meta.yml init; test.yml and main.nf for printing version

This commit is contained in:
Sviatoslav Sidorov 2021-03-16 11:54:42 +00:00
parent 2f675fbe7c
commit 390c835f9f
3 changed files with 24 additions and 39 deletions

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@ -1,20 +1,17 @@
name: fastqc
description: Run FastQC on sequenced reads
name: hifiasm
description: Run hifiasm on Pacbio HiFi reads
keywords:
- quality control
- qc
- adapters
- genome assembly
- pacbaio
- hifi
- long reads
- fastq
tools:
- fastqc:
- hifiasm:
description: |
FastQC gives general quality metrics about your reads.
It provides information about the quality score distribution
across your reads, the per base sequence content (%A/C/G/T).
You get information about adapter contamination and other
overrepresented sequences.
homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
hifiasm generates a genome assembly from long Pacbio HiFi reads. ...Haplotype resolution ...Using short reads.
homepage: https://github.com/chhylp123/hifiasm
documentation: https://github.com/chhylp123/hifiasm
params:
- outdir:
type: string

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nextflow.enable.dsl = 2
include { FASTQC } from '../../../software/fastqc/main.nf' addParams( options: [:] )
include { HIFIASM } from '../../../software/hifiasm/main.nf' addParams( options: [:] )
/*
* Test with single-end data
*/
workflow test_fastqc_single_end {
/* workflow test_fastqc_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] ]
FASTQC ( input )
}
} */
/*
* Test with paired-end data
* Test version printing
*/
workflow test_fastqc_paired_end {
workflow test_hifiasm_version {
def input = []
/* def input = []
input = [[id: 'test', single_end: false], // meta map
[file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true)]]
FASTQC (input)
file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true)]] */
HIFIASM ()
}

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- name: fastqc single-end
command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_single_end -c tests/config/nextflow.config
- name: hifiasm
command: nextflow run ./tests/software/hifiasm/ -entry test_hifiasm_version -c tests/config/nextflow.config
tags:
- fastqc
- fastqc_single_end
- hifiasm
- hifiasm_version
files:
- path: ./output/fastqc/test_fastqc.html
- path: ./output/fastqc/test_fastqc.zip
- name: fastqc paired-end
command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_paired_end -c tests/config/nextflow.config
tags:
- fastqc
- fastqc_paired_end
files:
- path: ./output/fastqc/test_1_fastqc.html
- path: ./output/fastqc/test_2_fastqc.html
- path: ./output/fastqc/test_2_fastqc.zip
- path: ./output/fastqc/test_1_fastqc.zip
- path: ./output/hifiasm/VERSION.txt