PHYLO_PIPELINE(1)

✨ PHYLO_PIPELINE(1) ✨

okay so bestie, we're in the User Commands section of the manual and this one is chef's kiss. it's called phylo_pipeline — the Phylo Pipeline of the PALEOMIX suite 🧬💖. let's get into it.

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🌸 SYNOPSIS 🌸

paleomix phylo_pipeline <command> [options] [makefiles]

that's the whole vibe. <command> + [options] + [makefiles], go off 💅

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🦋 DESCRIPTION 🦋

so the PALEOMIX pipelines are a lil family of pipelines and tools made to help you process High-Throughput Sequencing (HTS) data at speed, no cap:

• the BAM pipeline takes de-multiplexed reads from one or more samples, runs them through sequence processing and alignment, and spits out BAM alignment files that are useful downstream 🔥
• the Phylogenetic pipeline does genotyping and phylogenetic inference on BAM alignment files — whether you made them with the BAM pipeline or got them from somewhere else, doesn't matter, she's flexible ✨
• the Zonkey pipeline runs a whole suite of analyses on low coverage equine alignments, all to detect the presence of F1-hybrids in archaeological assemblages 🐴

on top of all that, PALEOMIX also helps you out with metagenomic analysis of the extracts. iconic.

and here's the thing — these pipelines were designed with ancient DNA (aDNA) in mind 🏺, and they include several features that are especially useful for analysing ancient samples. but you can absolutely use all of them for processing modern samples too, because consistent data processing is the moment 🙌

phylo_pipeline is the phylo pipeline of paleomix(1).

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💅 OPTIONS 💅

🎀 Commands 🎀

• phylo_pipeline help — Display this message. (yes queen, ask for help, it's free)
• phylo_pipeline example [...] — Copy example project to folder.
• phylo_pipeline makefile — Print makefile template.
• phylo_pipeline genotype [...] — Carry out genotyping according to makefile.
• phylo_pipeline msa [...] — Carry out multiple sequence alignment.
• phylo_pipeline phylogeny — Carry out phylogenetic inference.

⭐ Optional arguments ⭐

• --version — show program's version number and exit
• -h, --help — show this help message and exit
• --to-dot-file=DOT_FILE — Write dependency tree to the specified dot-file.

🌈 Progress reporting 🌈

• --progress-ui=PROGRESS_UI — Select method for displaying the progress of the pipeline:
  • 'running' = Display only currently running nodes
  • 'progress' = Display changes in state
  • 'summary' — one-line summary only

[Default is 'running']

• --ui-colors=UI_COLORS — Enable, disable, or force the use of color codes when printing the command-line UI. Unless forced, colors will only be printed if STDOUT is a TTY [Default is 'on']

📝 Logging 📝

• --log-file=LOG_FILE — Create the specified log-file and write any messages to this file. By default, a log-file will be generated in the folder specified using --temp-root, but only when messages are logged
• --log-level=LOG_LEVEL — Log messages to log-file at and above the specified level; one of 'info', 'warning', 'error', or 'debug' [warning]

🧚 Scheduling 🧚

• --samtools-max-threads=SAMTOOLS_MAX_THREADS — Maximum number of threads to use when genotyping or building pileups [1]
• --examl-max-threads=EXAML_MAX_THREADS — Maximum number of threads to use for each instance of ExaML [1]
• --max-threads=MAX_THREADS — Maximum number of threads to use in total [4]
• --dry-run — If passed, only a dry-run in performed, the dependency tree is printed, and no tasks are executed. (a lil sneak peek, zero commitment 💖)

👑 Required paths: 👑

• --temp-root=TEMP_ROOT — Location for temporary files and folders [/tmp/USERNAME/phylo_pipeline]
• --samples-root=SAMPLES_ROOT — Location of BAM files for each sample [./data/samples]
• --regions-root=REGIONS_ROOT — Location of BED files containing regions of interest [./data/regions]
• --prefix-root=PREFIX_ROOT — Location of prefixes (FASTAs) [./data/prefixes]
• --refseq-root=REFSEQ_ROOT — Location of reference sequences (FASTAs) [./data/refseqs]
• --destination=DESTINATION — The destination folder for result files [./results]

🔍 Files and executables: 🔍

• --list-input-files — List all input files used by pipeline for the makefile(s), excluding any generated by the pipeline itself.
• --list-output-files — List all output files generated by pipeline for the makefile(s).
• --list-executables — List all executables required by the pipeline, with version requirements (if any).

🍓 Config files: 🍓

• --write-config-file — Write config using current settings to $HOME/.paleomix/phylo_pipeline.ini

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🌟 SEE ALSO 🌟

• paleomix(1)

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💜 AUTHOR 💜

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

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okay that's the whole page bestie, you're officially educated 🎓✨ this was phylo_pipeline version 1.2.7, dated February 2017 — mwah, slay, periodt 💅🫶