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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 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.
*/
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 "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: \$(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 use 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 use 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 use 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"
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"

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process ELPREP_SPLIT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0':
'quay.io/biocontainers/elprep:5.1.2--he881be0_0' }"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("**.{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}"
meta.single_end ? args += " --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 \\
. \\
$args \\
--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"

21
modules/kraken2/kraken2/main.nf
View file

@ -10,11 +10,14 @@ 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
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:
@ -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

7
modules/picard/collecthsmetrics/main.nf
View file

@ -15,7 +15,7 @@ process PICARD_COLLECTHSMETRICS {
path target_intervals
output:
tuple val(meta), path("*collecthsmetrics.txt"), emit: hs_metrics
tuple val(meta), path("*_metrics") , emit: metrics
path "versions.yml" , emit: versions
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"

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

11
modules/stranger/main.nf
View file

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

9
modules/tabix/bgzip/main.nf
View file

@ -11,7 +11,7 @@ process TABIX_BGZIP {
tuple val(meta), path(input)
output:
tuple val(meta), path("*.gz"), emit: gz
tuple val(meta), path("${prefix}*"), emit: output
path "versions.yml" , emit: versions
when:
@ -19,9 +19,12 @@ process TABIX_BGZIP {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${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

32
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/**
@ -591,6 +603,10 @@ elprep/merge:
- modules/elprep/merge/**
- tests/modules/elprep/merge/**
elprep/split:
- modules/elprep/split/**
- tests/modules/elprep/split/**
emmtyper:
- modules/emmtyper/**
- tests/modules/emmtyper/**
@ -663,6 +679,10 @@ 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/**
@ -671,6 +691,10 @@ 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/**
@ -747,6 +771,10 @@ 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/**
@ -1559,6 +1587,10 @@ samtools/bam2fq:
- modules/samtools/bam2fq/**
- tests/modules/samtools/bam2fq/**
samtools/collatefastq:
- modules/samtools/collatefastq/**
- tests/modules/samtools/collatefastq/**
samtools/depth:
- modules/samtools/depth/**
- tests/modules/samtools/depth/**

18
tests/modules/amplify/predict/main.nf Normal file
View file

@ -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
View file

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

9
tests/modules/amplify/predict/test.yml Normal file
View file

@ -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
View file

@ -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
View file

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

14
tests/modules/antismash/antismashlitedownloaddatabases/test.yml Normal file
View file

@ -0,0 +1,14 @@
- name: antismash antismashlitedownloaddatabases test_antismash_antismashlitedownloaddatabases
command: nextflow run tests/modules/antismash/antismashlitedownloaddatabases -entry test_antismash_antismashlitedownloaddatabases -c tests/config/nextflow.config
tags:
- antismash/antismashlitedownloaddatabases
- antismash
files:
- path: output/antismash/versions.yml
md5sum: e2656c8d2bcc7469eba40eb1ee5c91b3
- 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

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

@ -0,0 +1,22 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BCLCONVERT } from '../../../modules/bclconvert/main.nf'
process STUB_BCLCONVERT_INPUT {
output:
path "SampleSheet.csv" ,emit: samplesheet
path "DDMMYY_SERIAL_FLOWCELL" ,emit: run_dir
stub:
"""
mkdir DDMMYY_SERIAL_FLOWCELL
echo "SampleSheet" > SampleSheet.csv
"""
}
workflow test_bclconvert {
STUB_BCLCONVERT_INPUT ()
BCLCONVERT (STUB_BCLCONVERT_INPUT.out.samplesheet, STUB_BCLCONVERT_INPUT.out.run_dir)
}

5
tests/modules/bclconvert/nextflow.config Normal file
View file

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

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

@ -0,0 +1,52 @@
- name: bclconvert test_bclconvert
command: nextflow run tests/modules/bclconvert -entry test_bclconvert -c tests/config/nextflow.config -stub-run
tags:
- bclconvert
files:
- path: output/bclconvert/InterOp/InterOp.bin
md5sum: d3dea0bb4ab1c8754af324f40b001481
- path: output/bclconvert/Logs/Errors.log
md5sum: 334645f09074b2597a692e395b716a9c
- path: output/bclconvert/Logs/FastqComplete.txt
md5sum: a4c4c6ce2d0de67d3b7ac7d1fcb512e4
- path: output/bclconvert/Logs/Info.log
md5sum: d238822d379f2277cac950ca986cb660
- path: output/bclconvert/Logs/Warnings.log
md5sum: aeefd2d631817e170f88f25ecaaf4664
- path: output/bclconvert/Reports/Adapter_Metrics.csv
md5sum: af62e9c7b44940cfd8ea11064a1f42ae
- path: output/bclconvert/Reports/Demultiplex_Stats.csv
md5sum: d11313931fcaabb5ce159462ad3dd1da
- path: output/bclconvert/Reports/IndexMetricsOut.bin
md5sum: 6bcee11c8145e3b1059ceaa91d2f5be7
- path: output/bclconvert/Reports/Index_Hopping_Counts.csv
md5sum: 697e40e0c0d48b4bd25f138ef60b0bde
- path: output/bclconvert/Reports/Quality_Metrics.csv
md5sum: 3902fd38f6b01f1ce0f0e8724238f8f2
- path: output/bclconvert/Reports/RunInfo.xml
md5sum: 5bef7c7e76360231b0c4afdfc915fd44
- path: output/bclconvert/Reports/SampleSheet.csv
md5sum: c579e7d2c9c917c4cfb875a0373c0936
- path: output/bclconvert/Reports/Top_Unknown_Barcodes.csv
md5sum: 39a5e7f6d21c12d6051afdc8261b6330
- path: output/bclconvert/Reports/fastq_list.csv
md5sum: 32c51ab10e013fd547928de57361ffcb
- path: output/bclconvert/sample1_S1_L001_R1_001.fastq.gz
md5sum: 9b831a39755935333f86f167527a094d
- path: output/bclconvert/sample1_S1_L001_R2_001.fastq.gz
md5sum: 082f4f767b7619f409ca7e752ef482bf
- path: output/bclconvert/sample1_S1_L002_R1_001.fastq.gz
md5sum: 837764c89db93dfb53cd663c4f26f3d7
- path: output/bclconvert/sample1_S1_L002_R2_001.fastq.gz
md5sum: 1a42cf6ba0bb8fc7770f278e6d1ab676
- path: output/bclconvert/sample2_S2_L001_R1_001.fastq.gz
md5sum: 475bc426b7cc48d0551d40e31457dc78
- path: output/bclconvert/sample2_S2_L001_R2_001.fastq.gz
md5sum: f670ccd7d9352e0e67fe1c1232429d94
- path: output/bclconvert/sample2_S2_L002_R1_001.fastq.gz
md5sum: ebd5ff6fa5603e7d704b5a10598de58c
- path: output/bclconvert/sample2_S2_L002_R2_001.fastq.gz
md5sum: 2f83b460f52620d2548c7ef8845b31d7
- path: output/stub/SampleSheet.csv
md5sum: c579e7d2c9c917c4cfb875a0373c0936
- path: output/bclconvert/versions.yml

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

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

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

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

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

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

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

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

2
tests/modules/picard/collecthsmetrics/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

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

3
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, [] )

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

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

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

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

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