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def VERSION = '1.0.3' // Version information not provided by tool
process AMPLIFY_PREDICT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::amplify=1.0.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/amplify:1.0.3--py36hdfd78af_0':
'quay.io/biocontainers/amplify:1.0.3--py36hdfd78af_0' }"
input:
tuple val(meta), path(faa)
path(model_dir)
output:
tuple val(meta), path('*.tsv'), emit: tsv
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 custom_model_dir = model_dir ? "-md ${model_dir}" : ""
"""
AMPlify \\
$args \\
${custom_model_dir} \\
-s '${faa}'
#rename output, because tool includes date and time in name
mv *.tsv ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
AMPlify: $VERSION
END_VERSIONS
"""
}

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name: "amplify_predict"
description: AMPlify is an attentive deep learning model for antimicrobial peptide prediction.
keywords:
- antimicrobial peptides
- AMPs
- prediction
- model
tools:
- "amplify":
description: "Attentive deep learning model for antimicrobial peptide prediction"
homepage: "https://github.com/bcgsc/AMPlify"
documentation: "https://github.com/bcgsc/AMPlify"
tool_dev_url: "https://github.com/bcgsc/AMPlify"
doi: "https://doi.org/10.1186/s12864-022-08310-4"
licence: "['GPL v3']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- faa:
type: file
description: amino acid sequences fasta
pattern: "*.{fa,fa.gz,faa,faa.gz,fasta,fasta.gz}"
- model_dir:
type: directory
description: Directory of where models are stored (optional)
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"
- tsv:
type: file
description: amino acid sequences with prediction (AMP, non-AMP) and probability scores
pattern: "*.{tsv}"
authors:
- "@louperelo"

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process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
label 'process_low'
conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' :
'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
/*
These files are normally downloaded/created by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH.
Reason: Upon execution, the tool checks if certain database files are present within the container and if not, it tries to create them in /usr/local/bin, for which only root user has write permissions. Mounting those database files with this module prevents the tool from trying to create them.
These files are also emitted as output channels in this module to enable the antismash-lite module to use them as mount volumes to the docker/singularity containers.
*/
containerOptions {
workflow.containerEngine == 'singularity' ?
"-B $database_css:/usr/local/lib/python3.8/site-packages/antismash/outputs/html/css,$database_detection:/usr/local/lib/python3.8/site-packages/antismash/detection,$database_modules:/usr/local/lib/python3.8/site-packages/antismash/modules" :
workflow.containerEngine == 'docker' ?
"-v \$PWD/$database_css:/usr/local/lib/python3.8/site-packages/antismash/outputs/html/css -v \$PWD/$database_detection:/usr/local/lib/python3.8/site-packages/antismash/detection -v \$PWD/$database_modules:/usr/local/lib/python3.8/site-packages/antismash/modules" :
''
}
input:
path database_css
path database_detection
path database_modules
output:
path("antismash_db") , emit: database
path("css"), emit: css_dir
path("detection"), emit: detection_dir
path("modules"), emit: modules_dir
path "versions.yml", emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
"""
download-antismash-databases \\
--database-dir antismash_db \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
END_VERSIONS
"""
}

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name: antismash_antismashlitedownloaddatabases
description: antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. This module downloads the antiSMASH databases.
keywords:
- secondary metabolites
- BGC
- biosynthetic gene cluster
- genome mining
- NRPS
- RiPP
- antibiotics
- prokaryotes
- bacteria
- eukaryotes
- fungi
- antismash
- database
tools:
- antismash:
description: antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell
homepage: https://docs.antismash.secondarymetabolites.org
documentation: https://docs.antismash.secondarymetabolites.org
tool_dev_url: https://github.com/antismash/antismash
doi: "10.1093/nar/gkab335"
licence: ["AGPL v3"]
input:
- database_css:
type: directory
description: |
antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
pattern: "css"
- database_detection:
type: directory
description: |
antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
pattern: "detection"
- database_modules:
type: directory
description: |
antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
pattern: "modules"
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- database:
type: directory
description: Download directory for antiSMASH databases
pattern: "antismash_db"
- css_dir:
type: directory
description: |
antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
pattern: "css"
- detection_dir:
type: directory
description: |
antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
pattern: "detection"
- modules_dir:
type: directory
description: |
antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
pattern: "modules"
authors:
- "@jasmezz"

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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"

4
modules/cat/fastq/main.nf
View file

@ -4,8 +4,8 @@ process CAT_FASTQ {
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
'biocontainers/biocontainers:v1.2.0_cv1' }"
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"
input:
tuple val(meta), path(reads, stageAs: "input*/*")

6
modules/custom/getchromsizes/main.nf
View file

@ -2,10 +2,10 @@ process CUSTOM_GETCHROMSIZES {
tag "$fasta"
label 'process_low'
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
input:
path fasta

89
modules/elprep/filter/main.nf Normal file
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@ -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
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@ -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
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@ -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"

41
modules/gamma/main.nf Normal file
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@ -0,0 +1,41 @@
def VERSION = '2.1' // Version information not provided by tool on CLI
process GAMMA {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gamma=2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gamma%3A2.1--hdfd78af_0':
'quay.io/biocontainers/gamma:2.1--hdfd78af_0' }"
input:
tuple val(meta), path(fasta)
path(db)
output:
tuple val(meta), path("*.gamma") , emit: gamma
tuple val(meta), path("*.psl") , emit: psl
tuple val(meta), path("*.gff") , optional:true , emit: gff
tuple val(meta), path("*.fasta"), optional:true , emit: fasta
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}"
"""
GAMMA.py \\
$args \\
$fasta \\
$db \\
$prefix
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gamma: $VERSION
END_VERSIONS
"""
}

63
modules/gamma/meta.yml Normal file
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@ -0,0 +1,63 @@
name: "gamma"
description: Gene Allele Mutation Microbial Assessment
keywords:
- gamma
- gene-calling
tools:
- "gamma":
description: "Tool for Gene Allele Mutation Microbial Assessment"
homepage: "https://github.com/rastanton/GAMMA"
documentation: "https://github.com/rastanton/GAMMA"
tool_dev_url: "https://github.com/rastanton/GAMMA"
doi: "10.1093/bioinformatics/btab607"
licence: "['Apache License 2.0']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: FASTA file
pattern: "*.{fa,fasta}"
- db:
type: file
description: Database in FASTA format
pattern: "*.{fa,fasta}"
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"
- gamma:
type: file
description: GAMMA file with annotated gene matches
pattern: "*.{gamma}"
- psl:
type: file
description: PSL file with all gene matches found
pattern: "*.{psl}"
- gff:
type: file
description: GFF file
pattern: "*.{gff}"
- fasta:
type: file
description: multifasta file of the gene matches
pattern: "*.{fasta}"
authors:
- "@sateeshperi"
- "@rastanton"

2
modules/gatk4/haplotypecaller/main.nf
View file

@ -17,7 +17,7 @@ process GATK4_HAPLOTYPECALLER {
output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
tuple val(meta), path("*.tbi") , emit: tbi
tuple val(meta), path("*.tbi") , optional:true, emit: tbi
path "versions.yml" , emit: versions
when:

4
modules/gatk4/splitncigarreads/main.nf
View file

@ -8,7 +8,7 @@ process GATK4_SPLITNCIGARREADS {
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
tuple val(meta), path(bam), path(bai), path(intervals)
path fasta
path fai
path dict
@ -23,6 +23,7 @@ process GATK4_SPLITNCIGARREADS {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def interval_command = intervals ? "--intervals $intervals" : ""
def avail_mem = 3
if (!task.memory) {
@ -35,6 +36,7 @@ process GATK4_SPLITNCIGARREADS {
--input $bam \\
--output ${prefix}.bam \\
--reference $fasta \\
$interval_command \\
--tmp-dir . \\
$args

7
modules/gatk4/splitncigarreads/meta.yml
View file

@ -23,6 +23,13 @@ input:
type: list
description: BAM/SAM/CRAM file containing reads
pattern: "*.{bam,sam,cram}"
- bai:
type: list
description: BAI/SAI/CRAI index file (optional)
pattern: "*.{bai,sai,crai}"
- intervals:
type: file
description: Bed file with the genomic regions included in the library (optional)
- fasta:
type: file
description: The reference fasta file

4
modules/gunzip/main.nf
View file

@ -4,8 +4,8 @@ process GUNZIP {
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
'biocontainers/biocontainers:v1.2.0_cv1' }"
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"
input:
tuple val(meta), path(archive)

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

22
modules/minimap2/align/main.nf
View file

@ -2,18 +2,22 @@ process MINIMAP2_ALIGN {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' :
'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' :
'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }"
input:
tuple val(meta), path(reads)
path reference
val bam_format
val cigar_paf_format
val cigar_bam
output:
tuple val(meta), path("*.paf"), emit: paf
path "versions.yml" , emit: versions
tuple val(meta), path("*.paf"), optional: true, emit: paf
tuple val(meta), path("*.bam"), optional: true, emit: bam
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
@ -22,13 +26,19 @@ process MINIMAP2_ALIGN {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
def cigar_paf = cigar_paf_format && !sam_format ? "-c" : ''
def set_cigar_bam = cigar_bam && sam_format ? "-L" : ''
"""
minimap2 \\
$args \\
-t $task.cpus \\
$reference \\
$input_reads \\
> ${prefix}.paf
$cigar_paf \\
$set_cigar_bam \\
$bam_output
cat <<-END_VERSIONS > versions.yml
"${task.process}":

18
modules/minimap2/align/meta.yml
View file

@ -29,6 +29,17 @@ input:
type: file
description: |
Reference database in FASTA format.
- bam_format:
type: boolean
description: Specify that output should be in BAM format
- cigar_paf_format:
type: boolean
description: Specify that output CIGAR should be in PAF format
- cigar_bam:
type: boolean
description: |
Write CIGAR with >65535 ops at the CG tag. This is recommended when
doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)
output:
- meta:
type: map
@ -39,9 +50,16 @@ output:
type: file
description: Alignment in PAF format
pattern: "*.paf"
- bam:
type: file
description: Alignment in BAM format
pattern: "*.bam"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@heuermh"
- "@sofstam"
- "@sateeshperi"
- "@jfy133"

5
modules/phantompeakqualtools/main.nf
View file

@ -22,11 +22,12 @@ process PHANTOMPEAKQUALTOOLS {
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
RUN_SPP=`which run_spp.R`
Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus
Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" $args2
cat <<-END_VERSIONS > versions.yml
"${task.process}":

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"

6
modules/rsem/calculateexpression/main.nf
View file

@ -2,10 +2,10 @@ process RSEM_CALCULATEEXPRESSION {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' :
'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' :
'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }"
input:
tuple val(meta), path(reads)

6
modules/rsem/preparereference/main.nf
View file

@ -2,10 +2,10 @@ process RSEM_PREPAREREFERENCE {
tag "$fasta"
label 'process_high'
conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' :
'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' :
'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }"
input:
path fasta, stageAs: "rsem/*"

35
modules/samtools/bamtocram/main.nf Normal file
View file

@ -0,0 +1,35 @@
//There is a -L option to only output alignments in interval, might be an option for exons/panel data?
process SAMTOOLS_BAMTOCRAM {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
input:
tuple val(meta), path(input), path(index)
path fasta
path fai
output:
tuple val(meta), path("*.cram"), path("*.crai"), emit: cram_crai
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}"
"""
samtools view --threads ${task.cpus} --reference ${fasta} -C $args $input > ${prefix}.cram
samtools index -@${task.cpus} ${prefix}.cram
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}

52
modules/samtools/bamtocram/meta.yml Normal file
View file

@ -0,0 +1,52 @@
name: samtools_bamtocram
description: filter/convert and then index CRAM file
keywords:
- view
- index
- bam
- cram
tools:
- samtools:
description: |
SAMtools is a set of utilities for interacting with and post-processing
short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
These files are generated as output by short read aligners like BWA.
homepage: http://www.htslib.org/
documentation: hhttp://www.htslib.org/doc/samtools.html
doi: 10.1093/bioinformatics/btp352
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: BAM/SAM file
pattern: "*.{bam,sam}"
- index:
type: file
description: BAM/SAM index file
pattern: "*.{bai,sai}"
- fasta:
type: file
description: Reference file to create the CRAM file
pattern: "*.{fasta,fa}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- cram_crai:
type: file
description: filtered/converted CRAM file + index
pattern: "*{.cram,.crai}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@FriederikeHanssen"
- "@maxulysse"

47
modules/samtools/collatefastq/main.nf Normal file
View file

@ -0,0 +1,47 @@
process SAMTOOLS_COLLATEFASTQ {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
input:
tuple val(meta), path(input)
output:
//TODO might be good to have ordered output of the fastq files, so we can
// make sure the we get the right files
tuple val(meta), path("*_{1,2}.fq.gz"), path("*_other.fq.gz"), path("*_singleton.fq.gz"), emit: reads
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
samtools collate \\
$args \\
--threads $task.cpus \\
-O \\
$input \\
. |
samtools fastq \\
$args2 \\
--threads $task.cpus \\
-1 ${prefix}_1.fq.gz \\
-2 ${prefix}_2.fq.gz \\
-0 ${prefix}_other.fq.gz \\
-s ${prefix}_singleton.fq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}

48
modules/samtools/collatefastq/meta.yml Normal file
View file

@ -0,0 +1,48 @@
name: samtools_collatefastq
description: |
The module uses collate and then fastq methods from samtools to
convert a SAM, BAM or CRAM file to FASTQ format
keywords:
- bam2fq
- samtools
- fastq
tools:
- samtools:
description: Tools for dealing with SAM, BAM and CRAM files
homepage: None
documentation: http://www.htslib.org/doc/1.1/samtools.html
tool_dev_url: None
doi: ""
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton)
or a single interleaved .fq.gz file if the user chooses not to split the reads.
pattern: "*.fq.gz"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@lescai"
- "@maxulysse"

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

16
modules/stranger/main.nf
View file

@ -9,6 +9,7 @@ process STRANGER {
input:
tuple val(meta), path(vcf)
path variant_catalog
output:
tuple val(meta), path("*.gz"), emit: vcf
@ -20,10 +21,23 @@ process STRANGER {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def options_variant_catalog = variant_catalog ? "--repeats-file $variant_catalog" : ""
"""
stranger \\
$args \\
$vcf | gzip --no-name > ${prefix}.vcf.gz
$vcf \\
$options_variant_catalog | gzip --no-name > ${prefix}.vcf.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
stranger: \$( stranger --version )
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.vcf.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":

4
modules/stranger/meta.yml
View file

@ -24,6 +24,10 @@ input:
type: file
description: VCF with repeat expansions
pattern: "*.{vcf.gz,vcf}"
- variant_catalog:
type: file
description: json file with repeat expansion sites to genotype
pattern: "*.{json}"
output:
- meta:

6
modules/stringtie/merge/main.nf
View file

@ -2,10 +2,10 @@ process STRINGTIE_MERGE {
label 'process_medium'
// Note: 2.7X indices incompatible with AWS iGenomes.
conda (params.enable_conda ? "bioconda::stringtie=2.1.7" : null)
conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0' :
'quay.io/biocontainers/stringtie:2.1.7--h978d192_0' }"
'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }"
input:
path stringtie_gtf

8
modules/stringtie/stringtie/main.nf
View file

@ -1,11 +1,11 @@
process STRINGTIE {
process STRINGTIE_STRINGTIE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::stringtie=2.1.7" : null)
conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0' :
'quay.io/biocontainers/stringtie:2.1.7--h978d192_0' }"
'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }"
input:
tuple val(meta), path(bam)

2
modules/stringtie/stringtie/meta.yml
View file

@ -1,4 +1,4 @@
name: stringtie
name: stringtie_stringtie
description: Transcript assembly and quantification for RNA-Se
keywords:
- transcript

11
modules/tabix/bgzip/main.nf
View file

@ -11,17 +11,20 @@ process TABIX_BGZIP {
tuple val(meta), path(input)
output:
tuple val(meta), path("*.gz"), emit: gz
path "versions.yml" , emit: versions
tuple val(meta), path("${prefix}*"), emit: output
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
prefix = task.ext.prefix ?: "${meta.id}"
in_bgzip = input.toString().endsWith(".gz")
command1 = in_bgzip ? '-d' : '-c'
command2 = in_bgzip ? '' : " > ${prefix}.${input.getExtension()}.gz"
"""
bgzip -c $args $input > ${prefix}.${input.getExtension()}.gz
bgzip $command1 $args -@${task.cpus} $input $command2
cat <<-END_VERSIONS > versions.yml
"${task.process}":

15
modules/tabix/bgzip/meta.yml
View file

@ -1,13 +1,14 @@
name: tabix_bgzip
description: Compresses files
description: Compresses/decompresses files
keywords:
- compress
- decompress
- bgzip
- tabix
tools:
- bgzip:
description: |
Bgzip compresses files in a similar manner to, and compatible with, gzip.
Bgzip compresses or decompresses files in a similar manner to, and compatible with, gzip.
homepage: https://www.htslib.org/doc/tabix.html
documentation: http://www.htslib.org/doc/bgzip.html
doi: 10.1093/bioinformatics/btp352
@ -18,19 +19,19 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- file:
- input:
type: file
description: text file
description: file to compress or to decompress
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- file:
- output:
type: file
description: Output compressed file
pattern: "*.{gz}"
description: Output compressed/decompressed file
pattern: "*."
- versions:
type: file
description: File containing software versions

2
modules/tiddit/sv/main.nf
View file

@ -24,7 +24,7 @@ process TIDDIT_SV {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def reference = fasta == "dummy_file.txt" ? "--ref $fasta" : ""
def reference = fasta ? "--ref $fasta" : ""
"""
tiddit \\
--sv \\

13
modules/trimgalore/main.nf
View file

@ -11,12 +11,13 @@ process TRIMGALORE {
tuple val(meta), path(reads)
output:
tuple val(meta), path("*.fq.gz") , emit: reads
tuple val(meta), path("*report.txt"), emit: log
path "versions.yml" , emit: versions
tuple val(meta), path("*{trimmed,val}*.fq.gz"), emit: reads
tuple val(meta), path("*report.txt") , emit: log
path "versions.yml" , emit: versions
tuple val(meta), path("*.html"), emit: html optional true
tuple val(meta), path("*.zip") , emit: zip optional true
tuple val(meta), path("*unpaired*.fq.gz") , emit: unpaired, optional: true
tuple val(meta), path("*.html") , emit: html , optional: true
tuple val(meta), path("*.zip") , emit: zip , optional: true
when:
task.ext.when == null || task.ext.when
@ -52,6 +53,7 @@ process TRIMGALORE {
$c_r1 \\
$tpc_r1 \\
${prefix}.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
@ -73,6 +75,7 @@ process TRIMGALORE {
$tpc_r2 \\
${prefix}_1.fastq.gz \\
${prefix}_2.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')

5
modules/trimgalore/meta.yml
View file

@ -37,6 +37,11 @@ output:
List of input adapter trimmed FastQ files of size 1 and 2 for
single-end and paired-end data, respectively.
pattern: "*.{fq.gz}"
- unpaired:
type: file
description: |
FastQ files containing unpaired reads from read 1 or read 2
pattern: "*unpaired*.fq.gz"
- html:
type: file
description: FastQC report (optional)

6
modules/untar/main.nf
View file

@ -2,10 +2,10 @@ process UNTAR {
tag "$archive"
label 'process_low'
conda (params.enable_conda ? "conda-forge::tar=1.34" : null)
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
'biocontainers/biocontainers:v1.2.0_cv2' }"
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"
input:
tuple val(meta), path(archive)

48
tests/config/pytest_modules.yml
View file

@ -26,6 +26,10 @@ allelecounter:
- modules/allelecounter/**
- tests/modules/allelecounter/**
amplify/predict:
- modules/amplify/predict/**
- tests/modules/amplify/predict/**
amps:
- modules/amps/**
- tests/modules/amps/**
@ -38,6 +42,10 @@ amrfinderplus/update:
- modules/amrfinderplus/update/**
- tests/modules/amrfinderplus/update/**
antismash/antismashlitedownloaddatabases:
- modules/antismash/antismashlitedownloaddatabases/**
- tests/modules/antismash/antismashlitedownloaddatabases/**
arriba:
- modules/arriba/**
- tests/modules/arriba/**
@ -166,6 +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/**
@ -587,6 +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/**
@ -655,10 +675,18 @@ freebayes:
- modules/freebayes/**
- tests/modules/freebayes/**
gamma:
- modules/gamma/**
- tests/modules/gamma/**
gatk4/applybqsr:
- modules/gatk4/applybqsr/**
- tests/modules/gatk4/applybqsr/**
gatk4/applybqsrspark:
- modules/gatk4/applybqsrspark/**
- tests/modules/gatk4/applybqsrspark/**
gatk4/applyvqsr:
- modules/gatk4/applyvqsr/**
- tests/modules/gatk4/applyvqsr/**
@ -667,6 +695,10 @@ gatk4/baserecalibrator:
- modules/gatk4/baserecalibrator/**
- tests/modules/gatk4/baserecalibrator/**
gatk4/baserecalibratorspark:
- modules/gatk4/baserecalibratorspark/**
- tests/modules/gatk4/baserecalibratorspark/**
gatk4/bedtointervallist:
- modules/gatk4/bedtointervallist/**
- tests/modules/gatk4/bedtointervallist/**
@ -743,6 +775,10 @@ gatk4/markduplicates:
- modules/gatk4/markduplicates/**
- tests/modules/gatk4/markduplicates/**
gatk4/markduplicatesspark:
- modules/gatk4/markduplicatesspark/**
- tests/modules/gatk4/markduplicatesspark/**
gatk4/mergebamalignment:
- modules/gatk4/mergebamalignment/**
- tests/modules/gatk4/mergebamalignment/**
@ -977,6 +1013,10 @@ 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/**
@ -1559,6 +1599,14 @@ samtools/bam2fq:
- modules/samtools/bam2fq/**
- tests/modules/samtools/bam2fq/**
samtools/bamtocram:
- modules/samtools/bamtocram/**
- tests/modules/samtools/bamtocram/**
samtools/collatefastq:
- modules/samtools/collatefastq/**
- tests/modules/samtools/collatefastq/**
samtools/depth:
- modules/samtools/depth/**
- tests/modules/samtools/depth/**

10
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 = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz"
@ -242,8 +245,8 @@ params {
test2_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz"
test2_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz"
test2_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz"
test_rnaseq_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.rnaseq_1.fastq.gz"
test_rnaseq_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.rnaseq_2.fastq.gz"
test_rnaseq_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz"
test_rnaseq_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz"
test_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table"
test2_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table"
@ -332,6 +335,7 @@ params {
'bacteroides_fragilis' {
'genome' {
genome_fna_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz"
genome_gbff_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz"
genome_paf = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf"
genome_mapping_potential_arg = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.mapping.potential.ARG"
@ -397,7 +401,7 @@ params {
hello = "${test_data_dir}/generic/txt/hello.txt"
}
'cnn' {
reference = "${test_data_dir}/generic/cnn/reference.cnn"
reference = "${test_data_dir}/generic/cnn/reference.cnn"
}
'cooler'{
test_pairix_pair_gz = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"

18
tests/modules/amplify/predict/main.nf Normal file
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@ -0,0 +1,18 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PRODIGAL } from '../../../modules/prodigal/main.nf' addParams( options: [:] )
include { AMPLIFY_PREDICT } from '../../../../modules/amplify/predict/main.nf' addParams( options: [:] )
workflow amplify_predict {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
]
model_dir = []
PRODIGAL ( input, "gff" )
AMPLIFY_PREDICT ( PRODIGAL.out.amino_acid_fasta, model_dir)
}

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

9
tests/modules/amplify/predict/test.yml Normal file
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@ -0,0 +1,9 @@
- name: amplify predict amplify_predict
command: nextflow run tests/modules/amplify/predict -entry amplify_predict -c tests/config/nextflow.config
tags:
- amplify/predict
- amplify
files:
- path: output/amplify/test.tsv
md5sum: 1951084ce1d410028be86754997e5852
- path: output/amplify/versions.yml

29
tests/modules/antismash/antismashlitedownloaddatabases/main.nf Normal file
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@ -0,0 +1,29 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { UNTAR as UNTAR1 } from '../../../../modules/untar/main.nf'
include { UNTAR as UNTAR2 } from '../../../../modules/untar/main.nf'
include { UNTAR as UNTAR3 } from '../../../../modules/untar/main.nf'
include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../../modules/antismash/antismashlitedownloaddatabases/main.nf'
workflow test_antismash_antismashlitedownloaddatabases {
input1 = [
[],
file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
]
input2 = [
[],
file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
]
input3 = [
[],
file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
]
UNTAR1 ( input1 )
UNTAR2 ( input2 )
UNTAR3 ( input3 )
ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] }, UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
}

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

17
tests/modules/antismash/antismashlitedownloaddatabases/test.yml Normal file
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@ -0,0 +1,17 @@
- name: antismash antismashlitedownloaddatabases test_antismash_antismashlitedownloaddatabases
command: nextflow run tests/modules/antismash/antismashlitedownloaddatabases -entry test_antismash_antismashlitedownloaddatabases -c tests/config/nextflow.config
tags:
- antismash
- antismash/antismashlitedownloaddatabases
files:
- path: output/antismash/versions.yml
md5sum: 24859c67023abab99de295d3675a24b6
- path: output/antismash/antismash_db
- path: output/antismash/antismash_db/clusterblast
- path: output/antismash/antismash_db/clustercompare
- path: output/antismash/antismash_db/pfam
- path: output/antismash/antismash_db/resfam
- path: output/antismash/antismash_db/tigrfam
- path: output/antismash/css
- path: output/antismash/detection
- path: output/antismash/modules

22
tests/modules/bclconvert/main.nf Normal file
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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

17
tests/modules/gamma/main.nf Normal file
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@ -0,0 +1,17 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GAMMA } from '../../../modules/gamma/main.nf'
workflow test_gamma {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
db = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
GAMMA ( input, db )
}

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

13
tests/modules/gamma/test.yml Normal file
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@ -0,0 +1,13 @@
- name: gamma test_gamma
command: nextflow run tests/modules/gamma -entry test_gamma -c tests/config/nextflow.config
tags:
- gamma
files:
- path: output/gamma/test.fasta
md5sum: df37b48466181311e0a679f3c5878484
- path: output/gamma/test.gamma
md5sum: 3256708fa517a65ed01d99e0e3c762ae
- path: output/gamma/test.psl
md5sum: 162a2757ed3b167ae1e0cdb24213f940
- path: output/gamma/versions.yml
md5sum: 3fefb5b46c94993362243c5f9a472057

18
tests/modules/gatk4/splitncigarreads/main.nf
View file

@ -6,7 +6,23 @@ include { GATK4_SPLITNCIGARREADS } from '../../../../modules/gatk4/splitncigarre
workflow test_gatk4_splitncigarreads {
input = [ [ id:'test' ], // 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)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK4_SPLITNCIGARREADS ( input, fasta, fai, dict )
}
workflow test_gatk4_splitncigarreads_intervals {
input = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['test_bed'], 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)

11
tests/modules/gatk4/splitncigarreads/test.yml
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@ -5,5 +5,14 @@
- gatk4/splitncigarreads
files:
- path: output/gatk4/test.bam
md5sum: ceed15c0bd64ff5c38d3816905933b0b
md5sum: 436d8e31285c6b588bdd1c7f1d07f6f2
- path: output/gatk4/versions.yml
- name: gatk4 splitncigarreads test_gatk4_splitncigarreads_intervals
command: nextflow run tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads_intervals -c tests/config/nextflow.config
tags:
- gatk4
- gatk4/splitncigarreads
files:
- path: output/gatk4/test.bam
md5sum: cd56e3225950f519fd47164cca60a0bb
- path: output/gatk4/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
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@ -0,0 +1,5 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

9
tests/modules/kaiju/kaiju2table/test.yml Normal file
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@ -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
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@ -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

10
tests/modules/minimap2/align/main.nf
View file

@ -9,8 +9,11 @@ workflow test_minimap2_align_single_end {
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
bam_format = true
cigar_paf_format = false
cigar_bam = false
MINIMAP2_ALIGN ( input, fasta )
MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam)
}
workflow test_minimap2_align_paired_end {
@ -19,6 +22,9 @@ workflow test_minimap2_align_paired_end {
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
bam_format = true
cigar_paf_format = false
cigar_bam = false
MINIMAP2_ALIGN ( input, fasta )
MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam )
}

16
tests/modules/minimap2/align/test.yml
View file

@ -1,17 +1,17 @@
- name: minimap2 align single-end
command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/minimap2/align/nextflow.config
- name: minimap2 align test_minimap2_align_single_end
command: nextflow run tests/modules/minimap2/align -entry test_minimap2_align_single_end -c tests/config/nextflow.config
tags:
- minimap2
- minimap2/align
files:
- path: ./output/minimap2/test.paf
md5sum: 70e8cf299ee3ecd33e629d10c1f588ce
- path: output/minimap2/test.bam
- path: output/minimap2/versions.yml
- name: minimap2 align paired-end
command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/minimap2/align/nextflow.config
- name: minimap2 align test_minimap2_align_paired_end
command: nextflow run tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c tests/config/nextflow.config
tags:
- minimap2
- minimap2/align
files:
- path: ./output/minimap2/test.paf
md5sum: 5e7b55a26bf0ea3a2843423d3e0b9a28
- path: output/minimap2/test.bam
- path: output/minimap2/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

4
tests/modules/rsem/calculateexpression/test.yml
View file

@ -42,7 +42,7 @@
- path: output/rsem/rsem/genome.transcripts.fa
md5sum: 050c521a2719c2ae48267c1e65218f29
- path: output/rsem/rsem/genomeParameters.txt
md5sum: 2fe3a030e1706c3e8cd4df3818e6dd2f
md5sum: df5a456e3242520cc36e0083a6a7d9dd
- path: output/rsem/rsem/sjdbInfo.txt
md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
- path: output/rsem/rsem/sjdbList.fromGTF.out.tab
@ -63,4 +63,4 @@
- path: output/rsem/test.stat/test.theta
md5sum: de2e4490c98cc5383a86ae8225fd0a28
- path: output/rsem/test.transcript.bam
md5sum: 7846491086c478858419667d60f18edd
md5sum: ed681d39f5700ffc74d6321525330d93

17
tests/modules/samtools/bamtocram/main.nf Normal file
View file

@ -0,0 +1,17 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_BAMTOCRAM } from '../../../../modules/samtools/bamtocram/main.nf'
workflow test_samtools_bamtocram {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], 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)
SAMTOOLS_BAMTOCRAM ( input, fasta, fai )
}

5
tests/modules/samtools/bamtocram/nextflow.config Normal file
View file

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

9
tests/modules/samtools/bamtocram/test.yml Normal file
View file

@ -0,0 +1,9 @@
- name: samtools bamtocram test_samtools_bamtocram
command: nextflow run ./tests/modules/samtools/bamtocram -entry test_samtools_bamtocram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/bamtocram/nextflow.config
tags:
- samtools/bamtocram
- samtools
files:
- path: output/samtools/test.cram
- path: output/samtools/test.cram.crai
- path: output/samtools/versions.yml

13
tests/modules/samtools/collatefastq/main.nf Normal file
View file

@ -0,0 +1,13 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_COLLATEFASTQ } from '../../../../modules/samtools/collatefastq/main.nf'
workflow test_samtools_collatefastq {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
SAMTOOLS_COLLATEFASTQ ( input )
}

5
tests/modules/samtools/collatefastq/nextflow.config Normal file
View file

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

14
tests/modules/samtools/collatefastq/test.yml Normal file
View file

@ -0,0 +1,14 @@
- name: samtools fastq test_samtools_collatefastq
command: nextflow run ./tests/modules/samtools/collatefastq -entry test_samtools_collatefastq -c ./tests/config/nextflow.config -c ./tests/modules/samtools/collatefastq/nextflow.config
tags:
- samtools
- samtools/collatefastq
files:
- path: output/samtools/test_1.fq.gz
md5sum: 829732de4e937edca90f27b07e5b501a
- path: output/samtools/test_2.fq.gz
md5sum: ef27d3809e495620fd93df894280c03a
- path: output/samtools/test_other.fq.gz
md5sum: 709872fc2910431b1e8b7074bfe38c67
- path: output/samtools/test_singleton.fq.gz
md5sum: 709872fc2910431b1e8b7074bfe38c67

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)

29
tests/modules/stranger/main.nf
View file

@ -5,15 +5,26 @@ nextflow.enable.dsl = 2
include { EXPANSIONHUNTER } from '../../../modules/expansionhunter/main.nf'
include { STRANGER } from '../../../modules/stranger/main.nf'
input = [ [ id:'test', gender:'male' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
variant_catalog = file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true)
workflow test_stranger {
input = [ [ id:'test', gender:'male' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
variant_catalog = file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true)
EXPANSIONHUNTER ( input, fasta, variant_catalog )
STRANGER ( EXPANSIONHUNTER.out.vcf )
STRANGER ( EXPANSIONHUNTER.out.vcf, variant_catalog )
}
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, [] )
}

26
tests/modules/stranger/test.yml
View file

@ -8,6 +8,30 @@
- path: output/expansionhunter/versions.yml
md5sum: f3962a6eecfddf9682414c0f605a885a
- path: output/stranger/test.vcf.gz
md5sum: bbe15159195681d5c18596d3ad85c78f
md5sum: 68b0ca1319851134ffa8793a4704dc11
- path: output/stranger/versions.yml
md5sum: 5ec35fd835fb1be50bc3e7c004310fc0
- name: stranger test_stranger_without_optional_variant_catalog
command: nextflow run tests/modules/stranger -entry test_stranger_without_optional_variant_catalog -c tests/config/nextflow.config
tags:
- stranger
files:
- path: output/expansionhunter/test.vcf
md5sum: cfd4a1d35c0e469b99eb6aaa6d22de76
- path: output/expansionhunter/versions.yml
md5sum: c95af9e6d8cd9bd2ce1090ca4e7a6020
- path: output/stranger/test.vcf.gz
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

12
tests/modules/stringtie/merge/main.nf
View file

@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
include { STRINGTIE_MERGE } from '../../../../modules/stringtie/merge/main.nf'
include { STRINGTIE_STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
include { STRINGTIE_MERGE } from '../../../../modules/stringtie/merge/main.nf'
/*
* Test with forward strandedness
@ -15,8 +15,8 @@ workflow test_stringtie_forward_merge {
]
annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE ( input, annotation_gtf )
STRINGTIE
STRINGTIE_STRINGTIE ( input, annotation_gtf )
STRINGTIE_STRINGTIE
.out
.transcript_gtf
.map { it -> it[1] }
@ -35,8 +35,8 @@ workflow test_stringtie_reverse_merge {
]
annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE ( input, annotation_gtf )
STRINGTIE
STRINGTIE_STRINGTIE ( input, annotation_gtf )
STRINGTIE_STRINGTIE
.out
.transcript_gtf
.map { it -> it[1] }

14
tests/modules/stringtie/merge/test.yml
View file

@ -5,7 +5,7 @@
- stringtie/merge
files:
- path: output/stringtie/stringtie.merged.gtf
md5sum: 9fab7049ef2eafdea246fc787d1def40
md5sum: d959eb2fab0db48ded7275e0a2e83c05
- path: output/stringtie/test.ballgown/e2t.ctab
md5sum: 9ae42e056c955a88a883e5e917840d77
- path: output/stringtie/test.ballgown/e_data.ctab
@ -17,11 +17,10 @@
- path: output/stringtie/test.ballgown/t_data.ctab
md5sum: 92a98902784e7406ffe054d2adbabc7c
- path: output/stringtie/test.coverage.gtf
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/stringtie/test.gene.abundance.txt
md5sum: 9708811bcefe0f6384293d6f419f3250
md5sum: 8bcd8e2730ed3337e2730186dbc184f3
- path: output/stringtie/test.transcripts.gtf
md5sum: 0e42709bfe30c2c7f2574ba664f5fa9f
md5sum: a914bd55b68a4b5f607738b17861e362
- name: stringtie merge test_stringtie_reverse_merge
command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config
@ -30,7 +29,7 @@
- stringtie/merge
files:
- path: output/stringtie/stringtie.merged.gtf
md5sum: afc461bb3cbc368f268a7a45c1b54497
md5sum: 6da479298d73d5b3216d4e1576a2bdf4
- path: output/stringtie/test.ballgown/e2t.ctab
md5sum: 9ae42e056c955a88a883e5e917840d77
- path: output/stringtie/test.ballgown/e_data.ctab
@ -42,8 +41,7 @@
- path: output/stringtie/test.ballgown/t_data.ctab
md5sum: 92a98902784e7406ffe054d2adbabc7c
- path: output/stringtie/test.coverage.gtf
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/stringtie/test.gene.abundance.txt
md5sum: 94b85145d60ab1b80a7f0f6cf08418b0
md5sum: f289f41b3ba1b9f0aa05d14408f1a5da
- path: output/stringtie/test.transcripts.gtf
md5sum: 3196e3d50fd461aae6408e0a70acae68
md5sum: 9dcdc9577c0fdbb25089eda210267546

6
tests/modules/stringtie/stringtie/main.nf
View file

@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
include { STRINGTIE_STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
//
// Test with forward strandedness
//
@ -13,7 +13,7 @@ workflow test_stringtie_forward {
]
annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE ( input, annotation_gtf )
STRINGTIE_STRINGTIE ( input, annotation_gtf )
}
//
@ -26,5 +26,5 @@ workflow test_stringtie_reverse {
]
annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE ( input, annotation_gtf )
STRINGTIE_STRINGTIE ( input, annotation_gtf )
}

2
tests/modules/stringtie/stringtie/test.yml
View file

@ -8,7 +8,6 @@
- path: ./output/stringtie/test.gene.abundance.txt
md5sum: 7d8bce7f2a922e367cedccae7267c22e
- path: ./output/stringtie/test.coverage.gtf
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/stringtie/test.ballgown/e_data.ctab
md5sum: 6b4cf69bc03f3f69890f972a0e8b7471
- path: ./output/stringtie/test.ballgown/i_data.ctab
@ -30,7 +29,6 @@
- path: ./output/stringtie/test.gene.abundance.txt
md5sum: 7385b870b955dae2c2ab78a70cf05cce
- path: ./output/stringtie/test.coverage.gtf
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/stringtie/test.ballgown/e_data.ctab
md5sum: 879b6696029d19c4737b562e9d149218
- path: ./output/stringtie/test.ballgown/i_data.ctab

10
tests/modules/tabix/bgzip/main.nf
View file

@ -4,10 +4,18 @@ nextflow.enable.dsl = 2
include { TABIX_BGZIP } from '../../../../modules/tabix/bgzip/main.nf'
workflow test_tabix_bgzip {
workflow test_tabix_bgzip_compress {
input = [ [ id:'test' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
]
TABIX_BGZIP ( input )
}
workflow test_tabix_bgzip_decompress {
input = [ [ id:'test' ], // meta map
[ file(params.test_data['sarscov2']['genome']['test_bed_gz'], checkIfExists: true) ]
]
TABIX_BGZIP ( input )
}

12
tests/modules/tabix/bgzip/test.yml
View file

@ -1,8 +1,16 @@
- name: tabix bgzip
command: nextflow run ./tests/modules/tabix/bgzip -entry test_tabix_bgzip -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgzip/nextflow.config
- name: tabix bgzip compress
command: nextflow run ./tests/modules/tabix/bgzip -entry test_tabix_bgzip_compress -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgzip/nextflow.config
tags:
- tabix
- tabix/bgzip
files:
- path: ./output/tabix/test.vcf.gz
md5sum: fc178eb342a91dc0d1d568601ad8f8e2
- name: tabix bgzip decompress
command: nextflow run ./tests/modules/tabix/bgzip -entry test_tabix_bgzip_decompress -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgzip/nextflow.config
tags:
- tabix
- tabix/bgzip
files:
- path: ./output/tabix/test.bed
md5sum: fe4053cf4de3aebbdfc3be2efb125a74

2
tests/modules/tiddit/sv/test.yml
View file

@ -9,6 +9,7 @@
- path: output/tiddit/test.signals.tab
md5sum: dab4b2fec4ddf8eb1c23005b0770150e
- path: output/tiddit/test.vcf
md5sum: bdce14ae8292bf3deb81f6f255baf859
- name: tiddit sv no ref
command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_no_ref -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
@ -21,3 +22,4 @@
- path: output/tiddit/test.signals.tab
md5sum: dab4b2fec4ddf8eb1c23005b0770150e
- path: output/tiddit/test.vcf
md5sum: 3d0e83a8199b2bdb81cfe3e6b12bf64b