CI
1ebb61f1e8
Build pipeline: vsh-ci-dev-jsbwk
Source commit: 1e1ffb315f
Source message: Merge pull request #17 from viash-hub/add_biobox_modules
- Migrate a number of components to biobox
- Fix tests
- Reduce size of test resources
- Prepare for Viash Hub
57 lines
1.6 KiB
YAML
57 lines
1.6 KiB
YAML
name: "getchromsizes"
|
|
info:
|
|
migration_info:
|
|
git_repo: https://github.com/nf-core/rnaseq.git
|
|
paths: [modules/nf-core/custom/getchromsizes/main.nf, modules/nf-core/custom/getchromsizes/meta.yml]
|
|
last_sha: 54721c6946daf6d602d7069dc127deef9cbe6b33
|
|
description: |
|
|
Generates a FASTA file of chromosome sizes and a fasta index file.
|
|
|
|
argument_groups:
|
|
- name: "Input"
|
|
arguments:
|
|
- name: "--fasta"
|
|
type: file
|
|
description: Genome fasta files
|
|
|
|
- name: "Output"
|
|
arguments:
|
|
- name: "--sizes"
|
|
type: file
|
|
direction: output
|
|
description: File containing chromosome lengths
|
|
- name: "--fai"
|
|
type: file
|
|
description: FASTA index file
|
|
direction: output
|
|
- name: "--gzi" # optional
|
|
type: file
|
|
description: Optional gzip index file for compressed inputs
|
|
direction: output
|
|
|
|
resources:
|
|
- type: bash_script
|
|
path: script.sh
|
|
test_resources:
|
|
- type: bash_script
|
|
path: test.sh
|
|
- path: /testData/minimal_test/reference/genome.fasta
|
|
|
|
engines:
|
|
- type: docker
|
|
image: ubuntu:22.04
|
|
setup:
|
|
- type: docker
|
|
run: |
|
|
apt-get update && \
|
|
apt-get install -y autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libncurses5-dev curl bzip2 && \
|
|
curl -fsSL https://github.com/samtools/samtools/releases/download/1.18/samtools-1.18.tar.bz2 -o samtools-1.18.tar.bz2 && \
|
|
tar -xjf samtools-1.18.tar.bz2 && \
|
|
rm samtools-1.18.tar.bz2 && \
|
|
cd samtools-1.18 && \
|
|
./configure && \
|
|
make && \
|
|
make install
|
|
runners:
|
|
- type: executable
|
|
- type: nextflow |