helixforge parallel tasks

Expand a command template over the plan → an executor-agnostic task file.

Step 2 of the chunked path. Expands a command template over every chunk in plan.json; the default template is a per-chunk helixforge reconcile built from the inputs you attach, so it works out of the box. Run the resulting file with any executor (GNU parallel, a Slurm array, xargs, HyperShell), then parallel aggregate the per-chunk outputs.

Template placeholders, substituted per chunk: {chunk_id} {region} {seqid} {start} {end} {start_0} {end_0} {size} {id_start} {novel_start} {output_dir} ({region}/{start_0}/{end_0} are internal 0-based; {seqid}/{start}/{end} are 1-based inclusive for the CLI.)

Output:

-o/--output: the task file, one command per chunk (one line each)
--wrapper: an optional reusable per-task wrapper script (with --wrapper-setup lines) so cluster setup runs once per task

Options

Option	Description
`--genome`	Genome FASTA (required). (required)
`--helixer`	Helixer GFF3 (required). (required)
`--helixer-h5`	Helixer confidence HDF5: a combined file, the '_input.h5' metadata half, or the '_predictions.h5' softmax half (the partner half is auto-detected as the sibling, or named via --helixer-input-h5).
`--helixer-input-h5`	Helixer '_input.h5' metadata half (coordinate mapping). Needed only when --helixer-h5 is a bare '_predictions.h5' whose '*_input.h5' sibling is not co-located. Mirrors 'confidence --input-h5'.
`--stringtie`	StringTie GTF, one per sample. Comma-separated or repeated. (repeatable)
`--stringtie-list`	File of StringTie GTF paths, one per line (blank lines and # comments ignored).
`--bam`	RNA-seq BAM. Comma-separated or repeated. (repeatable)
`--bam-list`	File of BAM paths, one per line (blank lines and # comments ignored).
`--bigwig`	Coverage bigWig. Comma-separated or repeated. (repeatable)
`--bigwig-list`	File of bigWig paths, one per line (blank lines and # comments ignored).
`--star-sj`	STAR SJ.out.tab. Comma-separated or repeated. (repeatable)
`--star-sj-list`	File of SJ.out.tab paths, one per line (blank lines and # comments ignored).
`--miniprot`	miniprot GFF for backstop CDS projection. Not a substitute for --protein-db; does not enable Mikado.
`--protein-db`	Protein FASTA for DIAMOND homology. Required (with StringTie) to enable Mikado reconciliation and isoform discovery.
`--te-annotation`	EDTA TE GFF3. Flags TE-overlapping models (TE_OVERLAP) and reclassifies good-ORF genes above --te-overlap-threshold as transposable_element. Uses the EDTA Classification order; knob/satellite/low-complexity never gate.
`--te-overlap-threshold`	Model-fraction TE overlap at/above which a good-ORF gene is reclassified transposable_element (default 0.5). (default: `0.5`)
`--te-class`	EDTA Classification order to treat as a TE (repeatable). Default covers true TE orders (LTR, DNA, MITE, TIR, Helitron, LINE, SINE) and excludes knob/satellite/low-complexity. (repeatable)
`--transdecoder-bin-dir`
`--backstop-transdecoder`, `--no-backstop-transdecoder`	(default: `False`)
`--portcullis-bin`
`--mikado-bin`	(default: `mikado`)
`--diamond-bin`	(default: `diamond`)
`--mikado-configure`, `--no-mikado-configure`	(default: `True`)
`--functional-annotation`, `--no-functional-annotation`	Run the opt-in functional-annotation hook (InterProScan / eggNOG). (default: `False`)
`--functional-tool`	Annotation tool(s) to run for --functional-annotation. (choices: interproscan/eggnog/both; default: `interproscan`)
`--functional-db`	eggNOG data dir (required for --functional-tool eggnog/both).
`--interproscan-bin`	InterProScan binary (bare command or absolute path). (default: `interproscan.sh`)
`--eggnog-bin`	eggNOG-mapper binary (bare command or absolute path). (default: `emapper.py`)
`--transl-table`	NCBI genetic-code table id for CDS validation (default 1 = standard nuclear code). (default: `1`)
`--transl-table-map`	Per-seqid genetic-code overrides; lines 'seqid=table' (e.g. chrMt=1, chrPt=11). 'seqid<TAB/space>table' also accepted. Overrides --transl-table for the named seqids.
`--scoring-profile`	(choices: strict/permissive; default: `strict`)
`--helixer-reference`, `--no-helixer-reference`	Inject Helixer as is_reference=true. (default: `True`)
`--helixer-support-weight`	Scale external helixer_support (0 disables coupling). (default: `1.0`)
`--output-prefix`	(default: `helixforge`)
`--report-path`
`--id-map-path`
`--work-dir`
`--region`	seqid or seqid:start-end.
`--chunk-id`
`--id-base`	Lowest HFG number for this chunk's reserved range. (default: `1`)
`--novel-base`	Lowest HFG number for this chunk's novel sub-range. (default: `90000`)
`--procs`	(default: `1`)
`--threads`	(default: `4`)
`--min-tpm`	(default: `0.5`)
`--min-samples`	(default: `1`)
`--coverage-threshold`	(default: `2.0`)
`--near-zero-coverage`	(default: `0.1`)
`--as-report`, `--no-as-report`	(default: `True`)
`--only-confirmed-introns`, `--allow-unconfirmed-introns`	(default: `True`)
`--max-isoforms`	(default: `5`)
`--keep-retained-introns`, `--drop-retained-introns`	(default: `False`)
`--pad`, `--no-pad`	Unify isoform termini (the strongest consistency lever). (default: `True`)
`--chimera-split`, `--no-chimera-split`	(default: `True`)
`--flank`	(default: `200`)
`--reciprocal-overlap`	(default: `0.5`)
`--min-cds-overlap`	(default: `0.6`)
`--min-cdna-overlap`	(default: `0.6`)
`--admit-novel`, `--no-admit-novel`	(default: `False`)
`--novel-evidence-floor`
`--trace-primary`, `--no-trace-primary`	Elect the canonical/primary isoform per gene by ranked-choice voting (TRaCE) instead of highest combined_score. (default: `False`)
`--trace-max-aed`	TRaCE: max AED for a sample to vote for a candidate. (default: `0.5`)
`--trace-min-tpm`	TRaCE: min TPM for a sample's assembled transcript to vote. (default: `0.5`)
`--trace-min-overlap`	TRaCE: min proportion-overlap for a sample transcript to vote. (default: `0.5`)
`--trace-weight-domain`	TRaCE: domain-coverage voter weight. (default: `9.0`)
`--trace-weight-protein`	TRaCE: protein (CDS) length voter weight. (default: `6.0`)
`--trace-weight-cdna`	TRaCE: transcript (cDNA) length voter weight. (default: `3.0`)
`--trace-use-domain`, `--no-trace-use-domain`	TRaCE: include the domain-coverage voter when per-isoform domain coverage is available. (default: `True`)
`--short-cds-threshold`	(default: `300`)
`--short-exon-threshold`	(default: `10`)
`--long-intron-threshold`	(default: `100000`)
`--junction-tolerance`	(default: `0`)
`--junction-min-reads`	(default: `3`)
`--plan`	plan.json from `parallel plan`. (required)
`--command`	Command template with chunk placeholders ({chunk_id} {region} {seqid} {start} {end} {start_0} {end_0} {size} {id_start} {novel_start} {output_dir}). Default: a per-chunk `helixforge reconcile` built from the attached inputs.
`-o`, `--output`	Task file to write (one command per chunk). (default: `tasks.txt`)
`--output-dir`	Per-chunk output directory ({output_dir} placeholder). (default: `chunks`)
`--wrapper`	Also write a reusable per-task wrapper script (setup once).
`--wrapper-setup`	Setup line for the wrapper (module load / conda activate); repeatable. (repeatable)
`--include-logging`	Redirect each task's stdout/stderr to /logs/.log. (default: `False`)
`--helixforge-bin`	helixforge binary used in the default command template. (default: `helixforge`)

Examples

  # default template (per-chunk reconcile from the attached inputs)
  helixforge parallel tasks --plan plan.json \
      --genome maize.fa --helixer helixer.gff3 --helixer-h5 preds.h5 \
      --stringtie-list stringtie.list -o tasks.txt
  parallel -j 16 < tasks.txt          # or: hs cluster tasks.txt --num-tasks 16

  # full override + cluster setup wrapper
  helixforge parallel tasks --plan plan.json --genome g.fa --helixer h.gff3 \
      --command 'helixforge reconcile --genome g.fa --helixer h.gff3 \
                 --region {region} --id-base {id_start} \
                 --output-prefix {output_dir}/{chunk_id}' \
      --wrapper run_chunk.sh --wrapper-setup 'module load helixforge' -o tasks.txt