mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
Merge branch 'nf-core:master' into master
This commit is contained in:
commit
20f9dfde69
19 changed files with 414 additions and 49 deletions
38
modules/bamtools/convert/main.nf
Normal file
38
modules/bamtools/convert/main.nf
Normal file
|
@ -0,0 +1,38 @@
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||||||
|
process BAMTOOLS_CONVERT {
|
||||||
|
tag "$meta.id"
|
||||||
|
label 'process_low'
|
||||||
|
|
||||||
|
conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
|
||||||
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
|
'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
|
||||||
|
'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
|
||||||
|
|
||||||
|
input:
|
||||||
|
tuple val(meta), path(bam)
|
||||||
|
|
||||||
|
output:
|
||||||
|
tuple val(meta), path("*.{bed,fasta,fastq,json,pileup,sam,yaml}"), emit: data
|
||||||
|
path "versions.yml" , emit: versions
|
||||||
|
|
||||||
|
script:
|
||||||
|
def args = task.ext.args ?: ''
|
||||||
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||||
|
def test = args ==~ /-format (bed|fasta|fastq|json|pileup|sam|yaml)/
|
||||||
|
if ( test == false ) error "-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml"
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||||||
|
m = args =~ /-format ([a-z]+)/
|
||||||
|
ext = m[0][1]
|
||||||
|
|
||||||
|
|
||||||
|
"""
|
||||||
|
bamtools \\
|
||||||
|
convert \\
|
||||||
|
$args \\
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||||||
|
-in $bam \\
|
||||||
|
-out ${prefix}.${ext}
|
||||||
|
|
||||||
|
cat <<-END_VERSIONS > versions.yml
|
||||||
|
"${task.process}":
|
||||||
|
bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
|
||||||
|
END_VERSIONS
|
||||||
|
"""
|
||||||
|
}
|
52
modules/bamtools/convert/meta.yml
Normal file
52
modules/bamtools/convert/meta.yml
Normal file
|
@ -0,0 +1,52 @@
|
||||||
|
name: bamtools_convert
|
||||||
|
description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
|
||||||
|
keywords:
|
||||||
|
- bamtools
|
||||||
|
- bamtools/convert
|
||||||
|
- bam
|
||||||
|
- convert
|
||||||
|
- bed
|
||||||
|
- fasta
|
||||||
|
- fastq
|
||||||
|
- json
|
||||||
|
- pileup
|
||||||
|
- sam
|
||||||
|
- yaml
|
||||||
|
tools:
|
||||||
|
- bamtools:
|
||||||
|
description: C++ API & command-line toolkit for working with BAM data
|
||||||
|
homepage: http://github.com/pezmaster31/bamtools
|
||||||
|
documentation: https://github.com/pezmaster31/bamtools/wiki
|
||||||
|
tool_dev_url: http://github.com/pezmaster31/bamtools
|
||||||
|
doi: ""
|
||||||
|
licence: ['MIT']
|
||||||
|
|
||||||
|
input:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- bam:
|
||||||
|
type: file
|
||||||
|
description: BAM file
|
||||||
|
pattern: "*.bam"
|
||||||
|
|
||||||
|
output:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- versions:
|
||||||
|
type: file
|
||||||
|
description: File containing software versions
|
||||||
|
pattern: "versions.yml"
|
||||||
|
## TODO nf-core: Delete / customise this example output
|
||||||
|
- out:
|
||||||
|
type: file
|
||||||
|
description: The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml)
|
||||||
|
pattern: "*.{bed,fasta,fastq,json,pileup,sam,yaml}"
|
||||||
|
|
||||||
|
authors:
|
||||||
|
- "@sguizard"
|
|
@ -41,7 +41,7 @@ process FREEBAYES {
|
||||||
$args \\
|
$args \\
|
||||||
$input > ${prefix}.vcf
|
$input > ${prefix}.vcf
|
||||||
|
|
||||||
gzip --no-name ${prefix}.vcf
|
bgzip ${prefix}.vcf
|
||||||
|
|
||||||
cat <<-END_VERSIONS > versions.yml
|
cat <<-END_VERSIONS > versions.yml
|
||||||
"${task.process}":
|
"${task.process}":
|
||||||
|
@ -60,7 +60,7 @@ process FREEBAYES {
|
||||||
$args \\
|
$args \\
|
||||||
$input > ${prefix}.vcf
|
$input > ${prefix}.vcf
|
||||||
|
|
||||||
gzip --no-name ${prefix}.vcf
|
bgzip ${prefix}.vcf
|
||||||
|
|
||||||
cat <<-END_VERSIONS > versions.yml
|
cat <<-END_VERSIONS > versions.yml
|
||||||
"${task.process}":
|
"${task.process}":
|
||||||
|
|
|
@ -8,8 +8,7 @@ process GATK4_MERGEBAMALIGNMENT {
|
||||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||||
|
|
||||||
input:
|
input:
|
||||||
tuple val(meta), path(aligned)
|
tuple val(meta), path(aligned), path(unmapped)
|
||||||
path unmapped
|
|
||||||
path fasta
|
path fasta
|
||||||
path dict
|
path dict
|
||||||
|
|
||||||
|
@ -28,10 +27,10 @@ process GATK4_MERGEBAMALIGNMENT {
|
||||||
}
|
}
|
||||||
"""
|
"""
|
||||||
gatk --java-options "-Xmx${avail_mem}g" MergeBamAlignment \\
|
gatk --java-options "-Xmx${avail_mem}g" MergeBamAlignment \\
|
||||||
ALIGNED=$aligned \\
|
-ALIGNED $aligned \\
|
||||||
UNMAPPED=$unmapped \\
|
-UNMAPPED $unmapped \\
|
||||||
R=$fasta \\
|
-R $fasta \\
|
||||||
O=${prefix}.bam \\
|
-O ${prefix}.bam \\
|
||||||
$args
|
$args
|
||||||
|
|
||||||
cat <<-END_VERSIONS > versions.yml
|
cat <<-END_VERSIONS > versions.yml
|
||||||
|
|
|
@ -2,10 +2,10 @@ process NEXTCLADE_DATASETGET {
|
||||||
tag "$dataset"
|
tag "$dataset"
|
||||||
label 'process_low'
|
label 'process_low'
|
||||||
|
|
||||||
conda (params.enable_conda ? "bioconda::nextclade=1.9.0" : null)
|
conda (params.enable_conda ? "bioconda::nextclade=1.10.1" : null)
|
||||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
'https://depot.galaxyproject.org/singularity/nextclade:1.9.0--h9ee0642_0' :
|
'https://depot.galaxyproject.org/singularity/nextclade:1.10.1--h9ee0642_0' :
|
||||||
'quay.io/biocontainers/nextclade:1.9.0--h9ee0642_0' }"
|
'quay.io/biocontainers/nextclade:1.10.1--h9ee0642_0' }"
|
||||||
|
|
||||||
input:
|
input:
|
||||||
val dataset
|
val dataset
|
||||||
|
|
|
@ -2,10 +2,10 @@ process NEXTCLADE_RUN {
|
||||||
tag "$meta.id"
|
tag "$meta.id"
|
||||||
label 'process_low'
|
label 'process_low'
|
||||||
|
|
||||||
conda (params.enable_conda ? "bioconda::nextclade=1.9.0" : null)
|
conda (params.enable_conda ? "bioconda::nextclade=1.10.1" : null)
|
||||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
'https://depot.galaxyproject.org/singularity/nextclade:1.9.0--h9ee0642_0' :
|
'https://depot.galaxyproject.org/singularity/nextclade:1.10.1--h9ee0642_0' :
|
||||||
'quay.io/biocontainers/nextclade:1.9.0--h9ee0642_0' }"
|
'quay.io/biocontainers/nextclade:1.10.1--h9ee0642_0' }"
|
||||||
|
|
||||||
input:
|
input:
|
||||||
tuple val(meta), path(fasta)
|
tuple val(meta), path(fasta)
|
||||||
|
|
|
@ -2,10 +2,10 @@ process PRODIGAL {
|
||||||
tag "$meta.id"
|
tag "$meta.id"
|
||||||
label 'process_low'
|
label 'process_low'
|
||||||
|
|
||||||
conda (params.enable_conda ? "bioconda::prodigal=2.6.3" : null)
|
conda (params.enable_conda ? "prodigal=2.6.3 pigz=2.6" : null)
|
||||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
'https://depot.galaxyproject.org/singularity/prodigal:2.6.3--h516909a_2' :
|
'https://depot.galaxyproject.org/singularity/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' :
|
||||||
'quay.io/biocontainers/prodigal:2.6.3--h516909a_2' }"
|
'quay.io/biocontainers/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' }"
|
||||||
|
|
||||||
input:
|
input:
|
||||||
tuple val(meta), path(genome)
|
tuple val(meta), path(genome)
|
||||||
|
@ -22,7 +22,7 @@ process PRODIGAL {
|
||||||
def args = task.ext.args ?: ''
|
def args = task.ext.args ?: ''
|
||||||
prefix = task.ext.prefix ?: "${meta.id}"
|
prefix = task.ext.prefix ?: "${meta.id}"
|
||||||
"""
|
"""
|
||||||
prodigal -i "${genome}" \\
|
pigz -cdf ${genome} | prodigal \\
|
||||||
$args \\
|
$args \\
|
||||||
-f $output_format \\
|
-f $output_format \\
|
||||||
-d "${prefix}.fna" \\
|
-d "${prefix}.fna" \\
|
||||||
|
@ -33,6 +33,7 @@ process PRODIGAL {
|
||||||
cat <<-END_VERSIONS > versions.yml
|
cat <<-END_VERSIONS > versions.yml
|
||||||
"${task.process}":
|
"${task.process}":
|
||||||
prodigal: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p')
|
prodigal: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p')
|
||||||
|
pigz: \$(pigz -V 2>&1 | sed 's/pigz //g')
|
||||||
END_VERSIONS
|
END_VERSIONS
|
||||||
"""
|
"""
|
||||||
}
|
}
|
||||||
|
|
|
@ -5,10 +5,10 @@ keywords:
|
||||||
tools:
|
tools:
|
||||||
- prodigal:
|
- prodigal:
|
||||||
description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
|
description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
|
||||||
homepage: {}
|
homepage: {https://github.com/hyattpd/Prodigal}
|
||||||
documentation: {}
|
documentation: {https://github.com/hyattpd/prodigal/wiki}
|
||||||
tool_dev_url: {}
|
tool_dev_url: {}
|
||||||
doi: ""
|
doi: "10.1186/1471-2105-11-119"
|
||||||
licence: ["GPL v3"]
|
licence: ["GPL v3"]
|
||||||
|
|
||||||
input:
|
input:
|
||||||
|
@ -17,10 +17,12 @@ input:
|
||||||
description: |
|
description: |
|
||||||
Groovy Map containing sample information
|
Groovy Map containing sample information
|
||||||
e.g. [ id:'test', single_end:false ]
|
e.g. [ id:'test', single_end:false ]
|
||||||
- bam:
|
- genome:
|
||||||
type: file
|
type: file
|
||||||
description: BAM/CRAM/SAM file
|
description: fasta/fasta.gz file
|
||||||
pattern: "*.{bam,cram,sam}"
|
- output_format:
|
||||||
|
type: string
|
||||||
|
description: Output format ("gbk"/"gff"/"sqn"/"sco")
|
||||||
|
|
||||||
output:
|
output:
|
||||||
- meta:
|
- meta:
|
||||||
|
@ -32,10 +34,22 @@ output:
|
||||||
type: file
|
type: file
|
||||||
description: File containing software versions
|
description: File containing software versions
|
||||||
pattern: "versions.yml"
|
pattern: "versions.yml"
|
||||||
- bam:
|
- nucleotide_fasta:
|
||||||
type: file
|
type: file
|
||||||
description: Sorted BAM/CRAM/SAM file
|
description: nucleotide sequences file
|
||||||
pattern: "*.{bam,cram,sam}"
|
pattern: "*.{fna}"
|
||||||
|
- amino_acid_fasta:
|
||||||
|
type: file
|
||||||
|
description: protein translations file
|
||||||
|
pattern: "*.{faa}"
|
||||||
|
- all_gene_annotations:
|
||||||
|
type: file
|
||||||
|
description: complete starts file
|
||||||
|
pattern: "*.{_all.txt}"
|
||||||
|
- gene_annotations:
|
||||||
|
type: file
|
||||||
|
description: gene annotations in output_format given as input
|
||||||
|
pattern: "*.{output_format}"
|
||||||
|
|
||||||
authors:
|
authors:
|
||||||
- "@grst"
|
- "@grst"
|
||||||
|
|
|
@ -46,6 +46,10 @@ bamaligncleaner:
|
||||||
- modules/bamaligncleaner/**
|
- modules/bamaligncleaner/**
|
||||||
- tests/modules/bamaligncleaner/**
|
- tests/modules/bamaligncleaner/**
|
||||||
|
|
||||||
|
bamtools/convert:
|
||||||
|
- modules/bamtools/convert/**
|
||||||
|
- tests/modules/bamtools/convert/**
|
||||||
|
|
||||||
bamtools/split:
|
bamtools/split:
|
||||||
- modules/bamtools/split/**
|
- modules/bamtools/split/**
|
||||||
- tests/modules/bamtools/split/**
|
- tests/modules/bamtools/split/**
|
||||||
|
|
104
tests/modules/bamtools/convert/main.nf
Normal file
104
tests/modules/bamtools/convert/main.nf
Normal file
|
@ -0,0 +1,104 @@
|
||||||
|
#!/usr/bin/env nextflow
|
||||||
|
|
||||||
|
nextflow.enable.dsl = 2
|
||||||
|
|
||||||
|
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_EXT_ERROR } from '../../../../modules/bamtools/convert/main.nf'
|
||||||
|
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_NOEXT_ERROR } from '../../../../modules/bamtools/convert/main.nf'
|
||||||
|
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_BED } from '../../../../modules/bamtools/convert/main.nf'
|
||||||
|
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTA } from '../../../../modules/bamtools/convert/main.nf'
|
||||||
|
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTQ } from '../../../../modules/bamtools/convert/main.nf'
|
||||||
|
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_JSON } from '../../../../modules/bamtools/convert/main.nf'
|
||||||
|
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_PILEUP } from '../../../../modules/bamtools/convert/main.nf'
|
||||||
|
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_SAM } from '../../../../modules/bamtools/convert/main.nf'
|
||||||
|
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_YAML } from '../../../../modules/bamtools/convert/main.nf'
|
||||||
|
|
||||||
|
workflow test_bamtools_convert_ext_error {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test', single_end:false ], // meta map
|
||||||
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
|
BAMTOOLS_CONVERT_EXT_ERROR ( input )
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_bamtools_convert_noext_error {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test', single_end:false ], // meta map
|
||||||
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
|
BAMTOOLS_CONVERT_NOEXT_ERROR ( input )
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_bamtools_convert_bed {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test', single_end:false ], // meta map
|
||||||
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
|
BAMTOOLS_CONVERT_BED ( input )
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_bamtools_convert_fasta {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test', single_end:false ], // meta map
|
||||||
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
|
BAMTOOLS_CONVERT_FASTA ( input )
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_bamtools_convert_fastq {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test', single_end:false ], // meta map
|
||||||
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
|
BAMTOOLS_CONVERT_FASTQ ( input )
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_bamtools_convert_json {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test', single_end:false ], // meta map
|
||||||
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
|
BAMTOOLS_CONVERT_JSON ( input )
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_bamtools_convert_pileup {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test', single_end:false ], // meta map
|
||||||
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
|
BAMTOOLS_CONVERT_PILEUP ( input )
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_bamtools_convert_sam {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test', single_end:false ], // meta map
|
||||||
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
|
BAMTOOLS_CONVERT_SAM ( input )
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_bamtools_convert_yaml {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test', single_end:false ], // meta map
|
||||||
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
|
BAMTOOLS_CONVERT_YAML ( input )
|
||||||
|
}
|
||||||
|
|
41
tests/modules/bamtools/convert/nextflow.config
Normal file
41
tests/modules/bamtools/convert/nextflow.config
Normal file
|
@ -0,0 +1,41 @@
|
||||||
|
process {
|
||||||
|
|
||||||
|
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||||
|
|
||||||
|
withName: BAMTOOLS_CONVERT_EXT_ERROR {
|
||||||
|
ext.args = "-format vcf"
|
||||||
|
}
|
||||||
|
|
||||||
|
withName: BAMTOOLS_CONVERT_NOEXT_ERROR {
|
||||||
|
ext.args = ""
|
||||||
|
}
|
||||||
|
|
||||||
|
withName: BAMTOOLS_CONVERT_BED {
|
||||||
|
ext.args = "-format bed"
|
||||||
|
}
|
||||||
|
|
||||||
|
withName: BAMTOOLS_CONVERT_FASTA {
|
||||||
|
ext.args = "-format fasta"
|
||||||
|
}
|
||||||
|
|
||||||
|
withName: BAMTOOLS_CONVERT_FASTQ {
|
||||||
|
ext.args = "-format fastq"
|
||||||
|
}
|
||||||
|
|
||||||
|
withName: BAMTOOLS_CONVERT_JSON {
|
||||||
|
ext.args = "-format json"
|
||||||
|
}
|
||||||
|
|
||||||
|
withName: BAMTOOLS_CONVERT_PILEUP {
|
||||||
|
ext.args = "-format pileup"
|
||||||
|
}
|
||||||
|
|
||||||
|
withName: BAMTOOLS_CONVERT_SAM {
|
||||||
|
ext.args = "-format sam"
|
||||||
|
}
|
||||||
|
|
||||||
|
withName: BAMTOOLS_CONVERT_YAML {
|
||||||
|
ext.args = "-format yaml"
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
90
tests/modules/bamtools/convert/test.yml
Normal file
90
tests/modules/bamtools/convert/test.yml
Normal file
|
@ -0,0 +1,90 @@
|
||||||
|
- name: bamtools convert test_bamtools_convert_ext_error
|
||||||
|
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_ext_error -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- bamtools
|
||||||
|
- bamtools/convert
|
||||||
|
exit_code: 1
|
||||||
|
|
||||||
|
- name: bamtools convert test_bamtools_convert_noext_error
|
||||||
|
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_noext_error -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- bamtools
|
||||||
|
- bamtools/convert
|
||||||
|
exit_code: 1
|
||||||
|
|
||||||
|
- name: bamtools convert test_bamtools_convert_bed
|
||||||
|
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_bed -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- bamtools
|
||||||
|
- bamtools/convert
|
||||||
|
files:
|
||||||
|
- path: output/bamtools/test.bed
|
||||||
|
md5sum: 4e34cc15bf31e700f5f3a9f8fffb6c81
|
||||||
|
- path: output/bamtools/versions.yml
|
||||||
|
md5sum: eb7a144b8a97965d3482f6f96b8a8243
|
||||||
|
|
||||||
|
- name: bamtools convert test_bamtools_convert_fasta
|
||||||
|
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_fasta -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- bamtools
|
||||||
|
- bamtools/convert
|
||||||
|
files:
|
||||||
|
- path: output/bamtools/test.fasta
|
||||||
|
md5sum: 52aeacf78571862b7e97c7d44ac8f827
|
||||||
|
- path: output/bamtools/versions.yml
|
||||||
|
md5sum: 42d19a2b2b07f05edb82b34369dfd754
|
||||||
|
|
||||||
|
- name: bamtools convert test_bamtools_convert_fastq
|
||||||
|
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_fastq -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- bamtools
|
||||||
|
- bamtools/convert
|
||||||
|
files:
|
||||||
|
- path: output/bamtools/test.fastq
|
||||||
|
md5sum: e591c48daad2c56638e5d6f21f1f71c5
|
||||||
|
- path: output/bamtools/versions.yml
|
||||||
|
md5sum: 13f0bf8a3e1f8f527f96dabaa5c8051e
|
||||||
|
|
||||||
|
- name: bamtools convert test_bamtools_convert_json
|
||||||
|
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_json -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- bamtools
|
||||||
|
- bamtools/convert
|
||||||
|
files:
|
||||||
|
- path: output/bamtools/test.json
|
||||||
|
md5sum: 04afed696f9f14da85a460353645d1f5
|
||||||
|
- path: output/bamtools/versions.yml
|
||||||
|
md5sum: 33d633dbd6209cb93c9b071f8c0ed3b3
|
||||||
|
|
||||||
|
- name: bamtools convert test_bamtools_convert_pileup
|
||||||
|
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_pileup -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- bamtools
|
||||||
|
- bamtools/convert
|
||||||
|
files:
|
||||||
|
- path: output/bamtools/test.pileup
|
||||||
|
md5sum: e5a3cb4a3e1bf980a575fafce6a2826f
|
||||||
|
- path: output/bamtools/versions.yml
|
||||||
|
md5sum: fd3ad0edd1e085b1a002e0593d1d5814
|
||||||
|
|
||||||
|
- name: bamtools convert test_bamtools_convert_sam
|
||||||
|
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_sam -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- bamtools
|
||||||
|
- bamtools/convert
|
||||||
|
files:
|
||||||
|
- path: output/bamtools/test.sam
|
||||||
|
md5sum: 61ab3d0de16a9da8b651f9c692e19d5e
|
||||||
|
- path: output/bamtools/versions.yml
|
||||||
|
md5sum: 4be470ce3cc0143ae5ae415b612a4965
|
||||||
|
|
||||||
|
- name: bamtools convert test_bamtools_convert_yaml
|
||||||
|
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_yaml -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- bamtools
|
||||||
|
- bamtools/convert
|
||||||
|
files:
|
||||||
|
- path: output/bamtools/test.yaml
|
||||||
|
md5sum: 68b56f198da036fef33e150eb773dc3b
|
||||||
|
- path: output/bamtools/versions.yml
|
||||||
|
md5sum: 1116abc088c5edf11bee393961c18b3e
|
|
@ -1,34 +1,49 @@
|
||||||
- name: freebayes test_freebayes
|
- name: freebayes test_freebayes
|
||||||
command: nextflow run ./tests/modules/freebayes -entry test_freebayes -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
|
command: nextflow run tests/modules/freebayes -entry test_freebayes -c tests/config/nextflow.config
|
||||||
tags:
|
tags:
|
||||||
- freebayes
|
- freebayes
|
||||||
files:
|
files:
|
||||||
- path: output/freebayes/test.vcf.gz
|
- path: output/freebayes/test.vcf.gz
|
||||||
|
md5sum: 81d3e6ce7b6343d088b779567c3803eb
|
||||||
|
- path: output/freebayes/versions.yml
|
||||||
|
md5sum: 53651eb835af65df829241257584a7d2
|
||||||
|
|
||||||
- name: freebayes test_freebayes_bed
|
- name: freebayes test_freebayes_bed
|
||||||
command: nextflow run ./tests/modules/freebayes -entry test_freebayes_bed -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
|
command: nextflow run tests/modules/freebayes -entry test_freebayes_bed -c tests/config/nextflow.config
|
||||||
tags:
|
tags:
|
||||||
- freebayes
|
- freebayes
|
||||||
files:
|
files:
|
||||||
- path: output/freebayes/test.vcf.gz
|
- path: output/freebayes/test.vcf.gz
|
||||||
|
md5sum: 02645d014a63485162a7789007373b2a
|
||||||
|
- path: output/freebayes/versions.yml
|
||||||
|
md5sum: becc93c8a0be580c09d55b955d60a5e1
|
||||||
|
|
||||||
- name: freebayes test_freebayes_cram
|
- name: freebayes test_freebayes_cram
|
||||||
command: nextflow run ./tests/modules/freebayes -entry test_freebayes_cram -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
|
command: nextflow run tests/modules/freebayes -entry test_freebayes_cram -c tests/config/nextflow.config
|
||||||
tags:
|
tags:
|
||||||
- freebayes
|
- freebayes
|
||||||
files:
|
files:
|
||||||
- path: output/freebayes/test.vcf.gz
|
- path: output/freebayes/test.vcf.gz
|
||||||
|
md5sum: 3d0bfcd2129c62f8863952fa4c1054db
|
||||||
|
- path: output/freebayes/versions.yml
|
||||||
|
md5sum: 2e5b266edfc6cab81353cfc72c00f67c
|
||||||
|
|
||||||
- name: freebayes test_freebayes_somatic
|
- name: freebayes test_freebayes_somatic
|
||||||
command: nextflow run ./tests/modules/freebayes -entry test_freebayes_somatic -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
|
command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic -c tests/config/nextflow.config
|
||||||
tags:
|
tags:
|
||||||
- freebayes
|
- freebayes
|
||||||
files:
|
files:
|
||||||
- path: output/freebayes/test.vcf.gz
|
- path: output/freebayes/test.vcf.gz
|
||||||
|
md5sum: 22fec868210ba3baf685b214bfd8e74b
|
||||||
|
- path: output/freebayes/versions.yml
|
||||||
|
md5sum: 8fbdb4c052fb3e42b5508a966125fa05
|
||||||
|
|
||||||
- name: freebayes test_freebayes_somatic_cram_intervals
|
- name: freebayes test_freebayes_somatic_cram_intervals
|
||||||
command: nextflow run ./tests/modules/freebayes -entry test_freebayes_somatic_cram_intervals -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
|
command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic_cram_intervals -c tests/config/nextflow.config
|
||||||
tags:
|
tags:
|
||||||
- freebayes
|
- freebayes
|
||||||
files:
|
files:
|
||||||
- path: output/freebayes/test.vcf.gz
|
- path: output/freebayes/test.vcf.gz
|
||||||
|
md5sum: 527cf2937067bbd4117d95fd472bb928
|
||||||
|
- path: output/freebayes/versions.yml
|
||||||
|
md5sum: af97e3dfdc086188739907c3460e49e0
|
||||||
|
|
|
@ -6,11 +6,11 @@ include { GATK4_MERGEBAMALIGNMENT } from '../../../../modules/gatk4/mergebamalig
|
||||||
|
|
||||||
workflow test_gatk4_mergebamalignment {
|
workflow test_gatk4_mergebamalignment {
|
||||||
input = [ [ id:'test' ], // meta map
|
input = [ [ id:'test' ], // meta map
|
||||||
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
|
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
|
||||||
|
file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
|
||||||
]
|
]
|
||||||
unmapped = file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
|
|
||||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||||
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
|
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
|
||||||
|
|
||||||
GATK4_MERGEBAMALIGNMENT ( input, unmapped, fasta, dict )
|
GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
|
||||||
}
|
}
|
||||||
|
|
|
@ -8,7 +8,8 @@ workflow test_nextclade_datasetget {
|
||||||
|
|
||||||
dataset = 'sars-cov-2'
|
dataset = 'sars-cov-2'
|
||||||
reference = 'MN908947'
|
reference = 'MN908947'
|
||||||
tag = '2022-01-05T19:54:31Z'
|
tag = '2022-01-18T12:00:00Z'
|
||||||
|
|
||||||
NEXTCLADE_DATASETGET ( dataset, reference, tag )
|
NEXTCLADE_DATASETGET ( dataset, reference, tag )
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
@ -9,12 +9,14 @@
|
||||||
- path: output/nextclade/sars-cov-2/primers.csv
|
- path: output/nextclade/sars-cov-2/primers.csv
|
||||||
md5sum: 5990c3483bf66ce607aeb90a44e7ef2e
|
md5sum: 5990c3483bf66ce607aeb90a44e7ef2e
|
||||||
- path: output/nextclade/sars-cov-2/qc.json
|
- path: output/nextclade/sars-cov-2/qc.json
|
||||||
md5sum: 018fa0c0b0d2e824954e37e01495d549
|
md5sum: c512f51fda0212b21ffff05779180963
|
||||||
- path: output/nextclade/sars-cov-2/reference.fasta
|
- path: output/nextclade/sars-cov-2/reference.fasta
|
||||||
md5sum: c7ce05f28e4ec0322c96f24e064ef55c
|
md5sum: c7ce05f28e4ec0322c96f24e064ef55c
|
||||||
- path: output/nextclade/sars-cov-2/sequences.fasta
|
- path: output/nextclade/sars-cov-2/sequences.fasta
|
||||||
md5sum: 41129d255b99e0e92bdf20e866b99a1b
|
md5sum: 41129d255b99e0e92bdf20e866b99a1b
|
||||||
- path: output/nextclade/sars-cov-2/tag.json
|
- path: output/nextclade/sars-cov-2/tag.json
|
||||||
md5sum: 2f6d8e806d9064571ee4188ef1304c9c
|
md5sum: 402ac2b87e2a6a64a3fbf5ad16497af3
|
||||||
- path: output/nextclade/sars-cov-2/tree.json
|
- path: output/nextclade/sars-cov-2/tree.json
|
||||||
md5sum: f8fb33ed62b59142ac20998eb599df6c
|
md5sum: b8f32f547ff9e2131d6fc66b68fc54b1
|
||||||
|
- path: output/nextclade/sars-cov-2/virus_properties.json
|
||||||
|
md5sum: 5f2de3949e07cb633f3d9e4a7654dc81
|
||||||
|
|
|
@ -9,7 +9,7 @@ workflow test_nextclade_run {
|
||||||
|
|
||||||
dataset = 'sars-cov-2'
|
dataset = 'sars-cov-2'
|
||||||
reference = 'MN908947'
|
reference = 'MN908947'
|
||||||
tag = '2022-01-05T19:54:31Z'
|
tag = '2022-01-18T12:00:00Z'
|
||||||
|
|
||||||
NEXTCLADE_DATASETGET ( dataset, reference, tag )
|
NEXTCLADE_DATASETGET ( dataset, reference, tag )
|
||||||
|
|
||||||
|
@ -20,3 +20,4 @@ workflow test_nextclade_run {
|
||||||
|
|
||||||
NEXTCLADE_RUN ( input, NEXTCLADE_DATASETGET.out.dataset )
|
NEXTCLADE_RUN ( input, NEXTCLADE_DATASETGET.out.dataset )
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
@ -6,8 +6,8 @@
|
||||||
files:
|
files:
|
||||||
- path: output/nextclade/test.json
|
- path: output/nextclade/test.json
|
||||||
- path: output/nextclade/test.csv
|
- path: output/nextclade/test.csv
|
||||||
md5sum: 3b87a4da190ba2e1fdc8418dc3a7ffdb
|
md5sum: 570c1aa2d5fd25c23d0042c1b06108e1
|
||||||
- path: output/nextclade/test.tsv
|
- path: output/nextclade/test.tsv
|
||||||
md5sum: 449393288e8734a02def139c550a8d9b
|
md5sum: dd76e1a4c760785489be4e4a860b4d00
|
||||||
- path: output/nextclade/test.tree.json
|
- path: output/nextclade/test.tree.json
|
||||||
md5sum: 9c6e33cb7ff860bee6194847bd2c855c
|
md5sum: 3591b4dc1542995a7ffcffcb1f52b524
|
||||||
|
|
|
@ -16,6 +16,9 @@ def _get_workflow_names():
|
||||||
# test_config = yaml.safe_load(f.read_text())
|
# test_config = yaml.safe_load(f.read_text())
|
||||||
test_config = yaml.load(f.read_text(), Loader=yaml.BaseLoader)
|
test_config = yaml.load(f.read_text(), Loader=yaml.BaseLoader)
|
||||||
for workflow in test_config:
|
for workflow in test_config:
|
||||||
|
# https://github.com/nf-core/modules/pull/1242 - added to cover tests
|
||||||
|
# that expect an error and therefore will not generate a versions.yml
|
||||||
|
if 'exit_code' not in workflow:
|
||||||
yield workflow["name"]
|
yield workflow["name"]
|
||||||
|
|
||||||
|
|
||||||
|
|
Loading…
Reference in a new issue