Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon

This commit is contained in:
JoseEspinosa 2021-02-02 09:15:20 +01:00
commit cee37852cd
38 changed files with 24146 additions and 24 deletions

42
.github/workflows/bowtie2_align.yml vendored Normal file
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@ -0,0 +1,42 @@
name: bowtie2_align
on:
push:
paths:
- software/bowtie2/align/**
- software/bowtie2/build/**
- .github/workflows/bowtie2_align.yml
- tests/software/bowtie2/**
pull_request:
paths:
- software/bowtie2/align/**
- software/bowtie2/build/**
- .github/workflows/bowtie2_align.yml
- tests/software/bowtie2/**
jobs:
ci_test:
runs-on: ubuntu-latest
strategy:
matrix:
nxf_version: [20.11.0-edge]
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.nxf_version }}
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: pytest --tag bowtie2_align --symlink --wt 2

40
.github/workflows/bowtie2_build.yml vendored Normal file
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name: bowtie2_build
on:
push:
paths:
- software/bowtie2/build/**
- .github/workflows/bowtie2_build.yml
- tests/software/bowtie2/**
pull_request:
paths:
- software/bowtie2/build/**
- .github/workflows/bowtie2_build.yml
- tests/software/bowtie2/**
jobs:
ci_test:
runs-on: ubuntu-latest
strategy:
matrix:
nxf_version: [20.11.0-edge]
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.nxf_version }}
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: pytest --tag bowtie2_build --symlink --wt 2

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@ -1,14 +1,14 @@
name: bowtie_index
name: bowtie_build
on:
push:
paths:
- software/bowtie/index/**
- .github/workflows/bowtie_index.yml
- software/bowtie/build/**
- .github/workflows/bowtie_build.yml
- tests/software/bowtie/**
pull_request:
paths:
- software/bowtie/index/**
- .github/workflows/bowtie_index.yml
- software/bowtie/build/**
- .github/workflows/bowtie_build.yml
- tests/software/bowtie/**
jobs:
@ -37,4 +37,4 @@ jobs:
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: pytest --tag bowtie_index --symlink --wt 2
- run: pytest --tag bowtie_build --symlink --wt 2

40
.github/workflows/fastp.yml vendored Normal file
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@ -0,0 +1,40 @@
name: fastp
on:
push:
paths:
- software/fastp/**
- .github/workflows/fastp.yml
- tests
pull_request:
paths:
- software/fastp/**
- .github/workflows/fastp.yml
- tests
jobs:
ci_test:
runs-on: ubuntu-latest
strategy:
matrix:
nxf_version: [20.11.0-edge]
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.nxf_version }}
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: pytest --tag fastp --symlink --wt 2

40
.github/workflows/quast.yml vendored Normal file
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@ -0,0 +1,40 @@
name: quast
on:
push:
paths:
- software/quast/**
- .github/workflows/quast.yml
- tests
pull_request:
paths:
- software/pquast/**
- .github/workflows/quest.yml
- tests
jobs:
ci_test:
runs-on: ubuntu-latest
strategy:
matrix:
nxf_version: [20.11.0-edge]
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.nxf_version }}
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: pytest --tag quast --symlink --wt 2

40
.github/workflows/seacr_callpeak.yml vendored Normal file
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@ -0,0 +1,40 @@
name: seacr_callpeak
on:
push:
paths:
- software/seacr/callpeak/**
- .github/workflows/seacr_callpeak.yml
- tests/software/seacr/**
pull_request:
paths:
- software/seacr/callpeak/**
- .github/workflows/seacr_callpeak.yml
- tests/software/seacr/**
jobs:
ci_test:
runs-on: ubuntu-latest
strategy:
matrix:
nxf_version: [20.11.0-edge]
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.nxf_version }}
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: pytest --tag seacr_callpeak --symlink --wt 2

1
.gitignore vendored
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@ -2,5 +2,6 @@
work/
results/
test_output/
output/
.DS_Store
*.code-workspace

3
.gitmodules vendored
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@ -1,3 +0,0 @@
[submodule "test-datasets"]
path = test-datasets
url = https://github.com/nf-core/test-datasets.git

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@ -4,7 +4,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process BOWTIE_INDEX {
process BOWTIE_BUILD {
tag "$fasta"
label 'process_high'
publishDir "${params.outdir}",
@ -22,11 +22,11 @@ process BOWTIE_INDEX {
path fasta
output:
path 'bowtie', emit: index
path 'bowtie' , emit: index
path '*.version.txt', emit: version
script:
def software = getSoftwareName(task.process)
def software = getSoftwareName(task.process)
"""
mkdir bowtie
bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName}

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@ -1,4 +1,4 @@
name: bowtie_index
name: bowtie_build
description: Create bowtie index for reference genome
keywords:
- index
@ -49,3 +49,4 @@ output:
pattern: "*.{version.txt}"
authors:
- "@kevinmenden"
- "@drpatelh"

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

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@ -0,0 +1,72 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process BOWTIE2_ALIGN {
tag "$meta.id"
label 'process_high'
publishDir "${params.outdir}",
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::bowtie2=2.4.2 bioconda::samtools=1.11 conda-forge::pigz=2.3.4' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0"
} else {
container "quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0"
}
input:
tuple val(meta), path(reads)
path index
output:
tuple val(meta), path('*.bam'), emit: bam
tuple val(meta), path('*.log'), emit: log
path '*.version.txt' , emit: version
tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
if (meta.single_end) {
def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
"""
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
bowtie2 \\
-x \$INDEX \\
-U $reads \\
--threads $task.cpus \\
$unaligned \\
$options.args \\
2> ${prefix}.bowtie2.log \\
| samtools view -@ $task.cpus $options.args2 -bhS -o ${prefix}.bam -
echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt
"""
} else {
def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
"""
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
bowtie2 \\
-x \$INDEX \\
-1 ${reads[0]} \\
-2 ${reads[1]} \\
--threads $task.cpus \\
$unaligned \\
$options.args \\
2> ${prefix}.bowtie2.log \\
| samtools view -@ $task.cpus $options.args2 -bhS -o ${prefix}.bam -
if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
fi
if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
fi
echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt
"""
}
}

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@ -0,0 +1,74 @@
name: bowtie2_align
description: Align reads to a reference genome using bowtie2
keywords:
- align
- fasta
- genome
- reference
tools:
- bowtie2:
description: |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
sequencing reads to long reference sequences.
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
doi: 10.1038/nmeth.1923
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
- save_unaligned:
type: boolean
description: Save unaligned reads
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- index:
type: file
description: Bowtie2 genome index files
pattern: "*.ebwt"
output:
- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.{bam}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
- fastq:
type: file
description: Unaligned FastQ files
pattern: "*.fastq.gz"
- log:
type: file
description: Aligment log
pattern: "*.log"
authors:
- "@joseespinosa"
- "@drpatelh"

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

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@ -0,0 +1,35 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process BOWTIE2_BUILD {
tag "$fasta"
label 'process_high'
publishDir "${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::bowtie2=2.4.2' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.2--py38h1c8e9b9_1'
} else {
container 'quay.io/biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1'
}
input:
path fasta
output:
path 'bowtie2' , emit: index
path '*.version.txt', emit: version
script:
def software = getSoftwareName(task.process)
"""
mkdir bowtie2
bowtie2-build $options.args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt
"""
}

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@ -0,0 +1,53 @@
name: bowtie2_build
description: Builds bowtie index for reference genome
keywords:
- build
- index
- fasta
- genome
- reference
tools:
- bowtie2:
description: |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
sequencing reads to long reference sequences.
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
doi: 10.1038/nmeth.1923
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
- fasta:
type: file
description: Input genome fasta file
output:
- index:
type: file
description: Bowtie2 genome index files
pattern: "*.bt2"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@joseespinosa"
- "@drpatelh"

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

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software/fastp/main.nf Normal file
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@ -0,0 +1,72 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process FASTP {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? 'bioconda::fastp=0.20.1' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/fastp:0.20.1--h8b12597_0'
} else {
container 'quay.io/biocontainers/fastp:0.20.1--h8b12597_0'
}
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path('*.trim.fastq.gz'), emit: reads
tuple val(meta), path('*.json') , emit: json
tuple val(meta), path('*.html') , emit: html
tuple val(meta), path('*.log') , emit: log
path '*.version.txt' , emit: version
tuple val(meta), path('*.fail.fastq.gz'), optional:true, emit: reads_fail
script:
// Added soft-links to original fastqs for consistent naming in MultiQC
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
if (meta.single_end) {
def fail_fastq = params.save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
"""
[ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
fastp \\
--in1 ${prefix}.fastq.gz \\
--out1 ${prefix}.trim.fastq.gz \\
--thread $task.cpus \\
--json ${prefix}.fastp.json \\
--html ${prefix}.fastp.html \\
$fail_fastq \\
$options.args \\
2> ${prefix}.fastp.log
echo \$(fastp --version 2>&1) | sed -e "s/fastp //g" > ${software}.version.txt
"""
} else {
def fail_fastq = params.save_trimmed_fail ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
"""
[ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
fastp \\
--in1 ${prefix}_1.fastq.gz \\
--in2 ${prefix}_2.fastq.gz \\
--out1 ${prefix}_1.trim.fastq.gz \\
--out2 ${prefix}_2.trim.fastq.gz \\
--json ${prefix}.fastp.json \\
--html ${prefix}.fastp.html \\
$fail_fastq \\
--thread $task.cpus \\
--detect_adapter_for_pe \\
$options.args \\
2> ${prefix}.fastp.log
echo \$(fastp --version 2>&1) | sed -e "s/fastp //g" > ${software}.version.txt
"""
}
}

79
software/fastp/meta.yml Normal file
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name: fastp
description: Perform adapter/quality trimming on sequencing reads
keywords:
- trimming
- quality control
- fastq
tools:
- fastq:
description: |
A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
documentation: https://github.com/OpenGene/fastp
doi: https://doi.org/10.1093/bioinformatics/bty560
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: The trimmed/modified fastq reads
pattern: "*trim.fastq.gz"
- json:
type: file
description: Results in JSON format
pattern: "*.json"
- html:
type: file
description: Results in HTML format
pattern: "*.thml"
- log:
type: file
description: fastq log file
pattern: "*.log"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
- reads_fail:
type: file
description: Reads the failed the preprocessing
pattern: "*fail.fastq.gz"
authors:
- "@drpatelh"
- "@kevinmenden"

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

48
software/quast/main.nf Normal file
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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process QUAST {
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? 'bioconda::quast=5.0.2' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2'
} else {
container 'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2'
}
input:
path consensus
path fasta
path gff
val use_fasta
val use_gff
output:
path "${prefix}" , emit: results
path '*.tsv' , emit: tsv
path '*.version.txt', emit: version
script:
def software = getSoftwareName(task.process)
prefix = options.suffix ?: software
def features = use_gff ? "--features $gff" : ''
def reference = use_fasta ? "-r $fasta" : ''
"""
quast.py \\
--output-dir $prefix \\
$reference \\
$features \\
--threads $task.cpus \\
$options.args \\
${consensus.join(' ')}
ln -s ${prefix}/report.tsv
echo \$(quast.py --version 2>&1) | sed 's/^.*QUAST v//; s/ .*\$//' > ${software}.version.txt
"""
}

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name: quast
description: Quality Assessment Tool for Genome Assemblies
keywords:
- quast
- assembly
- quality
tools:
- quast:
description: |
QUAST calculates quality metrics for genome assemblies
homepage: http://bioinf.spbau.ru/quast
doi:
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
- consensus:
type: file
description: |
Fasta file containing the assembly of interest
- fasta:
type: file
description: |
The genome assembly to be evaluated. Has to contain at least a non-empty string dummy value.
- use_fasta:
type: boolean
description: Whether to use the provided fasta reference genome file
- gff:
type: file
description: The genome GFF file. Has to contain at least a non-empty string dummy value.
- use_gff:
type: boolean
description: Whether to use the provided gff reference annotation file
output:
- quast:
type: directory
description: Directory containing complete quast report
pattern: "{prefix}.lineage_report.csv"
- report:
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@drpatelh"
- "@kevinmenden"

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

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@ -0,0 +1,42 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
def VERSION = '1.3'
process SEACR_CALLPEAK {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.29.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0"
} else {
container 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0'
}
input:
tuple val(meta), path(bedgraph), path(ctrlbedgraph)
output:
tuple val(meta), path("*.bed"), emit: bed
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
SEACR_1.3.sh \\
$bedgraph \\
$ctrlbedgraph \\
$options.args \\
$prefix
echo $VERSION > ${software}.version.txt
"""
}

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name: seacr_callpeak
description: Call peaks using SEACR on sequenced reads in bedgraph format
keywords:
- peak-caller
- peaks
- bedgraph
- cut&tag
- cut&run
- chromatin
- seacr
tools:
- seacr:
description: |
SEACR is intended to call peaks and enriched regions from sparse CUT&RUN
or chromatin profiling data in which background is dominated by "zeroes"
(i.e. regions with no read coverage).
homepage: https://github.com/FredHutch/SEACR
documentation: https://github.com/FredHutch/SEACR
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bedgraph:
type: file
description: |
The target bedgraph file from which the peaks will be calculated.
- ctrlbedgraph:
type: file
description: |
Control (IgG) data bedgraph file to generate an empirical threshold for peak calling.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Bed file containing the calculated peaks.
pattern: "*.bed"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@chris-cheshire"

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@ -2,32 +2,32 @@
nextflow.enable.dsl = 2
include { BOWTIE_INDEX } from '../../../software/bowtie/index/main.nf' addParams( options: [:] )
include { BOWTIE_BUILD } from '../../../software/bowtie/build/main.nf' addParams( options: [:] )
include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf' addParams( options: [:] )
workflow test_bowtie_index {
workflow test_bowtie_build {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE_INDEX ( fasta )
BOWTIE_BUILD ( fasta )
}
workflow test_bowtie_alignment_single_end {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE_INDEX ( fasta )
BOWTIE_BUILD ( fasta )
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
}
workflow test_bowtie_alignment_paired_end {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE_INDEX ( fasta )
BOWTIE_BUILD ( fasta )
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
}

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@ -1,8 +1,8 @@
- name: Run bowtie index
command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_index -c tests/config/nextflow.config
- name: Run bowtie build
command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_build -c tests/config/nextflow.config
tags:
- bowtie
- bowtie_index
- bowtie_build
files:
- path: output/bowtie/bowtie/NC_010473.1.ebwt
md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
@ -17,7 +17,7 @@
- path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
md5sum: f3c398bba5158f4039334a932d79c051
- name: Run bowtie index and align single-end
- name: Run bowtie build and align single-end
command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
tags:
- bowtie

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@ -0,0 +1,33 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BOWTIE2_BUILD } from '../../../software/bowtie2/build/main.nf' addParams( options: [:] )
include { BOWTIE2_ALIGN } from '../../../software/bowtie2/align/main.nf' addParams( options: [:] )
workflow test_bowtie2_build {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE2_BUILD ( fasta )
}
workflow test_bowtie2_alignment_single_end {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE2_BUILD ( fasta )
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
}
workflow test_bowtie2_alignment_paired_end {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE2_BUILD ( fasta )
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
}

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- name: Run bowtie2 build
command: nextflow run ./tests/software/bowtie2 -profile docker -entry test_bowtie2_build -c tests/config/nextflow.config
tags:
- bowtie2
- bowtie2_build
files:
- path: output/bowtie2/bowtie2/NC_010473.1.bt2
md5sum: 4db22d92e72111a5fbf609b3d9a43015
- path: output/bowtie2/bowtie2/NC_010473.2.bt2
md5sum: f4429ec74ee0064732c4bb26718a3eb1
- path: output/bowtie2/bowtie2/NC_010473.3.bt2
md5sum: cd201e81724f3099131aec16ef2cc53b
- path: output/bowtie2/bowtie2/NC_010473.4.bt2
md5sum: bbb9d6d21ad765d135f95290204e8433
- path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
- path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
- name: Run bowtie2 index and align single-end
command: nextflow run ./tests/software/bowtie2 -profile docker -entry test_bowtie2_alignment_single_end -c tests/config/nextflow.config
tags:
- bowtie2
- bowtie2_align
files:
- path: output/bowtie2/bowtie2/NC_010473.1.bt2
md5sum: 4db22d92e72111a5fbf609b3d9a43015
- path: output/bowtie2/bowtie2/NC_010473.2.bt2
md5sum: f4429ec74ee0064732c4bb26718a3eb1
- path: output/bowtie2/bowtie2/NC_010473.3.bt2
md5sum: cd201e81724f3099131aec16ef2cc53b
- path: output/bowtie2/bowtie2/NC_010473.4.bt2
md5sum: bbb9d6d21ad765d135f95290204e8433
- path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
- path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
- path: output/bowtie2/test.bowtie2.log
md5sum: 90041c264231be535042adb93a279356
- path: output/bowtie2/test.bam
md5sum: 906102f401d8234b6473790988fb09cf
- name: Run bowtie2 index and align paired-end
command: nextflow run ./tests/software/bowtie2 -profile docker -entry test_bowtie2_alignment_paired_end -c tests/config/nextflow.config
tags:
- bowtie2
- bowtie2_align
files:
- path: output/bowtie2/bowtie2/NC_010473.1.bt2
md5sum: 4db22d92e72111a5fbf609b3d9a43015
- path: output/bowtie2/bowtie2/NC_010473.2.bt2
md5sum: f4429ec74ee0064732c4bb26718a3eb1
- path: output/bowtie2/bowtie2/NC_010473.3.bt2
md5sum: cd201e81724f3099131aec16ef2cc53b
- path: output/bowtie2/bowtie2/NC_010473.4.bt2
md5sum: bbb9d6d21ad765d135f95290204e8433
- path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
- path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
- path: output/bowtie2/test.bowtie2.log
md5sum: 9f9eb40b5f57e0f2d5c874f2c1b5cfd5
- path: output/bowtie2/test.bam
md5sum: 732a33cd9816b38ea9b919c25eeb78f8

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@ -0,0 +1,30 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { FASTP } from '../../../software/fastp/main.nf' addParams( options: [:] )
/*
* Test with single-end data
*/
workflow test_fastp_se {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
FASTP( input )
}
/*
* Test with paired-end data
*/
workflow test_fastp_pe {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
FASTP( input )
}

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@ -0,0 +1,27 @@
- name: fastp_se
command: nextflow run ./tests/software/fastp -profile docker -entry test_fastp_se -c ./tests/config/nextflow.config
tags:
- fastp
- fastp_se
files:
- path: ./output/fastp/test.fastp.json
md5sum: b81d53bfa5c1553bed89f6475edcf437
- path: ./output/fastp/test.trim.fastq.gz
md5sum: 2f5516df477b123e3f78adb67effa3bc
- path: ./output/fastp/test.fastp.log
- path: ./output/fastp/test.fastp.html
- name: fastp_pe
command: nextflow run ./tests/software/fastp -profile docker -entry test_fastp_pe -c ./tests/config/nextflow.config
tags:
- fastp
- fastp_pe
files:
- path: ./output/fastp/test.fastp.html
- path: ./output/fastp/test.fastp.json
md5sum: 40db7fcbed478b0a96a1c5c1bb5f737b
- path: ./output/fastp/test.fastp.log
- path: ./output/fastp/test_1.trim.fastq.gz
md5sum: c8844c05194b50ae368e6825e997aa7f
- path: ./output/fastp/test_2.trim.fastq.gz
md5sum: 9238b07bb1609e939be7c8889b72c209

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@ -0,0 +1,25 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { QUAST } from '../../../software/quast/main.nf' addParams(options: [:])
workflow test_quast_ref {
consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
gff = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
def use_fasta = true
def use_gtf = true
QUAST( consensus, fasta, gff, use_fasta, use_gtf )
}
workflow test_quast_noref {
consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
gff = file('gff_dummy')
fasta = file('fasta_dummy')
def use_fasta = false
def use_gtf = false
QUAST( consensus, fasta, gff, use_fasta, use_gtf )
}

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- name: quast_ref
command: nextflow run ./tests/software/quast -profile docker -entry test_quast_ref -c ./tests/config/nextflow.config
tags:
- quast
- quast_reference
files:
- path: ./output/quast/quast/basic_stats/NGx_plot.pdf
- path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords.filtered
md5sum: ec9191d0acb5d5bce56b4842551a8598
- path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf
- path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
md5sum: c42838b1553759fb0460a9854e39da36
- path: ./output/quast/report.tsv
md5sum: b203a9d2c995bd66552eeb5cb0a98762
- path: ./output/quast/quast/report.tex
md5sum: 8168f197dfb2f781accdefaa0d90fc87
- path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf
- path: ./output/quast/quast/transposed_report.tex
md5sum: 0b8fd00649a5758024c8093d5919f71c
- path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords
md5sum: dda3fc0addc41ecc0d5183dee6f95886
- path: ./output/quast/quast/transposed_report.txt
md5sum: 73216314e65ef91c24422d5bdd0795e4
- path: ./output/quast/quast/report.html
- path: ./output/quast/quast/report.pdf
- path: ./output/quast/quast/contigs_reports/all_alignments_GCA_011545545-1_ASM1154554v1_cds_from_genomic.tsv
md5sum: c247152eb82b361106492642fd796e2c
- path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.used_snps.gz
md5sum: 7b1db1b433cd95243a949bcb72e7e3a6
- path: ./output/quast/quast/contigs_reports/unaligned_report.tex
md5sum: 48562e30903fcf33946e13b602b0e324
- path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.sf
- path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt
md5sum: 53c481fe8b3ef18280ea86cbded78b31
- path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.mis_contigs.info
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/quast/quast/contigs_reports/unaligned_report.tsv
md5sum: 769f2d9d7deb5e7a63e238d8ba0cfe13
- path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_cds_from_genomic_GC_content_plot.pdf
- path: ./output/quast/quast/genome_stats/features_cumulative_plot.pdf
- path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
- path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex
md5sum: 85614257e0bb62ac750f7872886b2fbf
- path: ./output/quast/quast/quast.log
- path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv
md5sum: 33144f8d064782864e8400e3a08b2a3a
- path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned.info
md5sum: a8505cf206bf53ca369f7e3073fee587
- path: ./output/quast/quast/genome_stats/GCA_011545545-1_ASM1154554v1_cds_from_genomic_genomic_features_any.txt
md5sum: 307b3bb1f42fc2f11a60a2e9846021d7
- path: ./output/quast/quast/icarus.html
md5sum: 6e57f5f7d07528496fc2f35b449951fe
- path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv
md5sum: 4d24cc0da823a100a076aef36f9fd75e
- path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stderr
- path: ./output/quast/quast/aligned_stats/cumulative_plot.pdf
- path: ./output/quast/quast/genome_stats/genome_info.txt
md5sum: bc3df27ad7356c045c9a108f9d4bcfbe
- path: ./output/quast/quast/genome_stats/features_frcurve_plot.pdf
- path: ./output/quast/quast/contigs_reports/misassemblies_report.txt
md5sum: 0784e0d31e9f2a165730cc0029023427
- path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stdout
- path: ./output/quast/quast/contigs_reports/unaligned_report.txt
md5sum: c1c26797084ea743ec5a224ab97adb1f
- path: ./output/quast/quast/genome_stats/GCA_011545545-1_ASM1154554v1_cds_from_genomic_gaps.txt
md5sum: c52381f09ea40b6141be5232494727b6
- path: ./output/quast/quast/icarus_viewers/alignment_viewer.html
md5sum: ad5176f21d3c4809a9a8f9c27bb8d70a
- path: ./output/quast/quast/contigs_reports/misassemblies_report.tex
md5sum: ffe19cf4d5332952f0627e9cd82e3375
- path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords_tmp
md5sum: ce66eaeb99fdc11e4d50efadc1816e04
- path: ./output/quast/quast/basic_stats/gc.icarus.txt
md5sum: b3a770802ff9b2dd4ee8e47bddb2df3e
- path: ./output/quast/quast/basic_stats/Nx_plot.pdf
- path: ./output/quast/quast/transposed_report.tsv
md5sum: 1754bd6c6fa8a0172a342a48dd3ca505
- path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
- path: ./output/quast/quast/report.txt
md5sum: e334b3390a5028cbf88fe4ccab2b6499
- path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf
- path: ./output/quast/quast/report.tsv
md5sum: b203a9d2c995bd66552eeb5cb0a98762
- path: ./output/quast/quast/contigs_reports/GCA_011545545_1_ASM1154554v1_cds_from_genomic.mis_contigs.fa
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/quast/quast/aligned_stats/NAx_plot.pdf
- name: quast_noref
command: nextflow run ./tests/software/quast -profile docker -entry test_quast_noref -c ./tests/config/nextflow.config
tags:
- quast
- quast_no_reference
files:
- path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
md5sum: d2680b8083139e62baf7af0f852d52b8
- path: ./output/quast/quast/transposed_report.txt
md5sum: b6b126e9dcfd8c8e7bd36dff9220caf0
- path: ./output/quast/report.tsv
md5sum: 55d2938fcdb678e97d441cf32b9c740e
- path: ./output/quast/quast/icarus.html
md5sum: dcb11b4c7b6c21190c1344c46288d3f4
- path: ./output/quast/quast/report.txt
md5sum: c8e87f40e888a0395be04f78532d9deb
- path: ./output/quast/quast/transposed_report.tsv
md5sum: 27b6c755be5d70e3eed22e1bf3f68ce5
- path: ./output/quast/quast/quast.log
- path: ./output/quast/quast/report.tex
md5sum: 69c31172ae6257663b22bb192ba84682
- path: ./output/quast/quast/report.pdf
- path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_cds_from_genomic_GC_content_plot.pdf
- path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
- path: ./output/quast/quast/report.tsv
md5sum: 55d2938fcdb678e97d441cf32b9c740e
- path: ./output/quast/quast/transposed_report.tex
md5sum: 213fb615afe21904e52d670e602c1f62
- path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
- path: ./output/quast/quast/basic_stats/Nx_plot.pdf
- path: ./output/quast/quast/report.html

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SEACR_CALLPEAK } from '../../../software/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] )
workflow test_seacr_callpeak {
def input = []
input = [[ id:'test_1'],
file("${launchDir}/tests/data/bedgraph/K27me3_1_to_chr20.bedgraph", checkIfExists: true),
file("${launchDir}/tests/data/bedgraph/IgG_1_to_chr20.bedgraph", checkIfExists: true) ]
SEACR_CALLPEAK ( input )
}
// For local testing
workflow {
test_seacr_callpeak()
}

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- name: Run seacr call peak test workflow
command: nextflow run ./tests/software/seacr/ -profile docker -entry test_seacr_callpeak -c tests/config/nextflow.config
tags:
- seacr
- seacr_callpeak
files:
- path: output/seacr/test_1.stringent.bed
md5sum: 3ac70475669eb6a7b8ca89e19a08a28e