millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-11-13 05:13:09 +00:00
Code Issues Releases Packages Activity

Merge branch 'master' into subwf/bam_qc

Browse source
This commit is contained in:
Matthias De Smet 2022-04-22 13:38:23 +02:00 committed by GitHub
commit e37b982bd7
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
40 changed files with 889 additions and 40 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

2
modules/bclconvert/.gitignore vendored Normal file
View file

@ -0,0 +1,2 @@
bcl-convert
*.rpm

15
modules/bclconvert/Dockerfile Normal file
View file

@ -0,0 +1,15 @@
# 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

30
modules/bclconvert/LICENSE Normal file
View file

@ -0,0 +1,30 @@
ILLUMINA END-USER SOFTWARE LICENSE AGREEMENT
IMPORTANT-READ CAREFULLY. THIS IS A LICENSE AGREEMENT THAT YOU ARE REQUIRED TO ACCEPT BEFORE, DOWNLOADING, INSTALLING AND USING ANY SOFTWARE MADE AVAILABLE FROM THE ILLUMINA SUPPORT CENTER (https://support.illumina.com).
CAREFULLY READ ALL THE TERMS AND CONDITIONS OF THIS LICENSE AGREEMENT BEFORE PROCEEDING WITH DOWNLOADING, INSTALLING, AND/OR USING THE SOFTWARE. YOU ARE NOT PERMITTED TO DOWNLOAD, INSTALL, AND/OR USE THE SOFTWARE UNTIL YOU HAVE AGREED TO BE BOUND BY ALL OF THE TERMS AND CONDITIONS OF THIS LICENSE AGREEMENT. YOU REPRESENT AND WARRANT THAT YOU ARE DULY AUTHORIZED TO ACCEPT THE TERMS AND CONDITIONS OF THIS LICENSE AGREEMENT ON BEHALF OF YOUR EMPLOYER.
Software made available through the Illumina Support Center is licensed, not sold, to you. Your license to each software program made available through the Illumina Support Center is subject to your prior acceptance of either this Illumina End-User Software License Agreement (“Agreement”), or a custom end user license agreement (“Custom EULA”), if one is provided with the software. Any software that is subject to this Agreement is referred to herein as the “Software.” By accepting this Agreement, you agree the terms and conditions of this Agreement will apply to and govern any and all of your downloads, installations, and uses of each Illumina software program made available through the Illumina Support Center, except that your download, installation, and use of any software provided with a Custom EULA will be governed by the terms and conditions of the Custom EULA.
This Agreement is made and entered into by and between Illumina, Inc., a Delaware corporation, having offices at 5200 Illumina Way, San Diego, CA 92122 (“Illumina”) and you as the end-user of the Software (hereinafter, “Licensee” or “you”). All software, firmware, and associated media, printed materials, and online and electronic documentation, including any updates or upgrades thereof, made available through the Illumina Support Center (collectively, “Software”) provided to Licensee are for use solely by Licensee and the provisions herein WILL apply with respect to such Software.
License Grant. Subject to the terms and conditions of this Agreement, Illumina grants to Licensee, under the following terms and conditions, a personal, non-exclusive, revocable, non-transferable, non-sublicensable license, for its internal end-use purposes only, in the ordinary course of Licensee’s business to use the Software in executable object code form only, solely at the Licensee’s facility to, install and use the Software on a single computer accessible only by Licensee (and not on any public network or server), where the single computer is owned, leased, or otherwise substantially controlled by Licensee, for the purpose of processing and analyzing data generated from an Illumina genetic sequencing instrument owned and operated solely by Licensee (the “Product”). In the case of Software provided by Illumina in non-compiled form, Illumina grants Licensee a personal, non-exclusive, non-sublicenseable, restricted right to compile, install, and use one copy of the Software solely for processing and analyzing data generated from the Product.
License Restrictions. Except as expressly permitted in Section 1, Licensee may not make, have made, import, use, copy, reproduce, distribute, display, publish, sell, re-sell, lease, or sub-license the Software, in whole or in part, except as expressly provided for in this Agreement. Licensee may not modify, improve, translate, reverse engineer, decompile, disassemble, or create derivative works of the Software or otherwise attempt to (a) defeat, avoid, by-pass, remove, deactivate, or otherwise circumvent any software protection mechanisms in the Software including, without limitation, any such mechanism used to restrict or control the functionality of the Software, or (b) derive the source code or the underlying ideas, algorithms, structure, or organization form of the Software. Licensee will not allow, at any time, including during and after the term of the license, the Software or any portions or copies thereof in any form to become available to any third parties. Licensee may use the Software solely with genomic data that is generated using the Product; Licensee may not use the Software with any data generated from other products or instruments. Licensee may not use the Software to perform any data analysis services for any third party.
Ownership. The Software is protected by United States and international intellectual property laws. All right, title, and interest in and to the Software (including associated intellectual property rights) are and will remain vested in Illumina or Illumina’s affiliated companies or licensors. Licensee acknowledges that no rights, license or interest to any Illumina trademarks are granted hereunder. Licensee acknowledges that unauthorized reproduction or distribution of the Software, or any portion of it, may result in severe civil and criminal penalties. Illumina reserves all rights in and to the Software not expressly granted to Licensee under this Agreement.
Upgrades/Updates. Illumina may, at its sole discretion, provide updates or upgrades to the Software. In that case, Licensee WILL have the same rights and obligations under such updates or upgrades as it has for the versions of the Software initially provided to Licensee hereunder. Licensee recognizes that Illumina is not obligated to provide any upgrades or updates to, or support for, the Software.
Data Integrity/Loss. Licensee is responsible for the integrity and availability, including preventing the loss of data that Licensee generates, uses, analyzes, manages, or stores in connection with or through its use of the Software, including without limitation, investigating and implementing industry appropriate policies and procedures regarding the provision of access to Licensee’s data, monitoring access and use of Licensee’s data, conducting routine backups and archiving of Licensee’s data, and ensuring the adequacy of anti-virus software. Accordingly, Licensee agrees that Illumina is not responsible for any inability to access, loss or corruption of data as a result of Licensee’s use of the Software, and Illumina has no liability to Licensee in connection with such inability to access, loss or corruption of data.
Term of License. This Agreement will be in effect from the time Licensee expressly accepts the terms and conditions of this license, or otherwise installs the Software, thereby accepting the terms and conditions contained herein, and will remain in effect until terminated. This license will otherwise terminate upon the conditions set forth in this Agreement, if revoked by Illumina, or if Licensee fails to comply with any term or condition of this Agreement including failure to pay any applicable license fee. Licensee agrees upon termination of this Agreement for any reason to immediately discontinue use of and un-install the Software and destroy all copies of the Software in its possession and/or under its control, and return or destroy, at Illumina’s option, any compact disks, floppy disks or other media provided by Illumina storing the Software thereon (together with any authorized copies thereof), as well as any documentation associated therewith
Limited Warranty. Illumina warrants that, for a period of 6 months from the date of download or installation of the Software by Licensee, the Software will perform in all material respects in accordance with the accompanying documentation available on the Illumina Support Center. EXCEPT AND TO THE EXTENT EXPRESSLY PROVIDED IN THE FOREGOING, AND TO THE FULLEST EXTENT PERMITTED BY APPLICABLE LAW, THE SOFTWARE IS PROVIDED “AS IS” AND ILLUMINA EXPRESSLY DISCLAIMS ALL WARRANTIES AND CONDITIONS REGARDING THE SOFTWARE AND RESULTS GENERATED BY THE SOFTWARE, INCLUDING WITHOUT LIMITATION, TO THE FULLEST EXTENT PERMITTED BY APPLICABLE LAW, ALL OTHER EXPRESS OR IMPLIED WARRANTIES OR CONDITIONS OF MERCHANTABLE QUALITY, NON-INFRINGEMENT, AND FITNESS FOR A PARTICULAR PURPOSE, AND THOSE ARISING BY STATUTE OR OTHERWISE IN LAW OR FROM A COURSE OF DEALING OR USAGE OF TRADE. ILLUMINA DOES NOT WARRANT THAT THE FUNCTIONS CONTAINED IN THE SOFTWARE WILL MEET LICENSEE"S REQUIREMENTS, OR THAT THE OPERATION OF THE SOFTWARE WILL BE ERROR FREE OR UNINTERRUPTED.
Limitation of Liability.
(a) ILLUMINA’S ENTIRE LIABILITY AND LICENSEE"S EXCLUSIVE REMEDY UNDER THE LIMITED WARRANTY PROVISION OF SECTION 7 ABOVE WILL BE, AT ILLUMINA’S OPTION, EITHER (i) RETURN OF THE PRICE PAID FOR THE SOFTWARE, OR (ii) REPAIR OR REPLACEMENT OF THE PORTIONS OF THE SOFTWARE THAT DO NOT COMPLY WITH ILLUMINA’S LIMITED WARRANTY. THIS LIMITED WARRANTY IS VOID AND ILLUMINA WILL HAVE NO LIABILITY AT ALL IF FAILURE OF THE SOFTWARE TO COMPLY WITH ILLUMINA LIMITED WARRANTY HAS RESULTED FROM: (w) FAILURE TO USE THE SOFTWARE IN ACCORDANCE WITH ILLUMINA’S THEN CURRENT USER MANUAL OR THIS AGREEMENT; (x) ACCIDENT, ABUSE, OR MISAPPLICATION; (y) PRODUCTS OR EQUIPMENT NOT SPECIFIED BY ILLUMINA AS BEING COMPATIBLE WITH THE SOFTWARE; OR (z) IF LICENSEE HAS NOT NOTIFIED ILLUMINA IN WRITING OF THE DEFECT WITHIN THE ABOVE WARRANTY PERIOD.
(b) TO THE FULLEST EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT WILL ILLUMINA BE LIABLE UNDER ANY THEORY OF CONTRACT, TORT, STRICT LIABILITY OR OTHER LEGAL OR EQUITABLE THEORY FOR ANY PERSONAL INJURY OR ANY INDIRECT, CONSEQUENTIAL, OR INCIDENTAL DAMAGES, EVEN IF ILLUMINA HAS BEEN ADVISED OF THE POSSIBILITY THEREOF INCLUDING, WITHOUT LIMITATION, LOST PROFITS, LOST DATA, INTERRUPTION OF BUSINESS, LOST BUSINESS REVENUE, OTHER ECONOMIC LOSS, OR ANY LOSS OF RECORDED DATA ARISING OUT OF THE USE OF OR INABILITY TO USE THE SOFTWARE. EXCEPT AND TO THE EXTENT EXPRESSLY PROVIDED IN SECTION 7 AND 8(a) ABOVE OR AS OTHERWISE PERMITTED BY LAW, IN NO EVENT WILL ILLUMINA’S TOTAL LIABILITY TO LICENSEE FOR ALL DAMAGES (OTHER THAN AS MAY BE REQUIRED BY APPLICABLE LAW IN CASES INVOLVING PERSONAL INJURY) EXCEED THE AMOUNT OF $500 USD. THE FOREGOING LIMITATIONS WILL APPLY EVEN IF THE ABOVE STATED REMEDY FAILS OF ITS ESSENTIAL PURPOSE.
Survival. The limitations of liability and ownership rights of Illumina contained herein and Licensee’s obligations following termination of this Agreement WILL survive the termination of this Agreement for any reason.
Research Use Only. The Software is labeled with a For Research Use Only or similar labeling statement and the performance characteristics of the Software have not been established and the Software is not for use in diagnostic procedures. Licensee acknowledges and agrees that (i) the Software has not been approved, cleared, or licensed by the United States Food and Drug Administration or any other regulatory entity whether foreign or domestic for any specific intended use, whether research, commercial, diagnostic, or otherwise, and (ii) Licensee must ensure it has any regulatory approvals that are necessary for Licensee’s intended uses of the Software. Licensee will comply with all applicable laws and regulations when using and maintaining the Software.
General. Licensee may not sublicense, assign, share, pledge, rent or transfer any of its rights under this Agreement in relation to the Software or any portion thereof including documentation. Illumina reserves the right to change this Agreement at any time. When Illumina makes any changes, Illumina will provide the updated Agreement, or a link to it, on Illumina’s website (www.illumina.com) and such updated Agreement WILL become effective immediately. Licensee’s continued access to or use of the Software represents Licensee’s agreement to any revised Agreement. If one or more provisions of this Agreement are found to be invalid or unenforceable, this Agreement WILL not be rendered inoperative but the remaining provisions WILL continue in full force and effect. This Agreement constitutes the entire agreement between the parties with respect to the subject matter of this Agreement and merges all prior communications except that a “hard-copy” form of licensing agreement relating to the Software previously agreed to in writing by Illumina and Licensee WILL supersede and govern in the event of any conflicting provisions.
Governing Law. This Agreement WILL be governed by and construed in accordance with the laws of the state of California, USA, without regard to its conflicts of laws principles, and independent of where a suit or action hereunder may be filed.
U.S. Government End Users. If Licensee is a branch agency or instrumentality of the United States Government, the following provision applies. The Software is a “commercial item” as that term is defined at 48 C.F.R. 2.101, consisting of “commercial computer software” and “commercial computer software documentation,” as such terms are used in 48 C.F.R. 12.212 or 48 C.F.R. 227.7202 (as applicable). Consistent with 48 C.F.R. 12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4, all United States Government end users acquire the Software with only those rights set forth herein.
Contact. Any questions regarding legal rights, duties, obligations, or restrictions associated with the software hereunder should be directed to Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, Attention: Legal Department, Phone: (858) 202-4500, Fax: (858) 202-4599, web site: www.illumina.com <http://www.illumina.com>.
Third Party Components. The Software may include third party software (“Third Party Programs”). Some of the Third Party Programs are available under open source or free software licenses. The License Agreement accompanying the Licensed Software does not alter any rights or obligations Licensee may have under those open source or free software licenses. The licenses that govern the terms and conditions of use of the Third Party Programs included in the Licensed Software are provided in the READ ME provided with the Software. The READ ME also contains copyright statements for the various open source software components (or portions thereof) that are distributed with the Licensed Software.
END OF END-USER SOFTWARE LICENSE AGREEMENT.

17
modules/bclconvert/README.md Normal file
View file

@ -0,0 +1,17 @@
# 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>
```

81
modules/bclconvert/main.nf Normal file
View file

@ -0,0 +1,81 @@
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
"""
}

45
modules/bclconvert/meta.yml Normal file
View file

@ -0,0 +1,45 @@
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"

89
modules/elprep/filter/main.nf Normal file
View file

@ -0,0 +1,89 @@
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
"""
}

106
modules/elprep/filter/meta.yml Normal file
View file

@ -0,0 +1,106 @@
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"

45
modules/elprep/split/main.nf Normal file
View file

@ -0,0 +1,45 @@
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
"""
}

43
modules/elprep/split/meta.yml Normal file
View file

@ -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
View file

@ -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
View file

@ -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
View file

@ -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
View file

@ -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
View file

@ -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
View file

@ -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
View file

@ -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