denovotranscript
nf-core/denovotranscript
A pipeline for de novo transcriptome assembly of short reads from bulk RNA-seq
Key tools
Run it
nfclaw run denovotranscript --input samplesheet.csv --outdir results -profile dockernextflow run pipelines/denovotranscript/upstream -profile docker --input samplesheet.csv --outdir resultsnfclaw run denovotranscript --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 (file path) | yes | matches ^\S+\.f(ast)?q\.gz$ | |
fastq_2 | string (file path) | no | matches ^\S+\.f(ast)?q\.gz$ |
--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. The schema declares AWS iGenomes at s3://ngi-igenomes/igenomes/; selecting --genome <id> uses the paths in the pipeline's reference configuration. Access to that remote source is required. To supply your own reference, use e.g. --fasta; the rnaquast_options group in reference.md lists every reference option. Set --igenomes-ignore true to disable the lookup entirely. Confirm the selected reference's paths and source in the pinned upstream/nextflow.config and upstream/conf/ before running.
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 denovotranscript --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 = '!>=24.04.2'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run denovotranscript ... --nxf-ver 24.04.2--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Demo
nfclaw run denovotranscript --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 (file path) | required | matches ^\S+\.f(ast)?q\.gz$ |
fastq_2 | string (file path) | optional | matches ^\S+\.f(ast)?q\.gz$ |
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
52 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.
31 parameters · 21 hidden
Assembly options6
Assemblers to use. Possible options include trinity, trinity_no_norm (trinity without normalized reads), and rnaspades.
Extra arguments for tr2aacds.pl. For example, '-MINAA=20'
Extra arguments to pass to Trinity command in addition to defaults. Applies to both trinity and trinity_no_norm.
Include soft filtered transcripts (in addition to the medium filtered transcripts) from rnaSPAdes in the input to EvidentialGene tr2aacds.
Include hard filtered transcripts (in addition to medium filtered transcripts) from rnaSPAdes in the input to EvidentialGene tr2aacds.
Set strand-specific type for rnaSPAdes. Use rf when first read in pair corresponds to reverse gene strand (antisense data, e.g. obtained via dUTP protocol) and fr otherwise (forward).
Busco options4
Path to BUSCO config file.
The BUSCO lineage to use, or auto to automatically select lineage
Path to local BUSCO lineages directory.
The mode to run BUSCO in. One of genome, proteins, or transcriptome
Fastqc Fastp options6
File in FASTA format containing possible adapters to remove. Accepted formats: *.{fasta,fna,fas,fa}
Extra arguements for fastp. For example, --trim_front1 15 --trim_front2 15 --trim_tail1 5 --trim_tail2 5{:bash}
Specify true to save all merged reads to the a file ending in *.merged.fastq.gz
Specify true to save files that failed to pass trimming thresholds ending in *.fail.fastq.gz
Skip the fastp process if true
Skip FastQC processes if true
Generic options1
Custom MultiQC yaml file containing HTML including a methods description.
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.
Path to fasta file (not compressed) containing a transcriptome assembly. Only needed if --skip_assembly is True.
Rnaquast options2
Path to FASTA genome file.
File with gene coordinates in GTF/GFF format (needs information about parent relations). rnaQUAST authors recommend to use files downloaded from GENCODE or Ensembl.
Salmon options1
Override library type inferred based on strandedness defined in meta object. A for auto.
Sortmerna options3
Enable the removal of reads derived from ribosomal RNA using SortMeRNA.
Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA.
If this option is specified, intermediate FastQ files containing non-rRNA reads will be saved in the results directory.
Transrate options1
Path to FASTA file of reference set of proteins or transcripts from a related species
Workflow options2
Whether the pipeline should only perform quality control, and skip assembly and quantification.
Whether the pipeline should skip assembly steps, and only perform quality control of reads and quantification. --transcript_fasta must be provided if True.
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. 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/denovotranscript/blob/1.2.1/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.