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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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process ELPREP_FILTER {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0':
'quay.io/biocontainers/elprep:5.1.2--he881be0_0' }"
input:
tuple val(meta), path(bam)
val(run_haplotypecaller)
val(run_bqsr)
path(reference_sequences)
path(filter_regions_bed)
path(reference_elfasta)
path(known_sites_elsites)
path(target_regions_bed)
path(intermediate_bqsr_tables)
val(bqsr_tables_only)
val(get_activity_profile)
val(get_assembly_regions)
output:
tuple val(meta), path("output/**.{bam,sam}") ,emit: bam
tuple val(meta), path("*.metrics.txt") ,optional: true, emit: metrics
tuple val(meta), path("*.recall") ,optional: true, emit: recall
tuple val(meta), path("*.vcf.gz") ,optional: true, emit: gvcf
tuple val(meta), path("*.table") ,optional: true, emit: table
tuple val(meta), path("*.activity_profile.igv") ,optional: true, emit: activity_profile
tuple val(meta), path("*.assembly_regions.igv") ,optional: true, emit: assembly_regions
path "versions.yml" ,emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = args.contains("--output-type sam") ? "sam" : "bam"
// filter args
def reference_sequences_cmd = reference_sequences ? " --replace-reference-sequences ${reference_sequences}" : ""
def filter_regions_cmd = filter_regions_bed ? " --filter-non-overlapping-reads ${filter_regions_bed}" : ""
// markdup args
def markdup_cmd = args.contains("--mark-duplicates") ? " --mark-optical-duplicates ${prefix}.metrics.txt": ""
// variant calling args
def haplotyper_cmd = run_haplotypecaller ? " --haplotypecaller ${prefix}.g.vcf.gz": ""
def fasta_cmd = reference_elfasta ? " --reference ${reference_elfasta}": ""
def known_sites_cmd = known_sites_elsites ? " --known-sites ${known_sites_elsites}": ""
def target_regions_cmd = target_regions_bed ? " --target-regions ${target_regions_bed}": ""
// bqsr args
def bqsr_cmd = run_bqsr ? " --bqsr ${prefix}.recall": ""
def bqsr_tables_only_cmd = bqsr_tables_only ? " --bqsr-tables-only ${prefix}.table": ""
def intermediate_bqsr_cmd = intermediate_bqsr_tables ? " --bqsr-apply .": ""
// misc
def activity_profile_cmd = get_activity_profile ? " --activity-profile ${prefix}.activity_profile.igv": ""
def assembly_regions_cmd = get_assembly_regions ? " --assembly-regions ${prefix}.assembly_regions.igv": ""
"""
elprep filter ${bam} output/${prefix}.${suffix} \\
${reference_sequences_cmd} \\
${filter_regions_cmd} \\
${markdup_cmd} \\
${haplotyper_cmd} \\
${fasta_cmd} \\
${known_sites_cmd} \\
${target_regions_cmd} \\
${bqsr_cmd} \\
${bqsr_tables_only_cmd} \\
${intermediate_bqsr_cmd} \\
${activity_profile_cmd} \\
${assembly_regions_cmd} \\
--nr-of-threads ${task.cpus} \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
elprep: \$(elprep 2>&1 | head -n2 | tail -n1 |sed 's/^.*version //;s/ compiled.*\$//')
END_VERSIONS
"""
}

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name: "elprep_filter"
description: "Filter, sort and markdup sam/bam files, with optional BQSR and variant calling."
keywords:
- sort
- bam
- sam
- filter
- variant calling
tools:
- "elprep":
description: "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4."
homepage: "https://github.com/ExaScience/elprep"
documentation: "https://github.com/ExaScience/elprep"
tool_dev_url: "https://github.com/ExaScience/elprep"
doi: "10.1371/journal.pone.0244471"
licence: "['AGPL v3']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: Input SAM/BAM file
pattern: "*.{bam,sam}"
- run_haplotypecaller:
type: boolean
description: Run variant calling on the input files. Needed to generate gvcf output.
- run_bqsr:
type: boolean
description: Run BQSR on the input files. Needed to generate recall metrics.
- reference_sequences:
type: file
description: Optional SAM header to replace existing header.
pattern: "*.sam"
- filter_regions_bed:
type: file
description: Optional BED file containing regions to filter.
pattern: "*.bed"
- reference_elfasta:
type: file
description: Elfasta file, required for BQSR and variant calling.
pattern: "*.elfasta"
- known_sites:
type: file
description: Optional elsites file containing known SNPs for BQSR.
pattern: "*.elsites"
- target_regions_bed:
type: file
description: Optional BED file containing target regions for BQSR and variant calling.
pattern: "*.bed"
- intermediate_bqsr_tables:
type: file
description: Optional list of BQSR tables, used when parsing files created by `elprep split`
pattern: "*.table"
- bqsr_tables_only:
type: boolean
description: Write intermediate BQSR tables, used when parsing files created by `elprep split`.
- get_activity_profile:
type: boolean
description: Get the activity profile calculated by the haplotypecaller to the given file in IGV format.
- get_assembly_regions:
type: boolean
description: Get the assembly regions calculated by haplotypecaller to the speficied file in IGV format.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bam:
type: file
description: Sorted, markdup, optionally BQSR BAM/SAM file
pattern: "*.{bam,sam}"
- metrics:
type: file
description: Optional duplicate metrics file generated by elprep
pattern: "*.{metrics.txt}"
- recall:
type: file
description: Optional recall metrics file generated by elprep
pattern: "*.{recall}"
- gvcf:
type: file
description: Optional GVCF output file
pattern: "*.{vcf.gz}"
- table:
type: file
description: Optional intermediate BQSR table output file
pattern: "*.{table}"
- activity_profile:
type: file
description: Optional activity profile output file
pattern: "*.{activity_profile.igv}"
- assembly_regions:
type: file
description: Optional activity regions output file
pattern: "*.{assembly_regions.igv}"
authors:
- "@matthdsm"

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process ELPREP_SPLIT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0':
'quay.io/biocontainers/elprep:5.1.2--he881be0_0' }"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("output/**.{bam,sam}"), emit: bam
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def single_end = meta.single_end ? " --single-end": ""
"""
# create directory and move all input so elprep can find and merge them before splitting
mkdir input
mv ${bam} input/
mkdir ${prefix}
elprep split \\
input \\
output/ \\
$args \\
$single_end \\
--nr-of-threads $task.cpus \\
--output-prefix $prefix
cat <<-END_VERSIONS > versions.yml
"${task.process}":
elprep: \$(elprep 2>&1 | head -n2 | tail -n1 |sed 's/^.*version //;s/ compiled.*\$//')
END_VERSIONS
"""
}

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modules/elprep/split/meta.yml Normal file
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@ -0,0 +1,43 @@
name: "elprep_split"
description: Split bam file into manageable chunks
keywords:
- bam
- split by chromosome
tools:
- "elprep":
description: "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4."
homepage: "https://github.com/ExaScience/elprep"
documentation: "https://github.com/ExaScience/elprep"
tool_dev_url: "https://github.com/ExaScience/elprep"
doi: "10.1371"
licence: "['AGPL v3']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: List of BAM/SAM files
pattern: "*.{bam,sam}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
#
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bam:
type: file
description: List of split BAM/SAM files
pattern: "*.{bam,sam}"
authors:
- "@matthdsm"

40
modules/kaiju/kaiju2table/main.nf Normal file
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@ -0,0 +1,40 @@
process KAIJU_KAIJU2TABLE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
'quay.io/biocontainers/kaiju:1.8.2--h2e03b76_0' }"
input:
tuple val(meta), path(results)
path db
val taxon_rank
output:
tuple val(meta), path('*.txt'), emit: summary
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
dbnodes=`find -L ${db} -name "*nodes.dmp"`
dbname=`find -L ${db} -name "*.fmi" -not -name "._*"`
kaiju2table $args \\
-t \$dbnodes \\
-n \$dbname \\
-r ${taxon_rank} \\
-o ${prefix}.txt \\
${results}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
END_VERSIONS
"""
}

50
modules/kaiju/kaiju2table/meta.yml Normal file
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@ -0,0 +1,50 @@
name: "kaiju_kaiju2table"
description: write your description here
keywords:
- classify
- metagenomics
tools:
- kaiju:
description: Fast and sensitive taxonomic classification for metagenomics
homepage: https://kaiju.binf.ku.dk/
documentation: https://github.com/bioinformatics-centre/kaiju/blob/master/README.md
tool_dev_url: https://github.com/bioinformatics-centre/kaiju
doi: "10.1038/ncomms11257"
licence: ["GNU GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- results:
type: file
description: File containing the kaiju classification results
pattern: "*.{txt}"
- taxon_rank:
type: string
description: |
Taxonomic rank to display in report
pattern: "phylum|class|order|family|genus|species"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- results:
type: file
description: |
Summary table for a given taxonomic rank
pattern: "*.{tsv}"
authors:
- "@sofstam"
- "@talnor"
- "@jfy133"

23
modules/kraken2/kraken2/main.nf
View file

@ -10,12 +10,15 @@ process KRAKEN2_KRAKEN2 {
input:
tuple val(meta), path(reads)
path db
val save_output_fastqs
val save_reads_assignment
output:
tuple val(meta), path('*classified*') , emit: classified
tuple val(meta), path('*unclassified*'), emit: unclassified
tuple val(meta), path('*report.txt') , emit: txt
path "versions.yml" , emit: versions
tuple val(meta), path('*classified*') , optional:true, emit: classified_reads_fastq
tuple val(meta), path('*unclassified*') , optional:true, emit: unclassified_reads_fastq
tuple val(meta), path('*classifiedreads*'), optional:true, emit: classified_reads_assignment
tuple val(meta), path('*report.txt') , emit: report
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
@ -26,19 +29,25 @@ process KRAKEN2_KRAKEN2 {
def paired = meta.single_end ? "" : "--paired"
def classified = meta.single_end ? "${prefix}.classified.fastq" : "${prefix}.classified#.fastq"
def unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq"
def classified_command = save_output_fastqs ? "--classified-out ${classified}" : ""
def unclassified_command = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
def readclassification_command = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : ""
def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : ""
"""
kraken2 \\
--db $db \\
--threads $task.cpus \\
--unclassified-out $unclassified \\
--classified-out $classified \\
--report ${prefix}.kraken2.report.txt \\
--gzip-compressed \\
$unclassified_command \\
$classified_command \\
$readclassification_command \\
$paired \\
$args \\
$reads
pigz -p $task.cpus *.fastq
$compress_reads_command
cat <<-END_VERSIONS > versions.yml
"${task.process}":

25
modules/kraken2/kraken2/meta.yml
View file

@ -27,25 +27,40 @@ input:
- db:
type: directory
description: Kraken2 database
- save_output_fastqs:
type: boolean
description: |
If true, optional commands are added to save classified and unclassified reads
as fastq files
- save_reads_assignment:
type: boolean
description: |
If true, an optional command is added to save a file reporting the taxonomic
classification of each input read
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- classified:
- classified_reads_fastq:
type: file
description: |
Reads classified to belong to any of the taxa
Reads classified as belonging to any of the taxa
on the Kraken2 database.
pattern: "*{fastq.gz}"
- unclassified:
- unclassified_reads_fastq:
type: file
description: |
Reads not classified to belong to any of the taxa
Reads not classified to any of the taxa
on the Kraken2 database.
pattern: "*{fastq.gz}"
- txt:
- classified_reads_assignment:
type: file
description: |
Kraken2 output file indicating the taxonomic assignment of
each input read
- report:
type: file
description: |
Kraken2 report containing stats about classified

9
modules/picard/collecthsmetrics/main.nf
View file

@ -15,8 +15,8 @@ process PICARD_COLLECTHSMETRICS {
path target_intervals
output:
tuple val(meta), path("*collecthsmetrics.txt"), emit: hs_metrics
path "versions.yml" , emit: versions
tuple val(meta), path("*_metrics") , emit: metrics
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
@ -41,7 +41,8 @@ process PICARD_COLLECTHSMETRICS {
-BAIT_INTERVALS $bait_intervals \\
-TARGET_INTERVALS $target_intervals \\
-INPUT $bam \\
-OUTPUT ${prefix}_collecthsmetrics.txt
-OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics
cat <<-END_VERSIONS > versions.yml
"${task.process}":
@ -52,7 +53,7 @@ process PICARD_COLLECTHSMETRICS {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}_collecthsmetrics.txt
touch ${prefix}.CollectHsMetrics.coverage_metrics
cat <<-END_VERSIONS > versions.yml
"${task.process}":

7
modules/picard/collecthsmetrics/meta.yml
View file

@ -57,10 +57,11 @@ output:
type: file
description: File containing software versions
pattern: "versions.yml"
- hs_metrics:
- metrics:
type: file
description: The metrics file.
pattern: "*_collecthsmetrics.txt"
description: Alignment metrics files generated by picard
pattern: "*_{metrics}"
authors:
- "@projectoriented"
- "@matthdsm"

2
modules/samtools/view/main.nf
View file

@ -8,7 +8,7 @@ process SAMTOOLS_VIEW {
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
input:
tuple val(meta), path(input)
tuple val(meta), path(input), path(index)
path fasta
output:

4
modules/samtools/view/meta.yml
View file

@ -25,6 +25,10 @@ input:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- index:
type: optional file
description: BAM.BAI/CRAM.CRAI file
pattern: "*.{.bai,.crai}"
- fasta:
type: optional file
description: Reference file the CRAM was created with

11
modules/stranger/main.nf
View file

@ -33,4 +33,15 @@ process STRANGER {
stranger: \$( stranger --version )
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.vcf.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
stranger: \$( stranger --version )
END_VERSIONS
"""
}

16
tests/config/pytest_modules.yml
View file

@ -174,6 +174,10 @@ bcftools/view:
- modules/bcftools/view/**
- tests/modules/bcftools/view/**
bclconvert:
- modules/bclconvert/**
- tests/modules/bclconvert/**
bedtools/bamtobed:
- modules/bedtools/bamtobed/**
- tests/modules/bedtools/bamtobed/**
@ -595,6 +599,14 @@ ectyper:
- modules/ectyper/**
- tests/modules/ectyper/**
elprep/filter:
- modules/elprep/filter/**
- tests/modules/elprep/filter/**
elprep/split:
- modules/elprep/split/**
- tests/modules/elprep/split/**
emmtyper:
- modules/emmtyper/**
- tests/modules/emmtyper/**
@ -997,6 +1009,10 @@ kaiju/kaiju:
- modules/kaiju/kaiju/**
- tests/modules/kaiju/kaiju/**
kaiju/kaiju2table:
- modules/kaiju/kaiju2table/**
- tests/modules/kaiju/kaiju2table/**
kallisto/index:
- modules/kallisto/index/**
- tests/modules/kallisto/index/**

3
tests/config/test_data.config
View file

@ -112,6 +112,7 @@ params {
}
'homo_sapiens' {
'genome' {
genome_elfasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome.elfasta"
genome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome.fasta"
genome_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/genome.fasta.fai"
genome_dict = "${test_data_dir}/genomics/homo_sapiens/genome/genome.dict"
@ -123,6 +124,7 @@ params {
genome_header = "${test_data_dir}/genomics/homo_sapiens/genome/genome.header"
genome_bed_gz = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz"
genome_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz.tbi"
genome_elsites = "${test_data_dir}/genomics/homo_sapiens/genome/genome.elsites"
transcriptome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/transcriptome.fasta"
genome2_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome2.fasta"
genome_chain_gz = "${test_data_dir}/genomics/homo_sapiens/genome/genome.chain.gz"
@ -136,6 +138,7 @@ params {
genome_21_multi_interval_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi"
genome_21_chromosomes_dir = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz"
dbsnp_146_hg38_elsites = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.elsites"
dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
dbsnp_146_hg38_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi"
gnomad_r2_1_1_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz"

22
tests/modules/bclconvert/main.nf Normal file
View file

@ -0,0 +1,22 @@
#!/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)
}

5
tests/modules/bclconvert/nextflow.config Normal file
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@ -0,0 +1,5 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

52
tests/modules/bclconvert/test.yml Normal file
View file

@ -0,0 +1,52 @@
- 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

18
tests/modules/elprep/filter/main.nf Normal file
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@ -0,0 +1,18 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { ELPREP_FILTER } from '../../../../modules/elprep/filter/main.nf'
workflow test_elprep_filter {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
]
reference_elfasta = file(params.test_data['homo_sapiens']['genome']['genome_elfasta'], checkIfExists: true)
known_sites_elsites = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_elsites'], checkIfExists: true)
target_regions_bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
ELPREP_FILTER ( input, true, true, [], [], reference_elfasta, known_sites_elsites, target_regions_bed, [], [], true, true)
}

7
tests/modules/elprep/filter/nextflow.config Normal file
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@ -0,0 +1,7 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: ELPREP_FILTER {
ext.args = "--mark-duplicates "
}
}

13
tests/modules/elprep/filter/test.yml Normal file
View file

@ -0,0 +1,13 @@
- name: elprep filter test_elprep_filter
command: nextflow run tests/modules/elprep/filter -entry test_elprep_filter -c tests/config/nextflow.config
tags:
- elprep
- elprep/filter
files:
- path: output/elprep/test.activity_profile.igv
- path: output/elprep/test.assembly_regions.igv
- path: output/elprep/output/test.bam
- path: output/elprep/test.g.vcf.gz
- path: output/elprep/test.metrics.txt
- path: output/elprep/test.recall
- path: output/elprep/versions.yml

15
tests/modules/elprep/split/main.nf Normal file
View file

@ -0,0 +1,15 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { ELPREP_SPLIT } from '../../../../modules/elprep/split/main.nf'
workflow test_elprep_split {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
]
ELPREP_SPLIT ( input )
}

9
tests/modules/elprep/split/nextflow.config Normal file
View file

@ -0,0 +1,9 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName : ELPREP_SPLIT {
ext.args = "--contig-group-size 1 --output-type bam"
}
}

10
tests/modules/elprep/split/test.yml Normal file
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@ -0,0 +1,10 @@
- name: elprep split test_elprep_split
command: nextflow run tests/modules/elprep/split -entry test_elprep_split -c tests/config/nextflow.config
tags:
- elprep
- elprep/split
files:
- path: output/elprep/output/splits/test-group00001.bam
- path: output/elprep/output/splits/test-unmapped.bam
- path: output/elprep/output/test-spread.bam
- path: output/elprep/versions.yml

21
tests/modules/kaiju/kaiju2table/main.nf Normal file
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@ -0,0 +1,21 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { UNTAR } from '../../../../modules/untar/main.nf'
include { KAIJU_KAIJU } from '../../../../modules/kaiju/kaiju/main.nf'
include { KAIJU_KAIJU2TABLE } from '../../../../modules/kaiju/kaiju2table/main.nf'
workflow test_kaiju_kaiju_single_end {
input = [
[ id:'test', single_end:true ], // meta map
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
]
db = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
taxon_rank = "species"
ch_db = UNTAR ( db )
KAIJU_KAIJU ( input, ch_db.untar.map{ it[1] } )
KAIJU_KAIJU2TABLE ( KAIJU_KAIJU.out.results, ch_db.untar.map{ it[1] }, taxon_rank )
}

5
tests/modules/kaiju/kaiju2table/nextflow.config Normal file
View file

@ -0,0 +1,5 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

9
tests/modules/kaiju/kaiju2table/test.yml Normal file
View file

@ -0,0 +1,9 @@
- name: kaiju kaiju2table test_kaiju_kaiju_single_end
command: nextflow run tests/modules/kaiju/kaiju2table -entry test_kaiju_kaiju_single_end -c tests/config/nextflow.config
tags:
- kaiju
- kaiju/kaiju2table
files:
- path: output/kaiju/test.txt
md5sum: 0d9f8fd36fcf2888296ae12632c5f0a8
- path: output/kaiju/versions.yml

14
tests/modules/kraken2/kraken2/main.nf
View file

@ -12,7 +12,7 @@ workflow test_kraken2_kraken2_single_end {
db = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
UNTAR ( db )
KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] } )
KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, true, false )
}
workflow test_kraken2_kraken2_paired_end {
@ -23,5 +23,15 @@ workflow test_kraken2_kraken2_paired_end {
db = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
UNTAR ( db )
KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] } )
KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, true, false )
}
workflow test_kraken2_kraken2_classifyreads {
input = [ [ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
]
db = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
UNTAR ( db )
KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, false, true )
}

40
tests/modules/kraken2/kraken2/test.yml
View file

@ -1,29 +1,43 @@
- name: kraken2 kraken2 single-end
command: nextflow run ./tests/modules/kraken2/kraken2 -entry test_kraken2_kraken2_single_end -c ./tests/config/nextflow.config -c ./tests/modules/kraken2/kraken2/nextflow.config
- name: kraken2 kraken2 test_kraken2_kraken2_single_end
command: nextflow run tests/modules/kraken2/kraken2 -entry test_kraken2_kraken2_single_end -c tests/config/nextflow.config
tags:
- kraken2
- kraken2/kraken2
files:
- path: output/kraken2/test.classified.fastq.gz
should_exist: true
- path: output/kraken2/test.unclassified.fastq.gz
should_exist: true
- path: output/kraken2/test.kraken2.report.txt
md5sum: 4227755fe40478b8d7dc8634b489761e
- path: output/kraken2/test.unclassified.fastq.gz
- path: output/kraken2/versions.yml
md5sum: 6e3ad947ac8dee841a89216071c181cc
- path: output/untar/versions.yml
- name: kraken2 kraken2 paired-end
command: nextflow run ./tests/modules/kraken2/kraken2 -entry test_kraken2_kraken2_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/kraken2/kraken2/nextflow.config
- name: kraken2 kraken2 test_kraken2_kraken2_paired_end
command: nextflow run tests/modules/kraken2/kraken2 -entry test_kraken2_kraken2_paired_end -c tests/config/nextflow.config
tags:
- kraken2
- kraken2/kraken2
files:
- path: output/kraken2/test.classified_1.fastq.gz
should_exist: true
- path: output/kraken2/test.classified_2.fastq.gz
should_exist: true
- path: output/kraken2/test.unclassified_1.fastq.gz
should_exist: true
- path: output/kraken2/test.unclassified_2.fastq.gz
should_exist: true
- path: output/kraken2/test.kraken2.report.txt
md5sum: 4227755fe40478b8d7dc8634b489761e
- path: output/kraken2/test.unclassified_1.fastq.gz
- path: output/kraken2/test.unclassified_2.fastq.gz
- path: output/kraken2/versions.yml
md5sum: 604482fe7a4519f890fae9c8beb1bd6e
- path: output/untar/versions.yml
- name: kraken2 kraken2 test_kraken2_kraken2_classifyreads
command: nextflow run tests/modules/kraken2/kraken2 -entry test_kraken2_kraken2_classifyreads -c tests/config/nextflow.config
tags:
- kraken2
- kraken2/kraken2
files:
- path: output/kraken2/test.kraken2.classifiedreads.txt
md5sum: e7a90531f0d8d777316515c36fe4cae0
- path: output/kraken2/test.kraken2.report.txt
md5sum: 4227755fe40478b8d7dc8634b489761e
- path: output/kraken2/versions.yml
md5sum: 3488c304259e83c5bea573403293fce9
- path: output/untar/versions.yml

2
tests/modules/picard/collecthsmetrics/main.nf
View file

@ -7,7 +7,7 @@ include { PICARD_COLLECTHSMETRICS } from '../../../../modules/picard/collecthsme
workflow test_picard_collecthsmetrics {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)

2
tests/modules/picard/collecthsmetrics/test.yml
View file

@ -5,4 +5,4 @@
- picard/collecthsmetrics
files:
# The file can't be md5'd consistently
- path: output/picard/test_collecthsmetrics.txt
- path: output/picard/test.CollectHsMetrics.coverage_metrics

7
tests/modules/samtools/view/main.nf
View file

@ -6,7 +6,8 @@ include { SAMTOOLS_VIEW } from '../../../../modules/samtools/view/main.nf'
workflow test_samtools_view {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
[]
]
SAMTOOLS_VIEW ( input, [] )
@ -14,8 +15,8 @@ workflow test_samtools_view {
workflow test_samtools_view_cram {
input = [ [ id: 'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)

5
tests/modules/stranger/main.nf
View file

@ -23,3 +23,8 @@ workflow test_stranger_without_optional_variant_catalog {
EXPANSIONHUNTER ( input, fasta, variant_catalog )
STRANGER ( EXPANSIONHUNTER.out.vcf, [] )
}
workflow test_stranger_without_optional_variant_catalog_stubs {
EXPANSIONHUNTER ( input, fasta, variant_catalog )
STRANGER ( EXPANSIONHUNTER.out.vcf, [] )
}

10
tests/modules/stranger/test.yml
View file

@ -25,3 +25,13 @@
md5sum: bbe15159195681d5c18596d3ad85c78f
- path: output/stranger/versions.yml
md5sum: 8558542a007e90ea5dcdceed3f12585d
- name: stranger test_stranger_without_optional_variant_catalog_stubs
command: nextflow run tests/modules/stranger -entry test_stranger_without_optional_variant_catalog -c tests/config/nextflow.config -stub-run
tags:
- stranger
files:
- path: output/expansionhunter/test.vcf
- path: output/expansionhunter/versions.yml
- path: output/stranger/test.vcf.gz
- path: output/stranger/versions.yml