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Merge branch 'master' into tcoffee_dev

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Phil Ewels 2020-07-11 13:12:17 +02:00
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34
.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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name: Build Docker Images
on:
push:
# Only on pushes to master (after PRs are merged)
branches: master
# Only if a conda environment file or a docker build file has been updated
paths:
- tools/*/environment.yml
- tools/*/Dockerfile
jobs:
build_docker:
runs-on: ubuntu-latest
steps:
# Check out the repo
- uses: actions/checkout@v1
# Find the tool wrappers that changed
# Annoyingly, matrix can't take dynamic variables
- name: Find changed tools
run: |
TOOLS=$( git diff --name-only HEAD~ | egrep -o 'tools\/[^\/]+\/' | sort | uniq | awk NF | tr '\r\n' ' ' )
# Save so that GitHub Actions can see this variable in the next step
echo "::set-env name=TOOLS::$TOOLS"
echo "Tools that appear to have been updated:"
echo $TOOLS
- name: Build images
run: |
echo "Tools that appear to have been updated:"
echo -e $TOOLS
echo '-----'
for TOOL in $TOOLS; do
echo $TOOL
done;
echo '-----'
for d in tools/*; do
for TOOL in $TOOLS; do
echo "$d -- $TOOL"
if echo $d/ | grep -q "$TOOL"; then
cd "$GITHUB_WORKSPACE/$d"
TOOLNAME=$(basename `pwd`)
# IMGNAME=docker.pkg.github.com/${GITHUB_REPOSITORY,,}/${TOOLNAME,,}:$GITHUB_SHA
# TODO: How do we have a proper version tag here?
IMGNAME=docker.pkg.github.com/${GITHUB_REPOSITORY,,}/${TOOLNAME,,}:latest
echo "Image name is: $IMGNAME"
echo "${{ secrets.GITHUB_TOKEN }}" | docker login -u ${{ github.actor }} --password-stdin docker.pkg.github.com
docker build -t $IMGNAME .
docker push $IMGNAME
fi;
done;
done;

8
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)
* [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
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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After

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2
test-datasets

@ -1 +1 @@
Subproject commit 5c3f5f2b1c5329f8effea41d29e4e2dabf6f573d
Subproject commit aae85a5c9c72238959108212481ce83bae569709

45
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
tools/cutadapt/meta.yml Normal file
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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
}

8
tools/fastqc/Dockerfile Normal file
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FROM nfcore/base:1.7
LABEL authors="phil.ewels@scilifelab.se" \
description="Docker image for nf-core modules fastqc"
# foobar
COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a
ENV PATH /opt/conda/envs/nf-core-modules-fastqc/bin:$PATH

9
tools/fastqc/environment.yml Normal file
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# You can use this file to create a conda environment for this pipeline:
# conda env create -f environment.yml
name: nf-core-modules-fastqc
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- fastqc=0.11.8

8
tools/samtools/Dockerfile Normal file
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FROM nfcore/base:1.7
LABEL authors="phil.ewels@scilifelab.se" \
description="Docker image for nf-core modules samtools"
# foobar
COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a
ENV PATH /opt/conda/envs/nf-core-modules-samtools/bin:$PATH

9
tools/samtools/environment.yml Normal file
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# You can use this file to create a conda environment for this pipeline:
# conda env create -f environment.yml
name: nf-core-modules-samtools
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- samtools=1.9

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tools/shovill/main.nf Normal file
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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'

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FROM nfcore/base:1.7
LABEL authors="phil.ewels@scilifelab.se" \
description="Docker image for nf-core modules trimgalore"
# foobar
COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a
ENV PATH /opt/conda/envs/nf-core-modules-trimgalore/bin:$PATH

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# You can use this file to create a conda environment for this pipeline:
# conda env create -f environment.yml
name: nf-core-modules-trimgalore
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- trim-galore=0.6.4