mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-22 08:12:03 +00:00
Merge remote-tracking branch 'upstream/master'
This commit is contained in:
Sviatoslav Sidorov
commit
46eb839553
45 changed files with 473 additions and 201 deletions
|
|
@ -22,17 +22,13 @@ process BISMARK_REPORT {
|
|||
tuple val(meta), path(align_report), path(dedup_report), path(splitting_report), path(mbias)
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||||
|
||||
output:
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||||
tuple val(meta), path("*{html,txt}"), emit: report
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||||
tuple val(meta), path("*report.{html,txt}"), emit: report
|
||||
path "*.version.txt" , emit: version
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||||
|
||||
script:
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||||
def software = getSoftwareName(task.process)
|
||||
"""
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||||
bismark2report \\
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||||
--alignment_report $align_report \\
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--dedup_report $dedup_report \\
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--splitting_report $splitting_report \\
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||||
--mbias_report $mbias
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bismark2report $options.args
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||||
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||||
echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt
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||||
"""
|
||||
|
|
|
|||
|
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@ -25,7 +25,7 @@ process BISMARK_SUMMARY {
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path(mbias)
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||||
|
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output:
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path("*{html,txt}") , emit: summary
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||||
path "*report.{html,txt}", emit: summary
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||||
path "*.version.txt" , emit: version
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||||
|
||||
script:
|
||||
|
|
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|||
|
|
@ -13,9 +13,9 @@ process BWAMETH_ALIGN {
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|||
|
||||
conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null)
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||||
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:
|
||||
|
|
|
|||
|
|
@ -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"
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||||
container "quay.io/biocontainers/bwameth:0.2.2--py_1"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
60
software/gubbins/functions.nf
Normal file
60
software/gubbins/functions.nf
Normal file
|
|
@ -0,0 +1,60 @@
|
|||
/*
|
||||
* -----------------------------------------------------
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||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
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||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
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||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
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||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
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||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
||||
44
software/gubbins/main.nf
Normal file
44
software/gubbins/main.nf
Normal file
|
|
@ -0,0 +1,44 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process GUBBINS {
|
||||
label 'process_medium'
|
||||
publishDir "${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
61
software/gubbins/meta.yml
Normal file
|
|
@ -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"
|
||||
|
||||
|
|
@ -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
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -24,7 +24,7 @@ process METHYLDACKEL_MBIAS {
|
|||
path fai
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.txt"), emit: txt
|
||||
tuple val(meta), path("*.mbias.txt"), emit: txt
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
|
|
@ -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
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
|
|
|
|||
|
|
@ -19,11 +19,12 @@ process RSEM_PREPAREREFERENCE {
|
|||
}
|
||||
|
||||
input:
|
||||
path fasta
|
||||
path fasta, stageAs: "rsem/*"
|
||||
path gtf
|
||||
|
||||
output:
|
||||
path "rsem" , emit: index
|
||||
path "rsem/*transcripts.fa", emit: transcript_fasta
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
|
|
@ -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 $task.cpus \\
|
||||
|
|
|
|||
|
|
@ -11,17 +11,16 @@ process SPADES {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::spades=3.15.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::spades=3.15.2" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/spades:3.15.0--h633aebb_0"
|
||||
container "https://depot.galaxyproject.org/singularity/spades:3.15.2--h95f258a_1"
|
||||
} else {
|
||||
container "quay.io/biocontainers/spades:3.15.0--h633aebb_0"
|
||||
container "quay.io/biocontainers/spades:3.15.2--h95f258a_1"
|
||||
}
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path hmm
|
||||
val coronaspades
|
||||
|
||||
output:
|
||||
tuple val(meta), path('*.scaffolds.fa') , optional:true, emit: scaffolds
|
||||
|
|
@ -37,9 +36,8 @@ process SPADES {
|
|||
def prefix = options.suffix ? "${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 \\
|
||||
|
|
|
|||
|
|
@ -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
52
software/subread/featurecounts/meta.yml
Normal file
|
|
@ -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"
|
||||
|
|
@ -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/(.*\$//' > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -246,6 +246,10 @@ gffread:
|
|||
- software/gffread/**
|
||||
- tests/software/gffread/**
|
||||
|
||||
gubbins:
|
||||
- software/gubbins/**
|
||||
- tests/software/gubbins/**
|
||||
|
||||
gunzip:
|
||||
- software/gunzip/**
|
||||
- tests/software/gunzip/**
|
||||
|
|
@ -466,6 +470,10 @@ stringtie:
|
|||
- software/stringtie/**
|
||||
- tests/software/stringtie/**
|
||||
|
||||
subread_featurecounts:
|
||||
- software/subread/featurecounts/**
|
||||
- tests/software/subread/featurecounts/**
|
||||
|
||||
tabix_bgzip:
|
||||
- software/tabix/bgzip/**
|
||||
- tests/software/tabix/bgzip/**
|
||||
|
|
|
|||
|
|
@ -9,6 +9,7 @@ params {
|
|||
genome_fasta_fai = "${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
8
tests/data/genomics/sarscov2/genome/alignment/test.fas
Normal file
File diff suppressed because one or more lines are too long
BIN
tests/data/genomics/sarscov2/genome/genome.gff3.gz
Normal file
BIN
tests/data/genomics/sarscov2/genome/genome.gff3.gz
Normal file
Binary file not shown.
|
|
@ -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 )
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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 )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
11
tests/software/gubbins/main.nf
Normal file
|
|
@ -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
23
tests/software/gubbins/test.yml
Normal file
|
|
@ -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
|
||||
|
|
@ -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 )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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 )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -4,5 +4,5 @@
|
|||
- methyldackel
|
||||
- methyldackel_mbias
|
||||
files:
|
||||
- path: output/methyldackel/test.txt
|
||||
- path: output/methyldackel/test.mbias.txt
|
||||
md5sum: 357bb944dc2cdffcc47fa0d34376e016
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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("${launchDir}/tests/data/genomics/homo_sapiens/illumina/bam/example_pe.bam", checkIfExists: true)
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
||||
]
|
||||
|
||||
OPTITYPE ( input )
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@ include { PANGOLIN } from '../../../software/pangolin/main.nf' addParams( option
|
|||
|
||||
workflow test_pangolin {
|
||||
input = [ [ id:'test' ], // meta map
|
||||
[ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ] ]
|
||||
[ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] ]
|
||||
|
||||
PANGOLIN ( input )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -4,4 +4,4 @@
|
|||
- pangolin
|
||||
files:
|
||||
- path: ./output/pangolin/test.pangolin.csv
|
||||
md5sum: 1d513775cec0901ebee1359c91035d3a
|
||||
md5sum: c8b1720f98c9e032908f61bbc05a0fe2
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@ include { QUALIMAP_BAMQC } from '../../../../software/qualimap/bamqc/main.nf' ad
|
|||
|
||||
workflow test_qualimap_bamqc {
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true)
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
|
||||
]
|
||||
gff = file("dummy_file.txt")
|
||||
use_gff = false
|
||||
|
|
|
|||
|
|
@ -5,9 +5,9 @@ nextflow.enable.dsl = 2
|
|||
include { QUAST } from '../../../software/quast/main.nf' addParams(options: [:])
|
||||
|
||||
workflow test_quast_ref {
|
||||
fasta = file("${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
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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 )
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -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
35
tests/software/subread/featurecounts/main.nf
Normal 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
35
tests/software/subread/featurecounts/test.yml
Normal 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
|
||||
|
|
@ -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 )
|
||||
|
|
|
|||
|
|
@ -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("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz", checkIfExists: true) ]
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
|
||||
]
|
||||
|
||||
TABIX_VCF ( input )
|
||||
|
|
|
|||
|
|
@ -14,8 +14,8 @@
|
|||
- tabix_tabix
|
||||
- gff
|
||||
files:
|
||||
- path: ./output/tabix/test_genome.gff3.gz.tbi
|
||||
md5sum: 30de27e3f44662272cfe6b3093126ea6
|
||||
- path: ./output/tabix/genome.gff3.gz.tbi
|
||||
md5sum: 4059fe4762568194cf293fc6df7b358b
|
||||
- name: tabix tabix vcf
|
||||
command: nextflow run ./tests/software/tabix/tabix -entry test_tabix_tabix_vcf -c tests/config/nextflow.config
|
||||
tags:
|
||||
|
|
|
|||
|
|
@ -6,17 +6,17 @@ include { TIDDIT_SV } from '../../../../software/tiddit/sv/main.nf' addParams( o
|
|||
|
||||
workflow test_tiddit_sv {
|
||||
input = [ [ id:'test' ], // meta map
|
||||
[ file("${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("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) ]
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
|
||||
]
|
||||
|
||||
TIDDIT_SV ( input, [], [] )
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@ include { UNICYCLER } from '../../../software/unicycler/main.nf' addParams( opti
|
|||
|
||||
workflow test_unicycler_single_end {
|
||||
input = [ [ id:'test', single_end:true ], // meta map
|
||||
[ file("${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 )
|
||||
|
|
|
|||
Loading…
Reference in a new issue