Merge branch 'master' into ivar-consensus

This commit is contained in:
Anders Goncalves da Silva 2021-02-12 11:51:24 -08:00
commit 24b212318b
36 changed files with 484 additions and 100 deletions

8
.github/filters.yml vendored
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@ -34,6 +34,10 @@ bedtools_genomecov:
- software/bedtools/genomecov/**
- tests/software/bedtools/genomecov/**
bedtools_getfasta:
- software/bedtools/getfasta/**
- tests/software/bedtools/getfasta/**
bedtools_intersect:
- software/bedtools/intersect/**
- tests/software/bedtools/intersect/**
@ -88,6 +92,10 @@ bwa_mem:
- software/bwa/mem/**
- tests/software/bwa/mem/**
cat_fastq:
- software/cat/fastq/**
- tests/software/cat/fastq/**
cutadapt:
- software/cutadapt/**
- tests/software/cutadapt/**

View file

@ -11,7 +11,7 @@ process BANDAGE_IMAGE {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? 'bioconda::bandage=0.8.1' : null)
conda (params.enable_conda ? 'bioconda::bandage=0.8.1=hc9558a2_2' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bandage:0.8.1--hc9558a2_2"
} else {

View file

@ -10,7 +10,7 @@ process BCFTOOLS_BGZIP {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
conda (params.enable_conda ? "bioconda::bcftools=1.11=h7c999a4_0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
} else {

View file

@ -10,7 +10,7 @@ process BCFTOOLS_CONSENSUS {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
conda (params.enable_conda ? "bioconda::bcftools=1.11=h7c999a4_0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
} else {

View file

@ -10,7 +10,7 @@ process BCFTOOLS_FILTER {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
conda (params.enable_conda ? "bioconda::bcftools=1.11=h7c999a4_0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
} else {

View file

@ -10,7 +10,7 @@ process BCFTOOLS_ISEC {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
conda (params.enable_conda ? "bioconda::bcftools=1.11=h7c999a4_0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
} else {

View file

@ -10,7 +10,7 @@ process BCFTOOLS_STATS {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
conda (params.enable_conda ? "bioconda::bcftools=1.11=h7c999a4_0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
} else {
@ -21,8 +21,8 @@ process BCFTOOLS_STATS {
tuple val(meta), path(vcf)
output:
tuple val(meta), path("*.txt"), emit: stats
path "*.version.txt" , emit: version
tuple val(meta), path("*stats.txt"), emit: stats
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)

View file

@ -52,7 +52,7 @@ output:
- stats:
type: file
description: Text output file containing stats
pattern: "*.{txt}"
pattern: "*_{stats.txt}"
- version:
type: file
description: File containing software version

View file

@ -10,7 +10,7 @@ process BCFTOOLS_TABIX {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
conda (params.enable_conda ? "bioconda::bcftools=1.11=h7c999a4_0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
} else {

View file

@ -0,0 +1,59 @@
/*
* -----------------------------------------------------
* Utility functions used in nf-core DSL2 module files
* -----------------------------------------------------
*/
/*
* Extract name of software tool from process name using $task.process
*/
def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
}
/*
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
*/
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
/*
* Tidy up and join elements of a list to return a path string
*/
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/')
}
/*
* Function to save/publish module results
*/
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
if (ioptions.publish_by_id) {
path_list.add(args.publish_id)
}
if (ioptions.publish_files instanceof Map) {
for (ext in ioptions.publish_files) {
if (args.filename.endsWith(ext.key)) {
def ext_list = path_list.collect()
ext_list.add(ext.value)
return "${getPathFromList(ext_list)}/$args.filename"
}
}
} else if (ioptions.publish_files == null) {
return "${getPathFromList(path_list)}/$args.filename"
}
}
}

View file

@ -0,0 +1,42 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process BEDTOOLS_GETFASTA {
tag "$bed"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? "bioconda::bedtools=2.30.0=hc088bd4_0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
} else {
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
}
input:
path bed
path fasta
output:
path "*.fa" , emit: fasta
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${bed.baseName}${options.suffix}" : "${bed.baseName}"
"""
bedtools \\
getfasta \\
$options.args \\
-fi $fasta \\
-bed $bed \\
-fo ${prefix}.fa
bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
"""
}

View file

@ -0,0 +1,54 @@
name: bedtools_getfasta
description: extract sequences in a FASTA file based on intervals defined in a feature file.
keywords:
- bed
- fasta
- getfasta
tools:
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
- bed:
type: file
description: Bed feature file
pattern: "*.{bed}"
- fasta:
type: file
description: Input fasta file
pattern: "*.{fa,fasta}"
output:
- fasta:
type: file
description: Output fasta file with extracted sequences
pattern: "*.{fa}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@joseespinosa"
- "@drpatelh"

View file

@ -11,7 +11,7 @@ process BEDTOOLS_MASKFASTA {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
conda (params.enable_conda ? "bioconda::bedtools=2.30.0=hc088bd4_0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
} else {

View file

@ -11,7 +11,7 @@ process BLAST_BLASTN {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? 'bioconda::blast=2.10.1' : null)
conda (params.enable_conda ? 'bioconda::blast=2.10.1=pl526he19e7b1_3' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/blast:2.10.1--pl526he19e7b1_3'
} else {

View file

@ -11,7 +11,7 @@ process BLAST_MAKEBLASTDB {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? 'bioconda::blast=2.10.1' : null)
conda (params.enable_conda ? 'bioconda::blast=2.10.1=pl526he19e7b1_3' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/blast:2.10.1--pl526he19e7b1_3'
} else {

View file

@ -22,13 +22,14 @@ process BWA_INDEX {
path fasta
output:
path "${fasta}.*" , emit: index
path "bwa" , emit: index
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
"""
bwa index $options.args $fasta
mkdir bwa
bwa index $options.args $fasta -p bwa/${fasta.baseName}
echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
"""
}

View file

@ -21,7 +21,6 @@ process BWA_MEM {
input:
tuple val(meta), path(reads)
path index
path fasta
output:
tuple val(meta), path("*.bam"), emit: bam
@ -32,13 +31,15 @@ process BWA_MEM {
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
"""
INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
bwa mem \\
$options.args \\
$read_group \\
-t $task.cpus \\
$fasta \\
\$INDEX \\
$reads \\
| samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
| samtools view $options.args2 -@ $task.cpus -bhS -o ${prefix}.bam -
echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
"""

View file

@ -51,10 +51,7 @@ input:
- index:
type: file
description: BWA genome index files
pattern: "*.{amb,ann,bwt,pac,sa}"
- fasta:
type: file
description: Input genome fasta file
pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
output:
- bam:
type: file

View file

@ -0,0 +1,59 @@
/*
* -----------------------------------------------------
* Utility functions used in nf-core DSL2 module files
* -----------------------------------------------------
*/
/*
* Extract name of software tool from process name using $task.process
*/
def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
}
/*
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
*/
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
/*
* Tidy up and join elements of a list to return a path string
*/
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/')
}
/*
* Function to save/publish module results
*/
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
if (ioptions.publish_by_id) {
path_list.add(args.publish_id)
}
if (ioptions.publish_files instanceof Map) {
for (ext in ioptions.publish_files) {
if (args.filename.endsWith(ext.key)) {
def ext_list = path_list.collect()
ext_list.add(ext.value)
return "${getPathFromList(ext_list)}/$args.filename"
}
}
} else if (ioptions.publish_files == null) {
return "${getPathFromList(path_list)}/$args.filename"
}
}
}

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@ -0,0 +1,46 @@
// Import generic module functions
include { initOptions; saveFiles } from './functions'
params.options = [:]
def options = initOptions(params.options)
process CAT_FASTQ {
tag "$meta.id"
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'merged_fastq', publish_id:meta.id) }
conda (params.enable_conda ? "conda-forge::sed=4.7=h1bed415_1000" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
} else {
container "biocontainers/biocontainers:v1.2.0_cv1"
}
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path("*.merged.fastq.gz"), emit: reads
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def readList = reads.collect{ it.toString() }
if (meta.single_end) {
if (readList.size > 1) {
"""
cat ${readList.sort().join(' ')} > ${prefix}.merged.fastq.gz
"""
}
} else {
if (readList.size > 2) {
def read1 = []
def read2 = []
readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
"""
cat ${read1.sort().join(' ')} > ${prefix}_1.merged.fastq.gz
cat ${read2.sort().join(' ')} > ${prefix}_2.merged.fastq.gz
"""
}
}
}

View file

@ -0,0 +1,55 @@
name: cat_fastq
description: Concatenates fastq files
keywords:
- fastq
- concatenate
tools:
- cat:
description: |
The cat utility reads files sequentially, writing them to the standard output.
documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: list
description: |
List of input FastQ files to be concatenated.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: Merged fastq file
pattern: "*.{merged.fastq.gz}"
authors:
- "@joseespinosa"
- "@drpatelh"

View file

@ -10,7 +10,7 @@ process GUNZIP {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
conda (params.enable_conda ? "conda-forge::sed=4.7=h1bed415_1000" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
} else {

View file

@ -11,19 +11,19 @@ process PANGOLIN {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? 'bioconda::pangolin=2.1.7=py_0' : null)
conda (params.enable_conda ? 'bioconda::pangolin=2.2.1=py_0 bioconda::pangolearn=2021.02.05=pyh3252c3a_0' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/pangolin:2.1.7--py_0'
container 'https://depot.galaxyproject.org/singularity/pangolin:2.2.1--py_0'
} else {
container 'quay.io/biocontainers/pangolin:2.1.7--py_0'
container 'quay.io/biocontainers/pangolin:2.2.1--py_0'
}
input:
tuple val(meta), path(fasta)
output:
tuple val(meta), path('*.lineage_report.csv'), emit: report
path '*.version.txt' , emit: version
tuple val(meta), path('*.csv'), emit: report
path '*.version.txt' , emit: version
script:
def software = getSoftwareName(task.process)
@ -31,7 +31,7 @@ process PANGOLIN {
"""
pangolin \\
$fasta\\
--outfile ${prefix}.lineage_report.csv \\
--outfile ${prefix}.pangolin.csv \\
$options.args
pangolin --version | sed "s/pangolin //g" > ${software}.version.txt

View file

@ -1,57 +1,54 @@
name: pangolin
description: Phylogenetic Assignment of Named Global Outbreak LINeages
keywords:
- covid
- pangolin
- lineage
- covid
- pangolin
- lineage
tools:
- star:
description: |
Phylogenetic Assignment of Named Global Outbreak LINeages
homepage: https://github.com/cov-lineages/pangolin#pangolearn-description
manual: https://github.com/cov-lineages/pangolin#pangolearn-description
- star:
description: |
Phylogenetic Assignment of Named Global Outbreak LINeages
homepage: https://github.com/cov-lineages/pangolin#pangolearn-description
manual: https://github.com/cov-lineages/pangolin#pangolearn-description
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
- meta:
type: map
description: |
Groovy Map containing sample information
- fasta:
type: file
description: |
The genome assembly to be evaluated
- meta:
type: map
description: |
Groovy Map containing sample information
- fasta:
type: file
description: |
The genome assembly to be evaluated
output:
- report:
type: file
description: The lineage report
pattern: "{prefix}.lineage_report.csv"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
- report:
type: file
description: Pangolin lineage report
pattern: "*.{csv}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@kevinmenden"
- "@kevinmenden"
- "@drpatelh"

View file

@ -25,7 +25,7 @@ process STRINGTIE {
output:
tuple val(meta), path("*.coverage.gtf") , emit: coverage_gtf
tuple val(meta), path("*.transcripts.gtf"), emit: transcript_gtf
tuple val(meta), path("*.txt") , emit: abundance
tuple val(meta), path("*.abundance.txt") , emit: abundance
tuple val(meta), path("*.ballgown") , emit: ballgown
path "*.version.txt" , emit: version
@ -45,7 +45,7 @@ process STRINGTIE {
$strandedness \\
-G $gtf \\
-o ${prefix}.transcripts.gtf \\
-A ${prefix}.gene_abundance.txt \\
-A ${prefix}.gene.abundance.txt \\
-C ${prefix}.coverage.gtf \\
-b ${prefix}.ballgown \\
$options.args

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@ -10,7 +10,7 @@ process UNTAR {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
conda (params.enable_conda ? "conda-forge::sed=4.7=h1bed415_1000" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
} else {

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@ -0,0 +1,12 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BEDTOOLS_GETFASTA } from '../../../../software/bedtools/getfasta/main.nf' addParams( options: [:] )
workflow test_bedtools_getfasta {
def bed = [ file("${launchDir}/tests/data/bed/C.bed", checkIfExists: true) ]
def fasta = [ file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) ]
BEDTOOLS_GETFASTA ( bed, fasta )
}

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@ -0,0 +1,8 @@
- name: bedtools getfasta
command: nextflow run ./tests/software/bedtools/getfasta -entry test_bedtools_getfasta -c tests/config/nextflow.config
tags:
- bedtools
- bedtools_getfasta
files:
- path: output/bedtools/C.fa
md5sum: 2257190c8d9fc6f177a518440cf1f3f3

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@ -5,10 +5,9 @@ nextflow.enable.dsl = 2
include { BEDTOOLS_MASKFASTA } from '../../../../software/bedtools/maskfasta/main.nf' addParams( options: [:] )
workflow test_bedtools_maskfasta {
def input,fasta = []
bed = [ [ id:'test'],
file("${launchDir}/tests/data/bed/C.bed", checkIfExists: true) ]
fasta = [ file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) ]
def bed = [ [ id:'test'],
file("${launchDir}/tests/data/bed/C.bed", checkIfExists: true) ]
def fasta = [ file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) ]
BEDTOOLS_MASKFASTA( bed, fasta )
}

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@ -4,11 +4,11 @@
- bwa
- bwa_index
files:
- path: output/bwa/NC_010473.fa.amb
- path: output/bwa/bwa/NC_010473.amb
md5sum: 942a990ae872f1c0b8d72dda2db405d5
- path: output/bwa/NC_010473.fa.bwt
- path: output/bwa/bwa/NC_010473.bwt
md5sum: 7301b52e2ecb893d429a49fa692447ae
- path: output/bwa/NC_010473.fa.pac
- path: output/bwa/bwa/NC_010473.pac
md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad
- path: output/bwa/NC_010473.fa.sa
md5sum: a47dcc92e750e2f16fbd979b8ff9538e
- path: output/bwa/bwa/NC_010473.sa
md5sum: a47dcc92e750e2f16fbd979b8ff9538e

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@ -15,8 +15,7 @@ workflow test_bwa_mem_single_end {
BWA_MEM (
input,
file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
file("${launchDir}/tests/data/index/E_coli/bwa/", checkIfExists: true)
)
}
@ -32,7 +31,6 @@ workflow test_bwa_mem_paired_end {
BWA_MEM (
input,
file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
file("${launchDir}/tests/data/index/E_coli/bwa/", checkIfExists: true)
)
}

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@ -6,7 +6,7 @@
- bwa_mem_single_end
files:
- path: output/bwa/test.bam
md5sum: 3ee21210bac387e0335008146e4728bc
md5sum: 52e81e5bd523d0b27fe533b21a0d80f5
- name: bwa mem paired-end
command: nextflow run ./tests/software/bwa/mem -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
@ -16,4 +16,4 @@
- bwa_mem_paired_end
files:
- path: output/bwa/test.bam
md5sum: 510d8acc6448c07cdacce8e64ec0904c
md5sum: 86d82fdb68ed384c656cfc62a253052f

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@ -0,0 +1,27 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { CAT_FASTQ } from '../../../../software/cat/fastq/main.nf' addParams( options: [:] )
workflow test_cat_fastq_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1_val_1.fq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ]]
CAT_FASTQ ( input )
}
workflow test_cat_fastq_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1_val_1.fq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2_val_2.fq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ]]
CAT_FASTQ ( input )
}

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@ -0,0 +1,21 @@
- name: cat fastq single-end
command: nextflow run ./tests/software/cat/fastq -entry test_cat_fastq_single_end -c tests/config/nextflow.config
tags:
- cat
- cat_fastq
- cat_fastqc_single_end
files:
- path: output/merged_fastq/test.merged.fastq.gz
md5sum: 7f753b793e5b0872758b1574db84d767
- name: cat fastq fastqc_paired_end
command: nextflow run ./tests/software/cat/fastq -entry test_cat_fastq_paired_end -c tests/config/nextflow.config
tags:
- cat
- cat_fastq
- cat_fastqc_paired_end
files:
- path: output/merged_fastq/test_1.merged.fastq.gz
md5sum: 7f753b793e5b0872758b1574db84d767
- path: output/merged_fastq/test_2.merged.fastq.gz
md5sum: c71ff917e002b1e852916a021d52921d

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@ -2,11 +2,11 @@
nextflow.enable.dsl = 2
include { PANGOLIN } from '../../../software/pangolin/main.nf' addParams(options: [:])
include { PANGOLIN } from '../../../software/pangolin/main.nf' addParams( options: [:] )
workflow test_pangolin {
input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) ] ]
PANGOLIN( input )
PANGOLIN ( input )
}

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@ -3,5 +3,5 @@
tags:
- pangolin
files:
- path: ./output/pangolin/test.lineage_report.csv
md5sum: a7423586a536a58f14fb4553f92b225e
- path: ./output/pangolin/test.pangolin.csv
md5sum: 097669de1843e27f4529d6db8bbed97b