment.
Specify input format. Default *FASTQ*. Options 'FASTQ' or 'BAM'.
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.
Specify if sorted bam file should be saved [false, true]. Default: false
Process Skipping options5
Keep read duplications marked by picard MarkDuplicates.
Store bam with marked duplicate reads.
Skip Picard MarkDuplicates and duplicate filtering
Skip MultiQC step.
Skip all QC steps except for MultiQC.
Read Trimming options8
Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads).
Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only).
Save the merged FastQ files in the results directory.
Save the trimmed FastQ files in the results directory.
Skip the adapter trimming step.
Instructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.
Instructs Trim Galore to remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed.
Instructs Trim Galore to apply the --nextseq=X option, to trim based on quality after removing poly-G tails.
Reference Genome options4
Path to the directory containg the BWA index files.
Path to FASTA genome file.
Name of iGenomes reference.
Save the index reference fasta in the results directory.
Unicycler options1
Store fastq intermediate files created during Uniycler run.
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/circdna/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.