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Merge remote-tracking branch 'upstream/master'

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This commit is contained in:
Sviatoslav Sidorov 2021-04-07 21:10:30 +01:00
commit 46eb839553
45 changed files with 473 additions and 201 deletions
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10
software/bismark/report/main.nf
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@ -22,17 +22,13 @@ process BISMARK_REPORT {
tuple val(meta), path(align_report), path(dedup_report), path(splitting_report), path(mbias)
output:
tuple val(meta), path("*{html,txt}"), emit: report
path "*.version.txt" , emit: version
tuple val(meta), path("*report.{html,txt}"), emit: report
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
"""
bismark2report \\
--alignment_report $align_report \\
--dedup_report $dedup_report \\
--splitting_report $splitting_report \\
--mbias_report $mbias
bismark2report $options.args
echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt
"""

4
software/bismark/summary/main.nf
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@ -25,8 +25,8 @@ process BISMARK_SUMMARY {
path(mbias)
output:
path("*{html,txt}") , emit: summary
path "*.version.txt", emit: version
path "*report.{html,txt}", emit: summary
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)

4
software/bwameth/align/main.nf
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@ -13,9 +13,9 @@ process BWAMETH_ALIGN {
conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bwameth:0.20--py35_0"
container "https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1"
} else {
container "quay.io/biocontainers/bwameth:0.20--py35_0"
container "quay.io/biocontainers/bwameth:0.2.2--py_1"
}
input:

4
software/bwameth/index/main.nf
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@ -13,9 +13,9 @@ process BWAMETH_INDEX {
conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bwameth:0.20--py35_0"
container "https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1"
} else {
container "quay.io/biocontainers/bwameth:0.20--py35_0"
container "quay.io/biocontainers/bwameth:0.2.2--py_1"
}
input:

60
software/gubbins/functions.nf Normal file
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@ -0,0 +1,60 @@
/*
* -----------------------------------------------------
* Utility functions used in nf-core DSL2 module files
* -----------------------------------------------------
*/
/*
* Extract name of software tool from process name using $task.process
*/
def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
}
/*
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
*/
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.args3 = args.args3 ?: ''
options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
/*
* Tidy up and join elements of a list to return a path string
*/
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/')
}
/*
* Function to save/publish module results
*/
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
if (ioptions.publish_by_id) {
path_list.add(args.publish_id)
}
if (ioptions.publish_files instanceof Map) {
for (ext in ioptions.publish_files) {
if (args.filename.endsWith(ext.key)) {
def ext_list = path_list.collect()
ext_list.add(ext.value)
return "${getPathFromList(ext_list)}/$args.filename"
}
}
} else if (ioptions.publish_files == null) {
return "${getPathFromList(path_list)}/$args.filename"
}
}
}

44
software/gubbins/main.nf Normal file
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@ -0,0 +1,44 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process GUBBINS {
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::gubbins=2.4.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gubbins:2.4.1--py38h197edbe_1"
} else {
container "quay.io/biocontainers/gubbins:2.4.1--py38h197edbe_1"
}
input:
path alignment
output:
path "*.fasta" , emit: fasta
path "*.gff" , emit: gff
path "*.vcf" , emit: vcf
path "*.csv" , emit: stats
path "*.phylip" , emit: phylip
path "*.recombination_predictions.embl" , emit: embl_predicted
path "*.branch_base_reconstruction.embl", emit: embl_branch
path "*.final_tree.tre" , emit: tree
path "*.node_labelled.final_tree.tre" , emit: tree_labelled
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
"""
run_gubbins.py \\
--threads $task.cpus \\
$options.args \\
$alignment
echo \$(run_gubbins.py --version 2>&1) > ${software}.version.txt
"""
}

61
software/gubbins/meta.yml Normal file
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@ -0,0 +1,61 @@
name: gubbins
description: Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies
loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the
putative point mutations outside of these regions.
keywords:
- recombination
- alignment
tools:
- gubbins:
description: Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
homepage: https://sanger-pathogens.github.io/gubbins/
documentation: https://sanger-pathogens.github.io/gubbins/
input:
- alignment:
type: file
description: fasta alignment file
pattern: "*.{fasta,fas,fa,aln}"
output:
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
- fasta:
type: file
description: Filtered variant alignment in fasta format
pattern: "*.{fasta}"
- embl_predicted:
type: file
description: Recombination predictions in embl format
pattern: "*.{recombination_predictions.embl}"
- gff:
type: file
description: Recombination predictions in gff format
pattern: "*.{gff}"
- embl_branch:
type: file
description: Branch base reconstruction
pattern: "*.{branch_base_reconstruction.embl}"
- vcf:
type: file
description: SNP distribution
pattern: "*.{vcf}"
- stats:
type: file
description: Per branch statistics
pattern: "*.{csv}"
- phylip:
type: file
description: Filtered variant alignment in phylip format
pattern: "*.{phylip}"
- tree:
type: file
description: Recombination removed RAxML phylogenetic tree
pattern: "*.{final_tree.tre}"
- tree_labelled:
type: file
description: Recombination removed RAxML phylogenetic tree (nodes labelled)
pattern: "*.{node_labelled.final_tree.tre}"
authors:
- "@avantonder"

2
software/methyldackel/extract/main.nf
View file

@ -35,6 +35,6 @@ process METHYLDACKEL_EXTRACT {
$fasta \\
$bam
echo \$(methyldackel --version 2>&1) | cut -f1 -d" " > ${software}.version.txt
echo \$(MethylDackel --version 2>&1) | cut -f1 -d" " > ${software}.version.txt
"""
}

8
software/methyldackel/mbias/main.nf
View file

@ -24,8 +24,8 @@ process METHYLDACKEL_MBIAS {
path fai
output:
tuple val(meta), path("*.txt"), emit: txt
path "*.version.txt" , emit: version
tuple val(meta), path("*.mbias.txt"), emit: txt
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
@ -37,8 +37,8 @@ process METHYLDACKEL_MBIAS {
$bam \\
$prefix \\
--txt \\
> ${prefix}.txt
> ${prefix}.mbias.txt
echo \$(methyldackel --version 2>&1) | cut -f1 -d" " > ${software}.version.txt
echo \$(MethylDackel --version 2>&1) | cut -f1 -d" " > ${software}.version.txt
"""
}

6
software/pangolin/main.nf
View file

@ -11,11 +11,11 @@ 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=2.3.2' : null)
conda (params.enable_conda ? 'bioconda::pangolin=2.3.8' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/pangolin:2.3.2--py_0'
container 'https://depot.galaxyproject.org/singularity/pangolin:2.3.8--py_0'
} else {
container 'quay.io/biocontainers/pangolin:2.3.2--py_0'
container 'quay.io/biocontainers/pangolin:2.3.8--py_0'
}
input:

9
software/rsem/preparereference/main.nf
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@ -19,12 +19,13 @@ process RSEM_PREPAREREFERENCE {
}
input:
path fasta
path fasta, stageAs: "rsem/*"
path gtf
output:
path "rsem" , emit: index
path "*.version.txt", emit: version
path "rsem" , emit: index
path "rsem/*transcripts.fa", emit: transcript_fasta
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
@ -33,7 +34,6 @@ process RSEM_PREPAREREFERENCE {
args.removeIf { it.contains('--star') }
def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
"""
mkdir rsem
STAR \\
--runMode genomeGenerate \\
--genomeDir rsem/ \\
@ -54,7 +54,6 @@ process RSEM_PREPAREREFERENCE {
"""
} else {
"""
mkdir rsem
rsem-prepare-reference \\
--gtf $gtf \\
--num-threads $task.cpus \\

10
software/spades/main.nf
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@ -11,17 +11,16 @@ process SPADES {
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::spades=3.15.0" : null)
conda (params.enable_conda ? "bioconda::spades=3.15.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/spades:3.15.0--h633aebb_0"
container "https://depot.galaxyproject.org/singularity/spades:3.15.2--h95f258a_1"
} else {
container "quay.io/biocontainers/spades:3.15.0--h633aebb_0"
container "quay.io/biocontainers/spades:3.15.2--h95f258a_1"
}
input:
tuple val(meta), path(reads)
path hmm
val coronaspades
output:
tuple val(meta), path('*.scaffolds.fa') , optional:true, emit: scaffolds
@ -37,9 +36,8 @@ process SPADES {
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def input_reads = meta.single_end ? "-s $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
def custom_hmms = params.spades_hmm ? "--custom-hmms $hmm" : ""
def command = coronaspades ? "coronaspades.py" : "spades.py"
"""
$command \\
spades.py \\
$options.args \\
--threads $task.cpus \\
$custom_hmms \\

5
software/spades/meta.yml
View file

@ -29,11 +29,6 @@ input:
type: file
description:
File or directory with amino acid HMMs for Spades HMM-guided mode.
- coronaspades:
type: boolean
description: |
Run coronaspades instead of default spades mode. coronaSPAdes is a special
mode of rnaviralSPAdes specifically aimed for SARS-CoV-2 de novo assembly.
output:
- meta:
type: map

52
software/subread/featurecounts/meta.yml Normal file
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@ -0,0 +1,52 @@
name: subread_featurecounts
description: Count reads that map to genomic features
keywords:
- counts
- fasta
- genome
- reference
tools:
- featurecounts:
description: featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. It can be used to count both RNA-seq and genomic DNA-seq reads.
homepage: http://bioinf.wehi.edu.au/featureCounts/
documentation: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf
doi: "10.1093/bioinformatics/btt656"
licence: ['GPL v3']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM/SAM file containing read alignments
pattern: "*.{bam}"
- annotation:
type: file
description: Genomic features annotation in GTF or SAF
pattern: "*.{gtf,saf}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- counts:
type: file
description: Counts of reads mapping to features
pattern: "*featureCounts.txt"
- summary:
type: file
description: Summary log file
pattern: "*.featureCounts.txt.summary"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@ntoda03"

3
software/tabix/bgzip/main.nf
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@ -30,6 +30,7 @@ process TABIX_BGZIP {
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
bgzip -c $options.args $input > ${prefix}.${input.getExtension()}.gz
echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/(.*\$//' > ${software}.version.txt
"""
}

8
tests/config/pytest_software.yml
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@ -246,6 +246,10 @@ gffread:
- software/gffread/**
- tests/software/gffread/**
gubbins:
- software/gubbins/**
- tests/software/gubbins/**
gunzip:
- software/gunzip/**
- tests/software/gunzip/**
@ -466,6 +470,10 @@ stringtie:
- software/stringtie/**
- tests/software/stringtie/**
subread_featurecounts:
- software/subread/featurecounts/**
- tests/software/subread/featurecounts/**
tabix_bgzip:
- software/tabix/bgzip/**
- tests/software/tabix/bgzip/**

3
tests/config/test_data.config
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@ -9,6 +9,7 @@ params {
genome_fasta_fai = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta.fai"
genome_dict = "${test_data_dir}/genomics/sarscov2/genome/genome.dict"
genome_gff3 = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3"
genome_gff3_gz = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3.gz"
genome_gtf = "${test_data_dir}/genomics/sarscov2/genome/genome.gtf"
genome_sizes = "${test_data_dir}/genomics/sarscov2/genome/genome.sizes"
transcriptome_fasta = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.fasta"
@ -24,6 +25,8 @@ params {
kraken2_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
test_wig_gz = "${test_data_dir}/genomics/sarscov2/genome/gcwiggle/test.wig.gz"
test_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/test.fas"
}
'illumina' {
test_single_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.bam"

8
tests/data/genomics/sarscov2/genome/alignment/test.fas Normal file
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tests/data/genomics/sarscov2/genome/genome.gff3.gz Normal file
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2
tests/software/blast/blastn/main.nf
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@ -6,7 +6,7 @@ include { BLAST_MAKEBLASTDB } from '../../../../software/blast/makeblastdb/main.
include { BLAST_BLASTN } from '../../../../software/blast/blastn/main.nf' addParams( options: [:] )
workflow test_blast_blastn {
input = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
BLAST_MAKEBLASTDB ( input )
BLAST_BLASTN ( [ [id:'test'], input ], BLAST_MAKEBLASTDB.out.db )

18
tests/software/blast/blastn/test.yml
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@ -5,18 +5,18 @@
- blast_blastn
files:
- path: ./output/blast/test.blastn.txt
- path: ./output/blast/blast_db/test_genome.fasta.nsq
- path: ./output/blast/blast_db/genome.fasta.nsq
md5sum: 982cbc7d9e38743b9b1037588862b9da
- path: ./output/blast/blast_db/test_genome.fasta.nin
- path: ./output/blast/blast_db/test_genome.fasta
- path: ./output/blast/blast_db/genome.fasta.nin
- path: ./output/blast/blast_db/genome.fasta
md5sum: 6e9fe4042a72f2345f644f239272b7e6
- path: ./output/blast/blast_db/test_genome.fasta.nhr
- path: ./output/blast/blast_db/genome.fasta.nhr
md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e
- path: ./output/blast/blast_db/test_genome.fasta.ndb
md5sum: 5134241fd6e34d01a6ab0f2d0986e8ed
- path: ./output/blast/blast_db/test_genome.fasta.not
- path: ./output/blast/blast_db/genome.fasta.ndb
md5sum: 45f2daf9769957ff80868dd3d80d30a3
- path: ./output/blast/blast_db/genome.fasta.not
md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
- path: ./output/blast/blast_db/test_genome.fasta.nto
- path: ./output/blast/blast_db/genome.fasta.nto
md5sum: 33cdeccccebe80329f1fdbee7f5874cb
- path: ./output/blast/blast_db/test_genome.fasta.ntf
- path: ./output/blast/blast_db/genome.fasta.ntf
md5sum: 1f6027d443e67a98ad0edc2d39971b0c

2
tests/software/blast/makeblastdb/main.nf
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@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
include { BLAST_MAKEBLASTDB } from '../../../../software/blast/makeblastdb/main.nf' addParams( options: ['args': '-dbtype nucl'] )
workflow test_blast_makeblastdb {
input = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
BLAST_MAKEBLASTDB ( input )
}

18
tests/software/blast/makeblastdb/test.yml
View file

@ -4,18 +4,18 @@
- blast
- blast_makeblastdb
files:
- path: ./output/blast/blast_db/test_genome.fasta.nsq
- path: ./output/blast/blast_db/genome.fasta.nsq
md5sum: 982cbc7d9e38743b9b1037588862b9da
- path: ./output/blast/blast_db/test_genome.fasta.nin
- path: ./output/blast/blast_db/test_genome.fasta
- path: ./output/blast/blast_db/genome.fasta.nin
- path: ./output/blast/blast_db/genome.fasta
md5sum: 6e9fe4042a72f2345f644f239272b7e6
- path: ./output/blast/blast_db/test_genome.fasta.nhr
- path: ./output/blast/blast_db/genome.fasta.nhr
md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e
- path: ./output/blast/blast_db/test_genome.fasta.ndb
md5sum: 5134241fd6e34d01a6ab0f2d0986e8ed
- path: ./output/blast/blast_db/test_genome.fasta.not
- path: ./output/blast/blast_db/genome.fasta.ndb
md5sum: 45f2daf9769957ff80868dd3d80d30a3
- path: ./output/blast/blast_db/genome.fasta.not
md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
- path: ./output/blast/blast_db/test_genome.fasta.nto
- path: ./output/blast/blast_db/genome.fasta.nto
md5sum: 33cdeccccebe80329f1fdbee7f5874cb
- path: ./output/blast/blast_db/test_genome.fasta.ntf
- path: ./output/blast/blast_db/genome.fasta.ntf
md5sum: 1f6027d443e67a98ad0edc2d39971b0c

4
tests/software/flash/main.nf
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@ -6,8 +6,8 @@ include { FLASH } from '../../../software/flash/main.nf' addParams( options: [ar
workflow test_flash {
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
FLASH ( input )

11
tests/software/gubbins/main.nf Normal file
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@ -0,0 +1,11 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GUBBINS } from '../../../software/gubbins/main.nf' addParams( options: [:] )
workflow test_gubbins {
input = file(params.test_data['sarscov2']['genome']['test_fas'], checkIfExists: true)
GUBBINS ( input )
}

23
tests/software/gubbins/test.yml Normal file
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@ -0,0 +1,23 @@
- name: gubbins
command: nextflow run ./tests/software/gubbins -entry test_gubbins -c tests/config/nextflow.config
tags:
- gubbins
files:
- path: output/gubbins/test.filtered_polymorphic_sites.fasta
md5sum: c9dff2294307eb2200a6e19efce47796
- path: output/gubbins/test.recombination_predictions.embl
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/gubbins/test.recombination_predictions.gff
md5sum: a2ca9c119674f4d121a8f78e4078fe05
- path: output/gubbins/test.branch_base_reconstruction.embl
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/gubbins/test.summary_of_snp_distribution.vcf
md5sum: afee50e92fb919a5df487fbda0b9dbb5
- path: output/gubbins/test.per_branch_statistics.csv
md5sum: 0f364b5e0b01a6be9b6a4407658ab25f
- path: output/gubbins/test.filtered_polymorphic_sites.phylip
md5sum: 85db9d0896cfec34a73641496b7498bb
- path: output/gubbins/test.final_tree.tre
md5sum: dce7164a0c69bb3d642a419907364aa3
- path: output/gubbins/test.node_labelled.final_tree.tre
md5sum: beef5ce05aca4598bb3f42caf126e045

8
tests/software/methyldackel/extract/main.nf
View file

@ -6,10 +6,10 @@ include { METHYLDACKEL_EXTRACT } from '../../../../software/methyldackel/extract
workflow test_methyldackel_extract {
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam.bai", checkIfExists: true) ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
fai = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam_bai'], checkIfExists: true) ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
METHYLDACKEL_EXTRACT ( input, fasta, fai )
}

9
tests/software/methyldackel/mbias/main.nf
View file

@ -6,11 +6,10 @@ include { METHYLDACKEL_MBIAS } from '../../../../software/methyldackel/mbias/mai
workflow test_methyldackel_mbias {
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam.bai", checkIfExists: true)
]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
fai = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam_bai'], checkIfExists: true) ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
METHYLDACKEL_MBIAS ( input, fasta, fai )
}

2
tests/software/methyldackel/mbias/test.yml
View file

@ -4,5 +4,5 @@
- methyldackel
- methyldackel_mbias
files:
- path: output/methyldackel/test.txt
- path: output/methyldackel/test.mbias.txt
md5sum: 357bb944dc2cdffcc47fa0d34376e016

4
tests/software/mosdepth/main.nf
View file

@ -6,8 +6,8 @@ include { MOSDEPTH } from '../../../software/mosdepth/main.nf' addParams( option
workflow test_mosdepth {
input = [ [ id:'test', single_end:true ],
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) ],
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
]
dummy = file("dummy_file.txt")
window = 100

4
tests/software/optitype/main.nf
View file

@ -2,11 +2,11 @@
nextflow.enable.dsl = 2
include { OPTITYPE } from ''../../../software/optitype/main.nf' addParams( options: ['args':'-e 1 -b 0.009', 'args2':'solver=glpk'] )
include { OPTITYPE } from '../../../software/optitype/main.nf' addParams( options: ['args':'-e 1 -b 0.009', 'args2':'solver=glpk'] )
workflow test_optitype {
input = [ [ id:'test', seq_type:'dna' ], // meta map
file("${launchDir}/tests/data/genomics/homo_sapiens/illumina/bam/example_pe.bam", checkIfExists: true)
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
OPTITYPE ( input )

2
tests/software/pangolin/main.nf
View file

@ -6,7 +6,7 @@ include { PANGOLIN } from '../../../software/pangolin/main.nf' addParams( option
workflow test_pangolin {
input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ] ]
[ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] ]
PANGOLIN ( input )
}

2
tests/software/pangolin/test.yml
View file

@ -4,4 +4,4 @@
- pangolin
files:
- path: ./output/pangolin/test.pangolin.csv
md5sum: 1d513775cec0901ebee1359c91035d3a
md5sum: c8b1720f98c9e032908f61bbc05a0fe2

4
tests/software/qualimap/bamqc/main.nf
View file

@ -6,10 +6,10 @@ include { QUALIMAP_BAMQC } from '../../../../software/qualimap/bamqc/main.nf' ad
workflow test_qualimap_bamqc {
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true)
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
]
gff = file("dummy_file.txt")
use_gff = false
QUALIMAP_BAMQC ( input, gff, use_gff )
}
}

8
tests/software/quast/main.nf
View file

@ -5,9 +5,9 @@ nextflow.enable.dsl = 2
include { QUAST } from '../../../software/quast/main.nf' addParams(options: [:])
workflow test_quast_ref {
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
gff = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
consensus = file("${launchDir}/tests/data/genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
gff = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
consensus = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
use_fasta = true
use_gtf = true
@ -17,7 +17,7 @@ workflow test_quast_ref {
workflow test_quast_noref {
fasta = file('fasta_dummy')
gff = file('gff_dummy')
consensus = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
consensus = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
use_fasta = false
use_gtf = false

78
tests/software/quast/test.yml
View file

@ -6,32 +6,32 @@
files:
- path: ./output/quast/report.tsv
- path: ./output/quast/quast/transposed_report.txt
md5sum: 73ae4f7cbe0da640819214cb013a79ef
md5sum: 5dee51af1e7f916200d0a80f0c66be60
- path: ./output/quast/quast/transposed_report.tex
md5sum: 117ed0d235b8e74b8f7ae8ed7b78c449
md5sum: 336ec8d7b403fe1e0519e3a39eadd691
- path: ./output/quast/quast/icarus.html
- path: ./output/quast/quast/transposed_report.tsv
md5sum: 475bf9987c421b72fe1675b54ae0bcbe
md5sum: 0e1b2eff1e8fd91a0bf80165d8f31ae5
- path: ./output/quast/quast/report.tex
md5sum: e4c1d12bfe94d5a10e2264397bb90f83
md5sum: a9aac7d2ac2263df7e4599e4431c7393
- path: ./output/quast/quast/report.txt
md5sum: 6295e6d462b1db45b1bb9f3f508275ad
md5sum: 2da78350f20819f2625bd467800700ad
- path: ./output/quast/quast/report.tsv
md5sum: b70404d2b4d4e905afcfe3d149a5bd15
md5sum: 38fb41afadc09ffcbef62e42fea49f5e
- path: ./output/quast/quast/report.html
- path: ./output/quast/quast/report.pdf
- path: ./output/quast/quast/quast.log
- path: ./output/quast/quast/genome_stats/test_transcriptome_genomic_features_any.txt
- path: ./output/quast/quast/genome_stats/transcriptome_genomic_features_any.txt
md5sum: 307b3bb1f42fc2f11a60a2e9846021d7
- path: ./output/quast/quast/genome_stats/features_cumulative_plot.pdf
- path: ./output/quast/quast/genome_stats/features_frcurve_plot.pdf
- path: ./output/quast/quast/genome_stats/genome_info.txt
md5sum: a4bb1f2792c175fc8d7fbf37f219e552
- path: ./output/quast/quast/genome_stats/test_transcriptome_gaps.txt
md5sum: d0193b322079565dc78608291e9c44d1
- path: ./output/quast/quast/genome_stats/transcriptome_gaps.txt
md5sum: c52381f09ea40b6141be5232494727b6
- path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
- path: ./output/quast/quast/basic_stats/Nx_plot.pdf
- path: ./output/quast/quast/basic_stats/test_transcriptome_GC_content_plot.pdf
- path: ./output/quast/quast/basic_stats/transcriptome_GC_content_plot.pdf
- path: ./output/quast/quast/basic_stats/gc.icarus.txt
md5sum: b3a770802ff9b2dd4ee8e47bddb2df3e
- path: ./output/quast/quast/basic_stats/NGx_plot.pdf
@ -39,45 +39,45 @@
- path: ./output/quast/quast/aligned_stats/cumulative_plot.pdf
- path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf
- path: ./output/quast/quast/aligned_stats/NAx_plot.pdf
- path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.mis_contigs.info
- path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.mis_contigs.info
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf
- path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.unaligned.info
- path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.unaligned.info
md5sum: a8505cf206bf53ca369f7e3073fee587
- path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex
md5sum: 4895cb02a010f1db85fc4992ac3c63b1
md5sum: d778f337899736cc62ed837b739b375c
- path: ./output/quast/quast/contigs_reports/misassemblies_report.txt
md5sum: d5c9dd22ce8f382649f74ba1f61d8a84
- path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.stdout
- path: ./output/quast/quast/contigs_reports/all_alignments_test_transcriptome.tsv
md5sum: 8b9a6d675a41bab6bf344dde2a20a939
- path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.stdout
- path: ./output/quast/quast/contigs_reports/all_alignments_transcriptome.tsv
md5sum: c247152eb82b361106492642fd796e2c
- path: ./output/quast/quast/contigs_reports/misassemblies_report.tex
md5sum: 0df52940978f10c0fc9ed5f6770f170e
- path: ./output/quast/quast/contigs_reports/test_transcriptome.mis_contigs.fa
md5sum: ec1f7a1d1fb4a1b465057cf897b90b51
- path: ./output/quast/quast/contigs_reports/transcriptome.mis_contigs.fa
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt
md5sum: d83abdf60e7ef02354a783dff4262d7d
md5sum: fdb440c653e2f0306286798cacceaadb
- path: ./output/quast/quast/contigs_reports/unaligned_report.tsv
md5sum: f2adf811a611abdcb9f10bd7801e61e1
md5sum: 81d9597314356363a6b4e0d67027345a
- path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv
md5sum: dd6e08408ea9a6830d47d5c21b84d587
md5sum: 3e8f449dd4481d1cfd4ce3ddab97b8e3
- path: ./output/quast/quast/contigs_reports/unaligned_report.txt
- path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv
md5sum: e77d87bafe0e2c881805f8dfcc5f2351
- path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.stderr
md5sum: a32a09a0df811d1a75fbfe124081d1ca
- path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.stderr
- path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf
- path: ./output/quast/quast/contigs_reports/unaligned_report.tex
md5sum: 6f9bd38e646b0a754b153e0dfe2c57b0
- path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.coords.filtered
md5sum: e8e3bcb86da2cbd8eded980de80fa45c
- path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords.filtered
md5sum: ec9191d0acb5d5bce56b4842551a8598
- path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.coords
- path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords
md5sum: dda3fc0addc41ecc0d5183dee6f95886
- path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.used_snps.gz
- path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.used_snps.gz
md5sum: 7b1db1b433cd95243a949bcb72e7e3a6
- path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.sf
- path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.unaligned
- path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.sf
- path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.unaligned
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.coords_tmp
- path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords_tmp
md5sum: ce66eaeb99fdc11e4d50efadc1816e04
- path: ./output/quast/quast/icarus_viewers/alignment_viewer.html
- path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
@ -89,26 +89,26 @@
- quast_no_reference
files:
- path: ./output/quast/report.tsv
md5sum: 94e7fd30b8147f1b9df4373ad865c0aa
md5sum: 074e239aac0f298cf4cd2a28a9bb5690
- path: ./output/quast/quast/transposed_report.txt
md5sum: 5496230d4bc3846616d7e08d52ffc081
md5sum: 8784d7c7349498e1507e09fbf554625d
- path: ./output/quast/quast/transposed_report.tex
md5sum: cf6a3b50575b510a7c42f5e745dd8674
md5sum: 4c2a9dd0c1d3cbb80a2ac2577b5d363b
- path: ./output/quast/quast/icarus.html
md5sum: ba0ddcdbcd743191d282e3986cb68735
md5sum: ecc0b67f3d4ff54568dfb83d8ac5911b
- path: ./output/quast/quast/transposed_report.tsv
md5sum: 4b128bbf595b07dd2e2d5230bf575d29
md5sum: f0b5f65b2050af83b6d170d384c7616b
- path: ./output/quast/quast/report.tex
md5sum: ac22b93fad7cdb6a812e5f670e815647
md5sum: 3da038cc5a02ef83e225c5277b87970b
- path: ./output/quast/quast/report.txt
md5sum: 283160faa1d8cd32064c49e3c6d738d5
md5sum: bd2faaef244f02aa072d544c0d6d6e71
- path: ./output/quast/quast/report.tsv
md5sum: 94e7fd30b8147f1b9df4373ad865c0aa
md5sum: 074e239aac0f298cf4cd2a28a9bb5690
- path: ./output/quast/quast/report.html
- path: ./output/quast/quast/report.pdf
- path: ./output/quast/quast/quast.log
- path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
- path: ./output/quast/quast/basic_stats/Nx_plot.pdf
- path: ./output/quast/quast/basic_stats/test_genome_GC_content_plot.pdf
- path: ./output/quast/quast/basic_stats/genome_GC_content_plot.pdf
- path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
- path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html

35
tests/software/spades/main.nf
View file

@ -2,43 +2,20 @@
nextflow.enable.dsl = 2
include { SPADES } from '../../../software/spades/main.nf' addParams( spades_hmm: false ,options: [:] )
include { SPADES } from '../../../software/spades/main.nf' addParams( spades_hmm: false ,options: ['args': '--rnaviral'] )
workflow test_spades_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
coronaspades = false
SPADES ( input, [], coronaspades )
SPADES ( input, [] )
}
workflow test_spades_paired_end {
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
coronaspades = false
SPADES ( input, [], coronaspades )
SPADES ( input, [] )
}
workflow test_coronospades_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
]
coronaspades = true
SPADES ( input, [], coronaspades )
}
workflow test_coronospades_paired_end {
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ]
]
coronaspades = true
SPADES ( input, [], coronaspades )
}

43
tests/software/spades/test.yml
View file

@ -5,13 +5,12 @@
- spades_single_end
files:
- path: output/spades/test.assembly.gfa
md5sum: f15ad4a198324de37c6010dafb3fe781
md5sum: b2616d2beba83ab7d361b54778d1e759
- path: output/spades/test.contigs.fa
md5sum: bc21771042b465c26dfc85beedc33d58
md5sum: 2690fefde046bc904e90df09a065257a
- path: output/spades/test.scaffolds.fa
md5sum: bc21771042b465c26dfc85beedc33d58
md5sum: 2690fefde046bc904e90df09a065257a
- path: output/spades/test.spades.log
- path: output/spades/warnings.log
- name: spades paired end
command: nextflow run ./tests/software/spades -entry test_spades_paired_end -c tests/config/nextflow.config
@ -20,39 +19,7 @@
- spades_paired_end
files:
- path: output/spades/test.assembly.gfa
md5sum: 5da5b04c6fce549c77a209034a9c1e72
md5sum: faf76135ee390606b899c0197dc38e04
- path: output/spades/test.contigs.fa
md5sum: 403b612d52edf390f662ab601873f09f
- path: output/spades/test.scaffolds.fa
md5sum: 49a9cbb29cee4d088e05e62eb4bc77c4
md5sum: 6148e25b33890c80f176f90f2dd88989
- path: output/spades/test.spades.log
- path: output/spades/warnings.log
- name: coronaspades single end
command: nextflow run ./tests/software/spades -entry test_coronospades_single_end -c tests/config/nextflow.config
tags:
- spades
- coronaspades_single_end
files:
- path: output/spades/test.assembly.gfa
md5sum: 46531ec9b845c1a1cb469627688fecb7
- path: output/spades/test.contigs.fa
md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
- path: output/spades/test.scaffolds.fa
md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
- path: output/spades/test.spades.log
- name: coronaspades paired end
command: nextflow run ./tests/software/spades -entry test_coronospades_single_end -c tests/config/nextflow.config
tags:
- spades
- coronaspades_paired_end
files:
- path: output/spades/test.assembly.gfa
md5sum: 46531ec9b845c1a1cb469627688fecb7
- path: output/spades/test.contigs.fa
md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
- path: output/spades/test.scaffolds.fa
md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
- path: output/spades/test.spades.log

35
tests/software/subread/featurecounts/main.nf Normal file
View file

@ -0,0 +1,35 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SUBREAD_FEATURECOUNTS } from '../../../../software/subread/featurecounts/main.nf' addParams( options: [args:'-t CDS'] )
workflow test_subread_featurecounts_forward {
def input = []
input = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
SUBREAD_FEATURECOUNTS ( input )
}
workflow test_subread_featurecounts_reverse {
def input = []
input = [ [ id:'test', single_end:true, strandedness:'reverse' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
SUBREAD_FEATURECOUNTS ( input )
}
workflow test_subread_featurecounts_unstranded {
def input = []
input = [ [ id:'test', single_end:true, strandedness:'unstranded' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
SUBREAD_FEATURECOUNTS ( input )
}

35
tests/software/subread/featurecounts/test.yml Normal file
View file

@ -0,0 +1,35 @@
- name: subread featurecounts test_subread_featurecounts_forward
command: nextflow run tests/software/subread/featurecounts -entry test_subread_featurecounts_forward -c tests/config/nextflow.config
tags:
- subread
- subread_featurecounts_forward
- subread_featurecounts
files:
- path: output/subread/test.featureCounts.txt.summary
md5sum: d78617192451a57f6ef249ddcaf13720
- path: output/subread/test.featureCounts.txt
md5sum: b0a1f7563afe49007f422d4c9ca5ee6c
- name: subread featurecounts test_subread_featurecounts_reverse
command: nextflow run tests/software/subread/featurecounts -entry test_subread_featurecounts_reverse -c tests/config/nextflow.config
tags:
- subread
- subread_featurecounts
- subread_featurecounts_reverse
files:
- path: output/subread/test.featureCounts.txt.summary
md5sum: 4217004d0b55f870f77092364f59e44d
- path: output/subread/test.featureCounts.txt
md5sum: 412840a8880cd29674b3d5404d3de19b
- name: subread featurecounts test_subread_featurecounts_unstranded
command: nextflow run tests/software/subread/featurecounts -entry test_subread_featurecounts_unstranded -c tests/config/nextflow.config
tags:
- subread
- subread_featurecounts
- subread_featurecounts_unstranded
files:
- path: output/subread/test.featureCounts.txt.summary
md5sum: ee585faeb1edfcd2188a5e486a0e98a9
- path: output/subread/test.featureCounts.txt
md5sum: 6b684e11a1e54bec7e1ee5e3f651d7fd

2
tests/software/tabix/bgzip/main.nf
View file

@ -6,7 +6,7 @@ include { TABIX_BGZIP } from '../../../../software/tabix/bgzip/main.nf' addParam
workflow test_tabix_bgzip {
input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
]
TABIX_BGZIP ( input )

6
tests/software/tabix/tabix/main.nf
View file

@ -8,7 +8,7 @@ include { TABIX_TABIX as TABIX_VCF } from '../../../../software/tabix/tabix/main
workflow test_tabix_tabix_bed {
input = [ [ id:'B.bed' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed.gz", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['genome']['test_bed_gz'], checkIfExists: true) ]
]
TABIX_BED ( input )
@ -16,7 +16,7 @@ workflow test_tabix_tabix_bed {
workflow test_tabix_tabix_gff {
input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gff3.gz", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true) ]
]
TABIX_GFF ( input )
@ -24,7 +24,7 @@ workflow test_tabix_tabix_gff {
workflow test_tabix_tabix_vcf {
input = [ [ id:'test.vcf' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
]
TABIX_VCF ( input )

4
tests/software/tabix/tabix/test.yml
View file

@ -14,8 +14,8 @@
- tabix_tabix
- gff
files:
- path: ./output/tabix/test_genome.gff3.gz.tbi
md5sum: 30de27e3f44662272cfe6b3093126ea6
- path: ./output/tabix/genome.gff3.gz.tbi
md5sum: 4059fe4762568194cf293fc6df7b358b
- name: tabix tabix vcf
command: nextflow run ./tests/software/tabix/tabix -entry test_tabix_tabix_vcf -c tests/config/nextflow.config
tags:

8
tests/software/tiddit/sv/main.nf
View file

@ -6,17 +6,17 @@ include { TIDDIT_SV } from '../../../../software/tiddit/sv/main.nf' addParams( o
workflow test_tiddit_sv {
input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
fai = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
TIDDIT_SV ( input, fasta, fai )
}
workflow test_tiddit_sv_no_ref {
input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
]
TIDDIT_SV ( input, [], [] )

6
tests/software/unicycler/main.nf
View file

@ -6,7 +6,7 @@ include { UNICYCLER } from '../../../software/unicycler/main.nf' addParams( opti
workflow test_unicycler_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
]
UNICYCLER ( input )
@ -14,8 +14,8 @@ workflow test_unicycler_single_end {
workflow test_unicycler_paired_end {
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
UNICYCLER ( input )