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bam2fastx.nf's Introduction

DOI

bam2fastx.nf

QUICK START - BASIC USAGE:

nextflow run https://github.com/grpiccoli/bam2fastx.nf --i_bam ccs.bam

OPTIONS:

Basic Options Default Value Description
--i_bam REQUIRED path to input pacbio bam file
--o_f q output format q=fastq a=fasta
--o_i output/indexes output directory for index file
--o_fx output/fastxs output directory for fastx files
Advanced Options
--m 1.GB RAM memory allocation
--p 2 CPU core allocation
--c_pbbam pbbam:1.6.0--h5b7e6e0_0 pbbam container url:tag
--c_bam2fastx pbbam:1.6.0--h5b7e6e0_0 bam2fastx container url:tag
HPC Options
--e local nextflow executor (slurm, local, etc)
--q quicktest queue/partition name
--t 1h max execution time

REQUIREMENTS:

  1. nextflow, instalation without sudo:
curl -s https://get.nextflow.io | bash
  1. singularity, instalation might require sudo: sylabs.io/guides/3.5/user-guide/quick_start.html

CITE

Guillermo R. Piccoli. (2021, April 27). grpiccoli/bam2fastx.nf: (Version 1.3.0). Zenodo. http://doi.org/10.5281/zenodo.4722467

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