Configuration

Configuration values use this precedence order:

1. an explicit command-line flag;
2. a CSRNA_* environment variable;
3. the built-in default.

--project falls back to CSRNA_PROJECT, then the current directory. Threads fall back to CSRNA_THREADS, then SLURM_CPUS_PER_TASK, then 20.

Required analysis values

The SLURM controller requires these values as flags:

Flag	Environment variable	Meaning
--project	CSRNA_PROJECT	Project root
--genome-index	CSRNA_GENOME_INDEX	STAR genome directory or HISAT2 index prefix
--genome	CSRNA_GENOME	HOMER genome name or genome FASTA path
--aligner	CSRNA_ALIGNER	star (default) or hisat2

submit_array.sh additionally requires --partition and --conda-env; those control SLURM and are not Python pipeline settings.

Common optional values

Flag	Environment variable	Default
--gtf	CSRNA_GTF	unset; RIT/RIE is skipped
--threads	CSRNA_THREADS	SLURM_CPUS_PER_TASK or 20
--trim-min	CSRNA_TRIM_MINLEN	20
--trim-max	CSRNA_TRIM_MAXLEN	58
--ntag-threshold	CSRNA_NTAG_THRESHOLD	7
--skip-chr	CSRNA_SKIP_CHR	chrEBV
--cleanup-intermediates	CSRNA_CLEANUP_INTERMEDIATES	off

See the CLI reference for every flag and its meaning.

Generated run record

Preparation writes <project>/config.txt. It records the effective settings, the samples HOMERun discovered, and the staged FASTQ paths. Check this file before troubleshooting later stages; it shows what the pipeline actually used.

GTF is optional

--gtf enables the RIT/RIE metric. Omitting it is valid and causes that step to be skipped. Supplying an unreadable path is an error caught during preparation.