Configuration

CatWeb Configuration Example

contexts:
- name: local
    prog_dirs:   '/data/pipelines'
    root_dirs:   '/work'
    output_dirs: '/work/output'
    images_dir:  '/data/images'

canonical_prog_dir: '/data/pipelines'
log_dir: '/home/ubuntu/sp3/catweb/logs'
db_target: '/db/catweb.sqlite'
download_url: 'https://download-cats.oxfordfun.com/files/'

nextflows:
- !include config.yaml.d/clockwork/variant_call.yaml

nfweb_api: { host: '127.0.0.1', port: '7100' }
fetch_api: { host: '127.0.0.1', port: '7200' }

authentication: ldap

ldap:
- name: 'ndm.local'
    host: '192.168.7.16'
    admins: ['denisv@ndm.local', 'fan@ndm.local']

users:
- name: compass

cluster_view:
disk_filter: "home|sda|sdb|sdc"
embeds:
    - title: 'Statistics'
    - img: 'https://stat-cats.oxfordfun.com/draw'

Explanation of the fields

Name

Explanation

  • contexts

  • contexts.name

  • contexts.prog_dirs

  • contexts.root_dirs

  • contexts.output_dirs

  • list of contexts

  • set as local

  • directory containing nextflow pipelines (will be - {prog_dirs}/{flow_name})

  • directory containing nextflow run files (will be - {root_dirs}/runs/{uuid}/)

  • directory containing nextflow outputs (will be - {output_dirs}/{uuid})

  • canonical_prog_dir

  • log_dir

  • db_target

  • download_url

  • ~prog_dir~ that is used by catweb to get nextflow pipeline versions from git

  • directory to put catweb configuration files into

  • sqlite database filepath

  • prefix for nginx file downloads (url will be - {download_url}/{uuid} - )

  • nextflows

  • nextflows.!include

  • list of flows

  • flows to include

  • nfweb_api.host

  • nfweb_api.port

  • hostname of nfweb api

  • port of nfweb api

  • fetch_api.host

  • fetch_api.port

  • hostname of fetch api

  • port of fetch api

  • ldap

  • ldap.name

  • ldap.host

  • ldap.admins

  • list of ldap

  • name of ldap configuration

  • hostname of ldap server

  • list of ldap admins

  • users.name

  • name of users

  • cluster_view

  • cluster_view.disk_filter

  • cluster_view.embeds

  • cluster_view.embeds.title

  • cluster_view.embeds.img

  • Catweb cluster view configuration

  • Regular expression identifying which disks to display

  • List of embeds

  • Title of embed

  • Link of embed

Pipeline Configuration Example

name: "Clockwork_VC"
display_name: "Clockwork variant call"
script: "vc.nf"
show: yes
root_dir: "clockworkcloud/"
prog_dir: "clockworkcloud/"
output_dir: "output/"
version: "0.1"
description: "Clockwork variant vall"
contexts:
- name: local
    arguments: "-process.executor slurm"
param:
description:
    - name: 'ref_dir'
    arg: "--ref_dir"
    type: switch
    desc: "Reference directory"
    globs:
        - /data/references/clockwork/qc_vc/*
    - name: 'indir'
    arg: '--input_dir'
    type: input-reqr
    desc: "Input directory"
    - name: 'readpat'
    arg: '--read_pattern'
    type: input-reqr
    desc: "Input file pattern"
output:
    parameter: "--output_dir"
count_tasks_per_sample: 5

Explanation of the fields

Field name

Field description

name

Name of pipeline

display_name

Name to display in catweb

script

Nextflow script filename

show

Toggle showing this script in catweb ( yes / no )

root_dir

Not used

prog_dir

Directory of nextflow pipeline relative to the context prog_dirs

description

Description of pipeline

  • contexts

  • contexts.name

  • contexts.arguments

  • List of contexts

  • Name of context

  • Arguments specific to this context

  • param

  • param.description

  • param.description.name

  • param.description.arg

  • param.description.type

  • param.description.desc

  • param.output

  • param.output.parameter

  • count_tasks_per_sample

  • List of params

  • Description of params

  • Name of parameter

  • Nextflow command-line key for parameter

  • switch or input-reqr

  • Description of parameter

  • output

  • Nextflow command-line key that determines the output directory

  • How many nextflow tasks (processes) there are per input sample