blit/_pkgdown.yml at main · WangLabCSU/blit · GitHub

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url: https://wanglabcsu.github.io/blit/
template:
  bootstrap: 5

reference:
  - title: "R6 class"
    desc: "Core R6 class for encapsulating command parameters and building command objects."
    contents:
    - Command

  - title: "Execute command"
    desc: "Functions for executing commands, including foreground, background, and parallel execution."
    contents:
    - exec
    - cmd_run
    - cmd_help
    - cmd_background
    - cmd_parallel

  - title: "Environment context"
    desc: "Set up the execution context, such as working directory, environment variables, and dependency management."
    contents:
    - cmd_wd
    - cmd_envvar
    - cmd_envpath
    - cmd_condaenv
    - conda
    - appmamba
    - install_appmamba
    - uninstall_appmamba
    - appmamba_rc
    - cmd_conda

  - title: "Schedule expressions"
    desc: "Define hooks to run before, after, or on success/failure of a command."
    contents:
    - cmd_on_start
    - cmd_on_exit
    - cmd_on_succeed
    - cmd_on_fail

  - title: "Genomic tools"
    desc: "Wrappers for common genomic data processing and analysis tools."
    contents:
    - allele_counter
    - bcftools
    - bedtools
    - bowtie2
    - bwa
    - samtools
    - seqkit
    - varscan
    - snpEff
    - gistic2

  - title: "Transcriptomic tools"
    desc: "Wrappers for transcriptome sequencing data processing and analysis tools."
    contents:
    - cellranger
    - fastp
    - fastq_pair
    - fastq_read_pair
    - kraken2
    - kraken_tools
    - trust4
    - trust4_imgt_annot
    - trust4_gene_names
    - pyscenic

  - title: "Development"
    desc: "Developer utilities for extending functionality and creating new command interfaces."
    contents:
    - make_command
    - arg
    - arg0

  - title: "Scripting interfaces"
    desc: "Interfaces to external scripting languages for seamless integration with existing scripts."
    contents:
    - python
    - perl