Module/bclconvert (#1485)

* bclconvert: initial commit

* add most of tool

* attempt at adding testing stub

* add dockerfile + instructions

* add container to module

* update readme

* more attempts at making stubs work

* finish stub run

* fix ci issues

* more fixes to stub

* add read version check to stub

* fix some tests

* update readme

* fix version number

* syntax fix

* revert edit to output directory

* Update modules/bclconvert/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/bclconvert/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* update meta.yaml

* update thread usage

* Update modules/bclconvert/main.nf

Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>

* Escape env variable

* Update modules/bclconvert/Dockerfile

Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>

* fix comments by @Emiller88

* fix task.cpus

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
This commit is contained in:
Matthias De Smet 2022-04-21 15:39:22 +02:00 committed by GitHub
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commit f4c69bc427
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modules/bclconvert/.gitignore vendored Normal file
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bcl-convert
*.rpm

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# Dockerfile to create container with bcl-convert
# Push to nfcore/bclconvert:<VER>
FROM debian:bullseye-slim
LABEL authors="Matthias De Smet <matthias.desmet@ugent.be>" \
description="Docker image containing bcl-convert"
# Disclaimer: this container is not provided nor supported by Illumina
# 'ps' command is need 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/*
COPY bcl-convert /usr/local/bin/bcl-convert
RUN chmod +x /usr/local/bin/bcl-convert

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# Updating the docker container and making a new module release
bcl-convert is a commercial tool from Illumina. The container provided for the bcl-convert nf-core module is not provided nor supported by Illumina. Updating the bcl-convert versions in the container and pushing the update to Dockerhub needs to be done manually.
1. Navigate to the appropriate download page. - [BCL Convert](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/downloads.html): download the rpm of the desired bcl-convert version with `curl` or `wget`.
2. Unpack the RPM package using `rpm2cpio bcl-convert-*.rpm | cpio -i --make-directories`. Place the executable located in `<unpack_dir>/usr/bin/bcl-convert` in the same folder where the Dockerfile lies.
3. Create and test the container:
```bash
docker build . -t nfcore/bclconvert:<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/bclconvert:<VERSION>
```

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process BCLCONVERT {
tag '$samplesheet'
label 'process_high'
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using bcl-convert. Please use docker or singularity containers."
}
container "nfcore/bclconvert:3.9.3"
input:
path samplesheet
path run_dir
output:
path "*.fastq.gz" ,emit: fastq
path "Reports/*.{csv,xml,bin}" ,emit: reports
path "Logs/*.{log,txt}" ,emit: logs
path "InterOp/*.bin" ,emit: interop
path "versions.yml" ,emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
"""
bcl-convert \
$args \\
--output-directory . \\
--bcl-input-directory ${run_dir} \\
--sample-sheet ${samplesheet} \\
--bcl-num-parallel-tiles ${task.cpus}
mkdir InterOp
cp ${run_dir}/InterOp/*.bin InterOp/
mv Reports/*.bin InterOp/
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bclconvert: \$(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //')
END_VERSIONS
"""
stub:
"""
echo "sample1_S1_L001_R1_001" > sample1_S1_L001_R1_001.fastq.gz
echo "sample1_S1_L001_R2_001" > sample1_S1_L001_R2_001.fastq.gz
echo "sample1_S1_L002_R1_001" > sample1_S1_L002_R1_001.fastq.gz
echo "sample1_S1_L002_R2_001" > sample1_S1_L002_R2_001.fastq.gz
echo "sample2_S2_L001_R1_001" > sample2_S2_L001_R1_001.fastq.gz
echo "sample2_S2_L001_R2_001" > sample2_S2_L001_R2_001.fastq.gz
echo "sample2_S2_L002_R1_001" > sample2_S2_L002_R1_001.fastq.gz
echo "sample2_S2_L002_R2_001" > sample2_S2_L002_R2_001.fastq.gz
mkdir Reports
echo "Adapter_Metrics" > Reports/Adapter_Metrics.csv
echo "Demultiplex_Stats" > Reports/Demultiplex_Stats.csv
echo "fastq_list" > Reports/fastq_list.csv
echo "Index_Hopping_Counts" > Reports/Index_Hopping_Counts.csv
echo "IndexMetricsOut" > Reports/IndexMetricsOut.bin
echo "Quality_Metrics" > Reports/Quality_Metrics.csv
echo "RunInfo" > Reports/RunInfo.xml
echo "SampleSheet" > Reports/SampleSheet.csv
echo "Top_Unknown_Barcodes" > Reports/Top_Unknown_Barcodes.csv
mkdir Logs
echo "Errors" > Logs/Errors.log
echo "FastqComplete" > Logs/FastqComplete.txt
echo "Info" > Logs/Info.log
echo "Warnings" > Logs/Warnings.log
mkdir InterOp/
echo "InterOp" > InterOp/InterOp.bin
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bclconvert: \$(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //')
END_VERSIONS
"""
}

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name: "bclconvert"
description: Demultiplex Illumina BCL files
keywords:
- demultiplex
- illumina
- fastq
tools:
- "bclconvert":
description: "Demultiplex Illumina BCL files"
homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html"
documentation: "https://support-docs.illumina.com/SW/BCL_Convert/Content/SW/FrontPages/BCL_Convert.htm"
licence: "ILLUMINA"
input:
- 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 FASTQ files
pattern: "*.{fastq.gz}"
- reports:
type: file
description: Demultiplexing Reports
pattern: "Reports/*.{csv,xml}"
- logs:
type: file
description: Log files
pattern: "Logs/*.{log,txt}"
- interop:
type: file
description: Interop files
pattern: "Interop/*.{bin}"
authors:
- "@matthdsm"

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@ -174,6 +174,10 @@ bcftools/view:
- modules/bcftools/view/** - modules/bcftools/view/**
- tests/modules/bcftools/view/** - tests/modules/bcftools/view/**
bclconvert:
- modules/bclconvert/**
- tests/modules/bclconvert/**
bedtools/bamtobed: bedtools/bamtobed:
- modules/bedtools/bamtobed/** - modules/bedtools/bamtobed/**
- tests/modules/bedtools/bamtobed/** - tests/modules/bedtools/bamtobed/**

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BCLCONVERT } from '../../../modules/bclconvert/main.nf'
process STUB_BCLCONVERT_INPUT {
output:
path "SampleSheet.csv" ,emit: samplesheet
path "DDMMYY_SERIAL_FLOWCELL" ,emit: run_dir
stub:
"""
mkdir DDMMYY_SERIAL_FLOWCELL
echo "SampleSheet" > SampleSheet.csv
"""
}
workflow test_bclconvert {
STUB_BCLCONVERT_INPUT ()
BCLCONVERT (STUB_BCLCONVERT_INPUT.out.samplesheet, STUB_BCLCONVERT_INPUT.out.run_dir)
}

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process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

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- name: bclconvert test_bclconvert
command: nextflow run tests/modules/bclconvert -entry test_bclconvert -c tests/config/nextflow.config -stub-run
tags:
- bclconvert
files:
- path: output/bclconvert/InterOp/InterOp.bin
md5sum: d3dea0bb4ab1c8754af324f40b001481
- path: output/bclconvert/Logs/Errors.log
md5sum: 334645f09074b2597a692e395b716a9c
- path: output/bclconvert/Logs/FastqComplete.txt
md5sum: a4c4c6ce2d0de67d3b7ac7d1fcb512e4
- path: output/bclconvert/Logs/Info.log
md5sum: d238822d379f2277cac950ca986cb660
- path: output/bclconvert/Logs/Warnings.log
md5sum: aeefd2d631817e170f88f25ecaaf4664
- path: output/bclconvert/Reports/Adapter_Metrics.csv
md5sum: af62e9c7b44940cfd8ea11064a1f42ae
- path: output/bclconvert/Reports/Demultiplex_Stats.csv
md5sum: d11313931fcaabb5ce159462ad3dd1da
- path: output/bclconvert/Reports/IndexMetricsOut.bin
md5sum: 6bcee11c8145e3b1059ceaa91d2f5be7
- path: output/bclconvert/Reports/Index_Hopping_Counts.csv
md5sum: 697e40e0c0d48b4bd25f138ef60b0bde
- path: output/bclconvert/Reports/Quality_Metrics.csv
md5sum: 3902fd38f6b01f1ce0f0e8724238f8f2
- path: output/bclconvert/Reports/RunInfo.xml
md5sum: 5bef7c7e76360231b0c4afdfc915fd44
- path: output/bclconvert/Reports/SampleSheet.csv
md5sum: c579e7d2c9c917c4cfb875a0373c0936
- path: output/bclconvert/Reports/Top_Unknown_Barcodes.csv
md5sum: 39a5e7f6d21c12d6051afdc8261b6330
- path: output/bclconvert/Reports/fastq_list.csv
md5sum: 32c51ab10e013fd547928de57361ffcb
- path: output/bclconvert/sample1_S1_L001_R1_001.fastq.gz
md5sum: 9b831a39755935333f86f167527a094d
- path: output/bclconvert/sample1_S1_L001_R2_001.fastq.gz
md5sum: 082f4f767b7619f409ca7e752ef482bf
- path: output/bclconvert/sample1_S1_L002_R1_001.fastq.gz
md5sum: 837764c89db93dfb53cd663c4f26f3d7
- path: output/bclconvert/sample1_S1_L002_R2_001.fastq.gz
md5sum: 1a42cf6ba0bb8fc7770f278e6d1ab676
- path: output/bclconvert/sample2_S2_L001_R1_001.fastq.gz
md5sum: 475bc426b7cc48d0551d40e31457dc78
- path: output/bclconvert/sample2_S2_L001_R2_001.fastq.gz
md5sum: f670ccd7d9352e0e67fe1c1232429d94
- path: output/bclconvert/sample2_S2_L002_R1_001.fastq.gz
md5sum: ebd5ff6fa5603e7d704b5a10598de58c
- path: output/bclconvert/sample2_S2_L002_R2_001.fastq.gz
md5sum: 2f83b460f52620d2548c7ef8845b31d7
- path: output/stub/SampleSheet.csv
md5sum: c579e7d2c9c917c4cfb875a0373c0936
- path: output/bclconvert/versions.yml