AMAP

Docs / Getting started

Quickstart

This walks from an installed Nextflow to an open report. If Nextflow or a container engine is still missing, start at installation.

1. Write a sample sheet#

AMAP reads a tab-separated file with two columns, sampleId and fasta:

samples.tsv
sampleId	fasta
G26689	/data/genomes/G26689.fasta
G26690	/data/genomes/G26690.fasta

The separator must be a real tab. Paths can be absolute, or relative to where you launch Nextflow. See preparing inputs for the details and the checks AMAP runs over them.

2. Check the inputs#

Cheap, and it catches the mistakes that would otherwise surface twenty minutes into a run:

nextflow run PathoGenOmics-Lab/AMAP -profile docker \
    --tsv samples.tsv --validate_only

3. Run it#

Pick what you have, and copy the command:

Where will it run?
Which genomes?
Anything else?

    
    
    
  
    

    The command for your machine and your genomes, with what each option does. The same as on the front page.
    

    Or start from one of these:
    

    nextflow run PathoGenOmics-Lab/AMAP -profile docker --tsv samples.tsv
    

    Without a scheduler profile every task is capped at the machine's CPUs and 16 GB, and with the scheduler profiles at 48 CPUs and 128 GB, whichever order the profiles come in; a larger request, such as the 50 GB the eggNOG annotation asks for, is lowered to the cap. Nextflow refuses to start a task asking for more memory than the machine has, so on a smaller machine, lower the ceiling:
    

    nextflow run PathoGenOmics-Lab/AMAP -profile docker \
    --tsv samples.tsv --max_cpus 4 --max_memory 12.GB
    

    The tutorial has the per-step figures and what to do when the machine cannot reach them.
    

    4. Read the results#
    

    Everything lands under results/ unless you set --outdir. The three things to open first:
    

    WhatWhere
    The full interactive reportresults/final_report.html
    Corrected annotation, per sampleresults/AMAP/{sampleId}/*-AMAP.gff3
    Protein sequences for downstream toolsresults/AMAP/{sampleId}/*-AMAP.clean.faa
    

    Which protein file do I want?
    *-AMAP.faa holds every gene, pseudogenes included, so it mirrors the annotation exactly. *-AMAP.clean.faa drops pseudogenes and sequences with internal stop codons, which is what orthology, phylogenomics and dN/dS tools expect. Reach for the clean one unless you specifically need the complete set.
    

    The outputs page covers every directory.
    

    5. Resume an interrupted run#
    

    Nextflow caches completed tasks. If a run dies, restart it with -resume and it picks up where it stopped:
    

    nextflow run PathoGenOmics-Lab/AMAP -profile docker --tsv samples.tsv -resume
    

    Keep the same parameters. Changing an input invalidates the cache for every task downstream of it, which is what you want, but it does mean the run redoes that work.
    

    Common variations#
    

    A non-MTBC organism. Lineage typing and Mycobrowser are specific to tuberculosis, so turn them off and supply your own reference:
    

    nextflow run PathoGenOmics-Lab/AMAP -profile docker \
    --tsv samples.tsv \
    --skip_typing --skip_mycobrowser \
    --genus Escherichia --species "Escherichia coli" \
    --ref_annotation my_reference.gbk --ref_genome my_reference.fasta
    

    See custom reference.
    

    Just the corrected genes. If you do not need functional annotation, duplications, the pangenome or the report, stop after the correction step. It is much faster, and leaves the corrected genes as a table with their proteins and sequences; the GFF3 and GenBank files come after eggNOG, so there are none:
    

    nextflow run PathoGenOmics-Lab/AMAP -profile docker \
    --tsv samples.tsv --skip_functional_annotation
    

    Next steps#
    


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