SLURM_SRST2(1)

💖 slurm_srst2 — the manual, but make it make sense 💖

okay bestie, so you've stumbled into slurm_srst2(1), a User Commands girly whose whole personality is running srst2 against a whole pile of read sets without you having to babysit each one. ✨ Let's get into it.

🌸 NAME 🌸

slurm_srst2 — running srst2 against multiple read sets

🎀 OPTIONS 🎀 (the quick lil synopsis, don't skip it)

slurm_srst2 [-h] [--walltime WALLTIME] [--memory MEMORY] [--rundir
RUNDIR] --script SCRIPT --output OUTPUT [--input_se INPUT_SE [INPUT_SE
...]]  [--input_pe INPUT_PE [INPUT_PE ...]] [--forward FORWARD]
[--reverse REVERSE] [--other_args OTHER_ARGS]

like… that's the whole vibe in one block. slay.

🦋 DESCRIPTION 🦋

Submit SRST2 jobs through SLURM (see srst(1)).

that's it, that's the pitch. it's giving "batch queen". 👑

✨ OPTIONS ✨

• -h, --help — show this help message and exit. the classic. the icon. when in doubt, ask for help. 🙈
• --walltime WALLTIME — wall time (default 0-1:0 = 1 h). so by default you get one whole hour of runtime, bestie. don't get greedy unless you say so. ⏳
• --memory MEMORY — mem (default 4096 = 4gb). yes, 4 whole gigabytes, handed to you like a lil snack. 🍓
• --rundir RUNDIR — directory to run in (default current dir). where the magic happens, literally where you're standing rn unless you tell it otherwise. 📁
• --script SCRIPT — path to srst2 (default srst2). point this at your actual script if it's not just chillin' on your PATH. 🫶
• --output OUTPUT — identifier for outputs (will be combined with read set identifiers). so your outputs get a name, and then the read set identifiers get glued onto it. teamwork, babes. 💅
• --input_se INPUT_SE [INPUT_SE ...] — Single end read file(s) for analysing (may be gzipped). feed it as many single-end files as your heart desires. gzipped? totally fine, no notes. 🌸
• --input_pe INPUT_PE [INPUT_PE ...] — Paired end read files for analysing (may be gzipped). the matched-set girlies. also very gzip-friendly. 🌈
• --forward FORWARD — Designator for forward reads (only used if NOT in MiSeq format sample_S1_L001_R1_001.fastq.gz; otherwise default is _1, i.e. expect forward reads as sample_1.fastq.gz). so: if you're living that MiSeq filename life, this option just sits there unbothered. if you're NOT, this is your moment. ⭐
• --reverse REVERSE — Designator for reverse reads (only used if NOT in MiSeq format sample_S1_L001_R2_001.fastq.gz; otherwise default is _2, i.e. expect forward reads as sample_2.fastq.gz). same deal, opposite direction. (yes, the original says "forward reads" in that second one too — we're keeping it exactly as written, no cap. 🫡)
• --other_args OTHER_ARGS — string containing all other arguments to pass to srst2. the ✨ catch-all ✨. everything else you wanna shove through goes right here. 🔥

💜 AUTHOR 💜

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

lowkey a whole serve. highkey a whole serve. fr fr.

and that's the page, bestie — this was slurm_srst2 version 0.1.6, dated December 2015, living in the SLURM_SRST2(1) section. go forth and submit those jobs. 🧚💖