CLI Reference

Alpha

HOMERun is in alpha testing. Nothing here is finalized, and some flags and behaviors are still rough or subject to change.

Full usage for the homerun command. This page mirrors homerun --help.

On start, homerun prints:

    __  __
   / / / /___  ____ ___  ___  _______  ______
  / /_/ / __ \/ __ `__ \/ _ \/ ___/ / / / __ \
 / __  / /_/ / / / / / /  __/ /  / /_/ / / / /
/_/ /_/\____/_/ /_/ /_/\___/_/   \__,_/_/ /_/

RNA-seq analysis pipeline for HPC clusters.
Version: 1.0.0

Usage

homerun [-h] [--project PROJECT] [--log-path LOG_PATH]
        [--steps {trim,align,tagdirs,tagdirs-combo,bedgraphs,tss,ritrie,qc,stability,report} ...]
        [--sample-index SAMPLE_INDEX] [--group-index GROUP_INDEX]
        [--skip-prepare] [--force] [--only-prepare]
        [--count-samples] [--count-groups] [--check-rerun] [--stage-raw]
        [--aligner {star,hisat2}] [--genome-index GENOME_INDEX] [--genome GENOME]
        [--gtf GTF] [--copy-src COPY_SRC] [--threads THREADS]
        [--trim-adapter TRIM_ADAPTER] [--trim-min TRIM_MIN] [--trim-max TRIM_MAX]
        [--ntag-threshold NTAG_THRESHOLD] [--skip-chr SKIP_CHR]
        [--cleanup-intermediates]
        [--star-filter-multimap STAR_FILTER_MULTIMAP]
        [--star-multimap-out STAR_MULTIMAP_OUT]
        [--star-multimap-order {Random,Old_2.4}]
        [--hisat2-strandness {F,R,FR,RF}]

Options

Flag	Description
-h, --help	Show the help message and exit.
--project PROJECT	Project root (default: $CSRNA_PROJECT or CWD).
--log-path LOG_PATH	Pipeline log file path (overrides CSRNA_LOG; else a timestamped file under <project>/logs/).
--steps STEP [STEP ...]	Run only these steps (still executed in canonical order). Choices: trim, align, tagdirs, tagdirs-combo, bedgraphs, tss, ritrie, qc, stability, report.
--sample-index N	0-based index into RawData R1 files. Restricts trim/align/tagdirs to one leaf run. Used by SLURM_ARRAY_TASK_ID.
--group-index N	0-based index into the sample list. Restricts tagdirs-combo/bedgraphs/tss to one Species/Sample group. Used by SLURM_ARRAY_TASK_ID.
--skip-prepare	Skip folder creation / raw copy / STARIndex setup.
--force, --overwrite	Allow rerunning on a project that already has pipeline outputs (Trimmed/, Aligned/, TagDirs/, bedGraphs/, TSS/, QC/). Without this flag, HOMERun refuses to start (and touches nothing) if any of those exist, to avoid overwriting a previous run. No effect on --count-samples/--count-groups/--stage-raw.
--only-prepare	Run prepare and exit.
--count-samples	Print the number of leaf runs (R1 files in RawData) and exit.
--count-groups	Print the number of Species/Sample groups and exit.
--check-rerun	Preflight for wrapper scripts: exit 1 (with a message) if every staged sample already has a populated QC/ and --force was not given — i.e. the run would touch nothing new. Exit 0 otherwise. Submits/runs nothing itself; call it before submitting SLURM jobs.
--stage-raw	Move loose *_R1* / *_R2* FASTQs into RawData/ and exit.

Config overrides

These override config.env values when given.

Flag	Description
--aligner {star,hisat2}	Aligner (overrides CSRNA_ALIGNER).
--genome-index GENOME_INDEX	STAR genomeDir or HISAT2 prefix (overrides CSRNA_GENOME_INDEX).
--genome GENOME	HOMER genome (overrides CSRNA_GENOME).
--gtf GTF	GTF annotation file for the RIT/RIE metric (overrides CSRNA_GTF).
--copy-src COPY_SRC	FASTQ copy source (overrides CSRNA_COPY_SRC).
--threads THREADS	Threads (overrides CSRNA_THREADS / SLURM_CPUS_PER_TASK).
--trim-adapter TRIM_ADAPTER	3′ adapter sequence.
--trim-min TRIM_MIN	Minimum read length after trimming.
--trim-max TRIM_MAX	Maximum read length after trimming.
--ntag-threshold NTAG_THRESHOLD	Minimum tags for TSS calling.
--skip-chr SKIP_CHR	Chromosome excluded from bedGraphs.
--cleanup-intermediates	Delete each sample's Trimmed/ and Aligned/ directories once the qc step has generated its tables from them (overrides CSRNA_CLEANUP_INTERMEDIATES). Off by default.

Alignment overrides

Flag	Description
--star-filter-multimap N	STAR outFilterMultimapNmax.
--star-multimap-out N	STAR outSAMmultNmax.
--star-multimap-order {Random,Old_2.4}	STAR outMultimapperOrder.
--hisat2-strandness {F,R,FR,RF}	HISAT2 RNA strandness.