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Module/bcl2fastq (#1883)

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* add bcl2fastq

* test fixes

* fixed tests

* add tests to workflow

* change container source
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Matthias De Smet 2 years ago committed by GitHub
parent f48a24770e
commit 9294259eea
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modules/bcl2fastq/.gitignore vendored
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bcl-convert
*.rpm

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modules/bcl2fastq/Dockerfile
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# Dockerfile to create container with bcl2fastq
# Push to nfcore/bcl2fastq:<VER>
FROM debian:bullseye-slim
LABEL authors="Matthias De Smet <matthias.desmet@ugent.be>" \
description="Docker image containing bcl2fastq"
# Disclaimer: this container is not provided nor supported by Illumina
# 'ps' command is needed by some nextflow executions to collect system stats
# Install procps and clean apt cache
RUN apt-get update \
&& apt-get install -y \
procps \
&& apt-get clean -y && rm -rf /var/lib/apt/lists/*
# Link hostname cmd to fix hardcoded path
RUN ln -s /bin/hostname /usr/bin/hostname
COPY bcl2fastq /usr/local/bin/bcl2fastq
RUN chmod +x /usr/local/bin/bcl2fastq

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modules/bcl2fastq/LICENSE
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modules/bcl2fastq/README.md
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# Updating the docker container and making a new module release
bcl2fastq is a commercial tool from Illumina. The container provided for the bcl2fastq nf-core module is not provided nor supported by Illumina. Updating the bcl2fastq versions in the container and pushing the update to Dockerhub needs to be done manually.
1. Navigate to the appropriate download page. - [bcl2fastq](https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software/downloads.html): download the rpm of the desired bcl2fastq version with `curl` or `wget`.
2. Unpack the RPM package using `rpm2cpio bcl2fastq2-*.rpm | cpio -i --make-directories`. Place the executable located in `<unpack_dir>/usr/bin/bcl2fastq` in the same folder where the Dockerfile lies.
3. Create and test the container:
```bash
docker build . -t nfcore/bcl2fastq:<VERSION>
```
4. Access rights are needed to push the container to the Dockerhub nfcore organization, please ask a core team member to do so.
```bash
docker push nfcore/bcl2fastq:<VERSION>
```

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modules/bcl2fastq/main.nf
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process BCL2FASTQ {
tag {"$meta.lane" ? "$meta.id"+"."+"$meta.lane" : "$meta.id" }
label 'process_high'
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using bcl2fastq. Please use docker or singularity containers."
}
container "nfcore/bcl2fastq:2.20.0.422"
input:
tuple val(meta), path(samplesheet), path(run_dir)
output:
tuple val(meta), path("**[!Undetermined]_S*_L00?_R?_00?.fastq.gz") ,emit: fastq
tuple val(meta), path("**_S*_L00?_I?_00?.fastq.gz") ,optional:true ,emit: fastq_idx
tuple val(meta), path("Undetermined_S0_L00?_R?_00?.fastq.gz") ,optional:true ,emit: undetermined
tuple val(meta), path("Undetermined_S0_L00?_I?_00?.fastq.gz") ,optional:true, emit: undetermined_idx
tuple val(meta), path("Reports") ,emit: reports
tuple val(meta), path("Stats") ,emit: stats
tuple val(meta), path("**/InterOp/*.bin") ,emit: interop
path("versions.yml") ,emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
"""
bcl2fastq \\
$args \\
--output-dir . \\
--runfolder-dir ${run_dir} \\
--sample-sheet ${samplesheet} \\
--processing-threads ${task.cpus}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bcl2fastq: \$(bcl2fastq -V 2>&1 | grep -m 1 bcl2fastq | sed 's/^.*bcl2fastq v//')
END_VERSIONS
"""
}

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modules/bcl2fastq/meta.yml
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name: "bcl2fastq"
description: Demultiplex Illumina BCL files
keywords:
- demultiplex
- illumina
- fastq
tools:
- "bcl2fastq":
description: "Demultiplex Illumina BCL files"
homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software"
documentation: "https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2-v2-20-software-guide-15051736-03.pdf"
licence: "ILLUMINA"
input:
- meta:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- samplesheet:
type: file
description: "Input samplesheet"
pattern: "*.{csv}"
- run_dir:
type: directory
description: "Input run directory containing RunInfo.xml and BCL data"
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- fastq:
type: file
description: Demultiplexed sample FASTQ files
pattern: "**_S*_L00?_R?_00?.fastq.gz"
- fastq_idx:
type: file
description: Optional demultiplexed index FASTQ files
pattern: "**_S*_L00?_I?_00?.fastq.gz"
- undetermined:
type: file
description: Optional undetermined sample FASTQ files
pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz"
- undetermined_idx:
type: file
description: Optional undetermined index FASTQ files
pattern: "Undetermined_S0_L00?_I?_00?.fastq.gz"
- reports:
type: file
description: Demultiplexing Reports
pattern: "Reports/*"
- stats:
type: file
description: Statistics files
pattern: "Stats/*"
- interop:
type: file
description: Interop files
pattern: "*.{bin}"
authors:
- "@matthdsm"

4
tests/config/pytest_modules.yml
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@ -210,6 +210,10 @@ bcftools/view:
- modules/bcftools/view/**
- tests/modules/bcftools/view/**
bcl2fastq:
- modules/bcl2fastq/**
- tests/modules/bcl2fastq/**
bclconvert:
- modules/bclconvert/**
- tests/modules/bclconvert/**

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tests/modules/bcl2fastq/main.nf
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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BCL2FASTQ } from '../../../modules/bcl2fastq/main.nf'
include { UNTAR } from '../../../modules/untar/main.nf'
workflow test_bcl2fastq {
ch_flowcell = Channel.value([
[id:'test', lane:1 ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_flowcell_samplesheet'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true)])
ch_flowcell
.multiMap { meta, ss, run ->
samplesheet: [meta, ss]
tar: [meta, run]
}.set{ ch_fc_split }
ch_flowcell_untar = ch_fc_split.samplesheet.join( UNTAR ( ch_fc_split.tar ).untar )
BCL2FASTQ (ch_flowcell_untar)
}

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tests/modules/bcl2fastq/nextflow.config
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process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: BCL2FASTQ {
ext.args = {[
"--tiles s_1_1101"
].join(" ").trim()}
}
withName: UNTAR {
publishDir = [ enabled: false ]
}
}

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tests/modules/bcl2fastq/test.yml
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- name: bcl2fastq test_bcl2fastq
command: nextflow run ./tests/modules/bcl2fastq -entry test_bcl2fastq -c ./tests/config/nextflow.config -c ./tests/modules/bcl2fastq/nextflow.config
tags:
- bcl2fastq
files:
- path: output/bcl2fastq/Sample1_S1_L001_R1_001.fastq.gz
md5sum: e92fce7b86c6447b053d72c5cb4be89c
- path: output/bcl2fastq/Stats/AdapterTrimming.txt
md5sum: 48ed2b914b1246c0b5d8667525550946
- path: output/bcl2fastq/Stats/ConversionStats.xml
md5sum: 8fe0f57f3f5d256a0762dba75ac62d05
- path: output/bcl2fastq/Stats/DemultiplexingStats.xml
md5sum: 2047ff18f5b9107c084de06e9ff943ad
- path: output/bcl2fastq/Stats/DemuxSummaryF1L1.txt
md5sum: 03e5fd0c1e3079c5f8c7b4d0501b37ff
- path: output/bcl2fastq/Stats/FastqSummaryF1L1.txt
md5sum: 0c6f2d87ee183b84d1051cde9a5643d1
- path: output/bcl2fastq/Stats/Stats.json
md5sum: 8e5f038b8aa9e465599d3575f930e604
- path: output/bcl2fastq/flowcell/InterOp/ControlMetricsOut.bin
md5sum: 6d77b38d0793a6e1ce1e85706e488953
- path: output/bcl2fastq/flowcell/InterOp/CorrectedIntMetricsOut.bin
md5sum: 2bbf84d3be72734addaa2fe794711434
- path: output/bcl2fastq/flowcell/InterOp/ErrorMetricsOut.bin
md5sum: 38c88def138e9bb832539911affdb286
- path: output/bcl2fastq/flowcell/InterOp/ExtractionMetricsOut.bin
md5sum: 7497c3178837eea8f09350b5cd252e99
- path: output/bcl2fastq/flowcell/InterOp/IndexMetricsOut.bin
md5sum: 9e688c58a5487b8eaf69c9e1005ad0bf
- path: output/bcl2fastq/flowcell/InterOp/QMetricsOut.bin
md5sum: 7e9f198d53ebdfbb699a5f94cf1ed51c
- path: output/bcl2fastq/flowcell/InterOp/TileMetricsOut.bin
md5sum: 83891751ec1c91a425a524b476b6ca3c
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