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Merge branch 'master' of github.com:nf-core/modules

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Phil Ewels 2020-07-11 13:08:33 +02:00
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.github/workflows/cutadapt.yml vendored Normal file
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name: cutadapt
on:
push: {}
pull_request:
paths: tools/cutadapt/*
jobs:
run_ci_test:
runs-on: ubuntu-latest
steps:
# Check out the repository
- uses: actions/checkout@v2
- name: Checkout submodules
shell: bash
run: |
auth_header="$(git config --local --get http.https://github.com/.extraheader)"
git submodule sync --recursive
git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Test module with paired-end data
run: |
cd tools/cutadapt/test_paired/
nextflow run . -ansi-log false
- name: Test module with single-end data
run: |
cd tools/cutadapt/test_single/
nextflow run . -ansi-log false

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README.md
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@ -14,6 +14,14 @@ A repository for hosting nextflow [`DSL2`](https://www.nextflow.io/docs/edge/dsl
* [Uploading to `nf-core/modules`](#uploading-to-nf-coremodules) * [Uploading to `nf-core/modules`](#uploading-to-nf-coremodules)
* [Help](#help) * [Help](#help)
## Terminology
The features offered by Nextflow DSL 2 can be used in various ways depending on the granularity with which you would like to write pipelines. Please see the listing below for the hierarchy and associated terminology we have decided to use when referring to DSL 2 components:
* *Module*: A `process`that can be used within different pipelines and is as atomic as possible i.e. cannot be split into another module. An example of this would be a module file containing the process definition for a single tool such as `FastQC`. This repository has been created to only host atomic module files that should be added to the `tools` sub-directory along with the required documentation, software and tests.
* *Sub-workflow*: A chain of multiple modules that offer a higher-level of functionality within the context of a pipeline. For example, a sub-workflow to run multiple QC tools with FastQ files as input. Sub-workflows should be shipped with the pipeline implementation and if required they should be shared amongst different pipelines directly from there. As it stands, this repository will not host sub-workflows.
* *Workflow*: What DSL 1 users would consider an end-to-end pipeline. For example, from one or more inputs to a series of outputs. This can either be implemented using a large monolithic script as with DSL 1, or by using a combination of DSL 2 individual modules and sub-workflows.
## Using existing modules ## Using existing modules
The Nextflow [`include`](https://www.nextflow.io/docs/edge/dsl2.html#modules-include) statement can be used within your pipelines in order to load module files that you have available locally. The Nextflow [`include`](https://www.nextflow.io/docs/edge/dsl2.html#modules-include) statement can be used within your pipelines in order to load module files that you have available locally.

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2
test-datasets

@ -1 +1 @@
Subproject commit e5fef88994b8d34c7bf4b07116e5f7a330d2ee3b Subproject commit aae85a5c9c72238959108212481ce83bae569709

16
tools/bwa/index/main.nf Normal file
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process bwa_index {
tag {fasta}
container 'quay.io/biocontainers/bwa:0.7.17--hed695b0_7'
input:
path(fasta)
output:
path("${fasta}.*")
script:
"""
bwa index ${fasta}
"""
}

25
tools/bwa/index/meta.yml Normal file
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name: bwa index
description: create indexes for BWA from a fasta file
keywords:
- index
tools:
- bwa:
description: |
BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
homepage: http://bio-bwa.sourceforge.net/
documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997
input:
-
- input:
type: file
description: Input fasta file
pattern: *.{fasta,fa}
output:
-
- index:
type: file
description: bwa indexes file
pattern: *.{fasta,fa}.{amb,ann,bwt,pac,sa}
authors:
- @maxulysse

16
tools/bwa/index/test/main.nf Normal file
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#!/usr/bin/env nextflow
nextflow.preview.dsl = 2
include '../../../nf-core/module_testing/check_process_outputs.nf' params(params)
include '../main.nf' params(params)
// Define input channels
input = '../../../test-datasets/tools/bwa/index/input/reference.fasta'
Channel
.from(input)
.set { ch_input }
// Run the workflow
workflow {
fastqc(ch_input)
// .check_output()
}

2
tools/bwa/index/test/nextflow.config Normal file
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docker.enabled = true
params.outdir = './results'

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tools/cutadapt/main.nf Normal file
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process cutadapt {
tag "${sample_id}"
container 'quay.io/biocontainers/cutadapt:1.16--py27_1'
input:
tuple val(sample_id), file(reads)
output:
tuple sample_id, file("trimmed_*.fastq")
script:
forward_fq = "trimmed_1.fastq"
reverse_fq = "trimmed_2.fastq"
if (params.singleEnd) {
processing = """
cutadapt \
-j ${task.cpus} \
-q $params.cutadapt_min_quality \
--minimum-length $params.cutadapt_min_length \
--output ${forward_fq} \
${reads}
"""
} else {
processing = """
cutadapt \
-j ${task.cpus} \
-q $params.cutadapt_min_quality \
--minimum-length $params.cutadapt_min_length \
--pair-filter=any \
--output ${forward_fq} \
--paired-output ${reverse_fq} ${reads}
"""
}
version = """
cutadapt --version &> v_cutadapt.txt
"""
return processing + version
}

36
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name: Cutadapt
description: cutadapt removes adapter sequences from high-throughput sequencing reads
keywords:
- Quality Control
- QC
- Adapters
tools:
- fastqc:
description: |
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence
from your high-throughput sequencing reads.
Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3’
sequencing adapter because the read is longer than the molecule that is sequenced. Amplicon reads
start with a primer sequence. Poly-A tails are useful for pulling out RNA from your sample, but
often you don’t want them to be in your reads.
homepage: https://cutadapt.readthedocs.io/en/stable/
documentation: https://cutadapt.readthedocs.io/en/stable/
input:
-
- sample_id:
type: string
description: Sample identifier
- reads:
type: file
description: Input FastQ file, or pair of files
output:
-
- sample_id:
type: string
description: Sample identifier
- reads:
type: file
description: trimmed FastQ file, or pair of files
authors:
- @piotr-faba-ardigen

14
tools/cutadapt/test_paired/main.nf Normal file
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#!/usr/bin/env nextflow
nextflow.preview.dsl = 2
include '../main.nf' params(params)
// Define input channels
Channel
.fromFilePairs('../../../test-datasets/tools/cutadapt/input/*_{1,2}.fastq' )
.set { ch_read_files }
// Run the workflow
workflow {
cutadapt(ch_read_files)
}

9
tools/cutadapt/test_paired/nextflow.config Normal file
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docker.enabled = true
params.outdir = './results'
params{
//preprocessing options
cutadapt_min_length = 40
cutadapt_min_quality = 25
singleEnd = false
}

21
tools/cutadapt/test_single/main.nf Normal file
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#!/usr/bin/env nextflow
nextflow.preview.dsl = 2
include '../main.nf' params(params)
// Define input channels
readPaths = [
['SRR4238351', '../../../test-datasets/tools/cutadapt/input/SRR4238351_subsamp.fastq.gz'],
['SRR4238355', '../../../test-datasets/tools/cutadapt/input/SRR4238355_subsamp.fastq.gz'],
['SRR4238359', '../../../test-datasets/tools/cutadapt/input/SRR4238359_subsamp.fastq.gz'],
['SRR4238379', '../../../test-datasets/tools/cutadapt/input/SRR4238379_subsamp.fastq.gz']
]
Channel
.from(readPaths)
.map { row -> [ row[0], [ file(row[1]) ] ] }
.set { ch_read_files }
// Run the workflow
workflow {
cutadapt(ch_read_files)
}

9
tools/cutadapt/test_single/nextflow.config Normal file
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docker.enabled = true
params.outdir = './results'
params{
//preprocessing options
cutadapt_min_length = 40
cutadapt_min_quality = 25
singleEnd = true
}

19
tools/gatk/dict/main.nf Normal file
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process gatk_dict {
tag {fasta}
container 'quay.io/biocontainers/gatk4-spark:4.1.4.1--1'
input:
path(fasta)
output:
path("${fasta.baseName}.dict")
script:
"""
gatk --java-options "-Xmx${task.memory.toGiga()}g" \
CreateSequenceDictionary \
--REFERENCE ${fasta} \
--OUTPUT ${fasta.baseName}.dict
"""
}

25
tools/gatk/dict/meta.yml Normal file
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name: gatk dict
description: create a dictionary file from a fasta file
keywords:
- dictionary
tools:
- gatk:
description: |
The GATK toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping, developed in the Data Sciences Platform at the Broad Institute.
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
input:
-
- input:
type: file
description: Input fasta file
pattern: *.{fasta,fa}
output:
-
- dict:
type: file
description: gatk dictionary file
pattern: *.{fasta,fa}.{dict}
authors:
- @maxulysse

13
tools/gatk/dict/test/main.nf Normal file
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#!/usr/bin/env nextflow
nextflow.preview.dsl = 2
include '../../../nf-core/module_testing/check_process_outputs.nf' params(params)
include '../main.nf' params(params)
// Define input channels
input = '../../../test-datasets/tools/bwa/index/input/reference.fasta'
// Run the workflow
workflow {
gatk_dict(input)
// .check_output()
}

2
tools/gatk/dict/test/nextflow.config Normal file
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docker.enabled = true
params.outdir = './results'

16
tools/htslib/tabix/main.nf Normal file
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@ -0,0 +1,16 @@
process htslib_tabix {
tag {vcf}
container 'quay.io/biocontainers/tabix:0.2.6--ha92aebf_0'
input:
path(vcf)
output:
path("${vcf}.tbi")
script:
"""
tabix -p vcf ${vcf}
"""
}

26
tools/htslib/tabix/meta.yml Normal file
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name: htslib tabix
description: create tabix index from a bgzip vcf file
keywords:
- index
- tabix
tools:
- bwa:
description: |
Generic indexer for TAB-delimited genome position files.
homepage: https://www.htslib.org/
documentation: https://www.htslib.org/doc/tabix.1.html
doi: 10.1093/bioinformatics/btq671
input:
-
- input:
type: file
description: Input vcf.gz file
pattern: *.{vcf.gz}
output:
-
- index:
type: file
description: tabix index file
pattern: *.{vcf.gz.tbi}
authors:
- @maxulysse

13
tools/htslib/tabix/test/main.nf Normal file
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@ -0,0 +1,13 @@
#!/usr/bin/env nextflow
nextflow.preview.dsl = 2
include '../../../nf-core/module_testing/check_process_outputs.nf' params(params)
include '../main.nf' params(params)
// Define input channels
input = '../../../test-datasets/tools/file.vcf.gz'
// Run the workflow
workflow {
tabix_index(ch_read_files)
// .check_output()
}

2
tools/htslib/tabix/test/nextflow.config Normal file
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@ -0,0 +1,2 @@
docker.enabled = true
params.outdir = './results'

16
tools/samtools/faidx/main.nf Normal file
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process samtools_faidx {
tag {fasta}
container 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
input:
path(fasta)
output:
path("${fasta}.fai")
script:
"""
samtools faidx ${fasta}
"""
}

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name: samtools faidx
description: index a fasta file
keywords:
- faidx
tools:
- samtools:
description: |
SAMtools is a set of utilities for interacting with and post-processing
short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
These files are generated as output by short read aligners like BWA.
homepage: http://www.htslib.org/
documentation: hhttp://www.htslib.org/doc/samtools.html
doi: 10.1093/bioinformatics/btp352
input:
-
- input:
type: file
description: Input fasta file
pattern: *.{fasta,fa}
output:
-
- faidx:
type: file
description: samtools index fasta file
pattern: *.fasta.fai
authors:
- @maxulysse

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#!/usr/bin/env nextflow
nextflow.preview.dsl = 2
include '../../../nf-core/module_testing/check_process_outputs.nf' params(params)
include '../main.nf' params(params)
// Define input channels
input = '../../../test-datasets/tools/bwa/index/input/reference.fasta'
// Run the workflow
workflow {
samtools_faidx(input)
// .check_output()
}

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docker.enabled = true
params.outdir = './results'

7
tools/samtools/index/main.nf
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@ -7,15 +7,14 @@ process samtools_index {
path(bam) path(bam)
output: output:
path "*.sorted.bam" path "*.bai"
script: script:
def suff_mem = ("${(task.memory.toBytes() - 6000000000) / task.cpus}" > 2000000000) ? 'true' : 'false' def suff_mem = ("${(task.memory.toBytes() - 6000000000) / task.cpus}" > 2000000000) ? 'true' : 'false'
def avail_mem = (task.memory && suff_mem) ? "-m" + "${(task.memory.toBytes() - 6000000000) / task.cpus}" : '' def avail_mem = (task.memory && suff_mem) ? "-m" + "${(task.memory.toBytes() - 6000000000) / task.cpus}" : ''
""" """
samtools sort $bam \\ samtools index $bam \\
-@ ${task.cpus} ${avail_mem} \\ -@ ${task.cpus} ${avail_mem}
-o ${bam.baseName}.sorted.bam
samtools --version &> v_samtools.txt samtools --version &> v_samtools.txt
""" """

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tools/samtools/index/meta.yml
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@ -1,7 +1,7 @@
name: samtools sort name: samtools index
description: Sort a BAM or CRAM file description: index a BAM or CRAM file
keywords: keywords:
- sort - index
tools: tools:
- samtools: - samtools:
description: | description: |

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process shovill {
tag { shovill }
publishDir "${params.outdir}", pattern: '*.fasta', mode: 'copy'
container "quay.io/biocontainers/shovill:1.0.9--0"
input:
tuple(sample_id, path(forward), path(reverse))
output:
path("${sample_id}.fasta")
script:
"""
shovill --R1 ${forward} --R2 ${reverse} --outdir shovill_out
mv shovill_out/contigs.fa ${sample_id}.fasta
"""
}

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name: Shovill
description: Create a bacterial assembly from paired fastq using shovill
keywords:
- Genome Assembly
- Bacterial Isolates
tools:
- fastqc:
description: |
Shovill assembles bacterial isolate genomes from Illumina
paired-end reads. Shovill uses the SPAdes genome assembler,
providing pre and post-processing to the SPAdes assembly.
It also supports SKESA, Velvet and Megahit.
homepage: https://github.com/tseemann/shovill
documentation: https://github.com/tseemann/shovill/blob/master/README.md
input:
-
- sample_id:
type: string
description: Sample identifier
- reads:
type: file
description: pair of fastq files
output:
-
- assembly:
type: file
description: fasta file
pattern: ${sample_id}.fasta
authors:
- @annacprice

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#!/usr/bin/env nextflow
nextflow.preview.dsl = 2
// import shovill
include {shovill} from '../main.nf' params(params)
// define input channel
readsPath = '../../../test-datasets/tools/shovill/input/SRR3609257_{1,2}.fastq.gz'
Channel
.fromFilePairs( "${readsPath}", flat: true )
.set{ ch_reads }
// main workflow
workflow {
shovill(ch_reads)
}

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// docker
docker.enabled = true
// output directory
params.outdir = './results'