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64
.github/ISSUE_TEMPLATE/bug_report.md vendored
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@ -1,64 +0,0 @@
---
name: Bug report
about: Report something that is broken or incorrect
title: "[BUG]"
---
<!--
# nf-core/module bug report
Hi there!
Thanks for telling us about a problem with the modules.
Please delete this text and anything that's not relevant from the template below:
-->
## Check Documentation
I have checked the following places for your error:
- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
- [ ] [nf-core/module documentation](https://github.com/nf-core/modules/blob/master/README.md)
## Description of the bug
<!-- A clear and concise description of what the bug is. -->
## Steps to reproduce
Steps to reproduce the behaviour:
1. Command line: <!-- [e.g. `nextflow run ...`] -->
2. See error: <!-- [Please provide your error message] -->
## Expected behaviour
<!-- A clear and concise description of what you expected to happen. -->
## Log files
Have you provided the following extra information/files:
- [ ] The command used to run the module
- [ ] The `.nextflow.log` file <!-- this is a hidden file in the directory where you launched the module -->
## System
- Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
- Executor: <!-- [e.g. slurm, local, awsbatch...] -->
- OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->
- Version <!-- [e.g. 7, 10.13.6, 18.3...] -->
## Nextflow Installation
- Version: <!-- [e.g. 19.10.0] -->
## Container engine
- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
- version: <!-- [e.g. 1.0.0] -->
- Image tag: <!-- [e.g. nfcore/module:2.6] -->
## Additional context
<!-- Add any other context about the problem here. -->

52
.github/ISSUE_TEMPLATE/bug_report.yml vendored Normal file
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@ -0,0 +1,52 @@
name: Bug report
description: Report something that is broken or incorrect
labels: bug
body:
- type: checkboxes
attributes:
label: Have you checked the docs?
description: I have checked the following places for my error
options:
- label: "[nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)"
required: true
- label: "[nf-core modules documentation](https://nf-co.re/docs/contributing/modules)"
required: true
- type: textarea
id: description
attributes:
label: Description of the bug
description: A clear and concise description of what the bug is.
validations:
required: true
- type: textarea
id: command_used
attributes:
label: Command used and terminal output
description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
render: console
placeholder: |
$ nextflow run ...
Some output where something broke
- type: textarea
id: files
attributes:
label: Relevant files
description: |
Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
- type: textarea
id: system
attributes:
label: System information
description: |
* Nextflow version _(eg. 21.10.3)_
* Hardware _(eg. HPC, Desktop, Cloud)_
* Executor _(eg. slurm, local, awsbatch)_
* Container engine and version: _(e.g. Docker 1.0.0, Singularity, Conda, Podman, Shifter or Charliecloud)_
* OS and version: _(eg. CentOS Linux, macOS, Ubuntu 22.04)_
* Image tag: <!-- [e.g. nfcore/cellranger:2.6] -->

32
.github/ISSUE_TEMPLATE/feature_request.md vendored
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@ -1,32 +0,0 @@
---
name: Feature request
about: Suggest an idea for nf-core/modules
title: "[FEATURE]"
---
<!--
# nf-core/modules feature request
Hi there!
Thanks for suggesting a new feature for the modules!
Please delete this text and anything that's not relevant from the template below:
-->
## Is your feature request related to a problem? Please describe
<!-- A clear and concise description of what the problem is. -->
<!-- e.g. [I'm always frustrated when ...] -->
## Describe the solution you'd like
<!-- A clear and concise description of what you want to happen. -->
## Describe alternatives you've considered
<!-- A clear and concise description of any alternative solutions or features you've considered. -->
## Additional context
<!-- Add any other context about the feature request here. -->

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.github/ISSUE_TEMPLATE/feature_request.yml vendored Normal file
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@ -0,0 +1,32 @@
name: Feature request
description: Suggest an idea for nf-core/modules
labels: feature
title: "[FEATURE]"
body:
- type: textarea
id: description
attributes:
label: Is your feature request related to a problem? Please describe
description: A clear and concise description of what the bug is.
placeholder: |
<!-- e.g. [I'm always frustrated when ...] -->
validations:
required: true
- type: textarea
id: solution
attributes:
label: Describe the solution you'd like
description: A clear and concise description of the solution you want to happen.
- type: textarea
id: alternatives
attributes:
label: Describe alternatives you've considered
description: A clear and concise description of any alternative solutions or features you've considered.
- type: textarea
id: additional_context
attributes:
label: Additional context
description: Add any other context about the feature request here.

26
.github/ISSUE_TEMPLATE/new_module.md vendored
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@ -1,26 +0,0 @@
---
name: New module
about: Suggest a new module for nf-core/modules
title: "new module: TOOL/SUBTOOL"
label: new module
---
<!--
# nf-core/modules new module suggestion
Hi there!
Thanks for suggesting a new module for the modules!
Please delete this text and anything that's not relevant from the template below:
Replace TOOL with the bioconda name for the tool in the following text, so that the link is functional.
Replace TOOL/SUBTOOL in the issue title so that it's understandable.
-->
I think it would be good to have a module for [TOOL](https://bioconda.github.io/recipes/TOOL/README.html)
- [ ] This module does not exist yet with the [`nf-core modules list`](https://github.com/nf-core/tools#list-modules) command
- [ ] There is no [open pull request](https://github.com/nf-core/modules/pulls) for this module
- [ ] There is no [open issue](https://github.com/nf-core/modules/issues) for this module
- [ ] If I'm planning to work on this module, I added myself to the `Assignees` to facilitate tracking who is working on the module

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@ -0,0 +1,36 @@
name: New module
description: Suggest a new module for nf-core/modules
title: "new module: TOOL/SUBTOOL"
labels: new module
body:
- type: checkboxes
attributes:
label: Is there an existing module for this?
description: This module does not exist yet with the [`nf-core modules list`](https://github.com/nf-core/tools#list-modules) command
options:
- label: I have searched for the existing module
required: true
- type: checkboxes
attributes:
label: Is there an open PR for this?
description: There is no [open pull request](https://github.com/nf-core/modules/pulls) for this module
options:
- label: I have searched for existing PRs
required: true
- type: checkboxes
attributes:
label: Is there an open issue for this?
description: There is no [open issue](https://github.com/nf-core/modules/issues) for this module
options:
- label: I have searched for existing issues
required: true
- type: checkboxes
attributes:
label: Are you going to work on this?
description: If I'm planning to work on this module, I added myself to the `Assignees` to facilitate tracking who is working on the module
options:
- label: If I'm planning to work on this module, I added myself to the `Assignees` to facilitate tracking who is working on the module
required: false

12
modules/antismash/antismashlitedownloaddatabases/main.nf
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@ -27,9 +27,7 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
output:
path("antismash_db") , emit: database
path("css"), emit: css_dir
path("detection"), emit: detection_dir
path("modules"), emit: modules_dir
path("antismash_dir"), emit: antismash_dir
path "versions.yml", emit: versions
when:
@ -37,11 +35,19 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
script:
def args = task.ext.args ?: ''
conda = params.enable_conda
"""
download-antismash-databases \\
--database-dir antismash_db \\
$args
if [[ $conda = false ]]; \
then \
cp -r /usr/local/lib/python3.8/site-packages/antismash antismash_dir; \
else \
cp -r \$(python -c 'import antismash;print(antismash.__file__.split("/__")[0])') antismash_dir; \
fi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
antismash-lite: \$(antismash --version | sed 's/antiSMASH //')

16
modules/antismash/antismashlitedownloaddatabases/meta.yml
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@ -50,21 +50,11 @@ output:
type: directory
description: Download directory for antiSMASH databases
pattern: "antismash_db"
- css_dir:
- antismash_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"
antismash installation folder which is being modified during the antiSMASH database downloading step. The modified 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 and installation folder in pipelines.
pattern: "antismash_dir"
authors:
- "@jasmezz"

16
modules/bamtools/split/main.nf
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@ -2,10 +2,10 @@ process BAMTOOLS_SPLIT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hd03093a_0' :
'quay.io/biocontainers/bamtools:2.5.2--hd03093a_0' }"
input:
tuple val(meta), path(bam)
@ -20,11 +20,15 @@ process BAMTOOLS_SPLIT {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def input_list = bam.collect{"-in $it"}.join(' ')
"""
bamtools \\
split \\
-in $bam \\
$args
merge \\
$input_list \\
| bamtools \\
split \\
-stub $prefix \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":

3
modules/bamtools/split/meta.yml
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@ -23,7 +23,7 @@ input:
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: A BAM file to split
description: A list of one or more BAM files to merge and then split
pattern: "*.bam"
output:
@ -43,3 +43,4 @@ output:
authors:
- "@sguizard"
- "@matthdsm"

40
modules/diamond/blastp/main.nf
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@ -2,20 +2,26 @@ process DIAMOND_BLASTP {
tag "$meta.id"
label 'process_medium'
// Dimaond is limited to v2.0.9 because there is not a
// singularity version higher than this at the current time.
conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null)
conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' :
'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }"
'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
input:
tuple val(meta), path(fasta)
path db
path db
val out_ext
val blast_columns
output:
tuple val(meta), path('*.txt'), emit: txt
path "versions.yml" , emit: versions
tuple val(meta), path('*.blast'), optional: true, emit: blast
tuple val(meta), path('*.xml') , optional: true, emit: xml
tuple val(meta), path('*.txt') , optional: true, emit: txt
tuple val(meta), path('*.daa') , optional: true, emit: daa
tuple val(meta), path('*.sam') , optional: true, emit: sam
tuple val(meta), path('*.tsv') , optional: true, emit: tsv
tuple val(meta), path('*.paf') , optional: true, emit: paf
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
@ -23,6 +29,21 @@ process DIAMOND_BLASTP {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def columns = blast_columns ? "${blast_columns}" : ''
switch ( out_ext ) {
case "blast": outfmt = 0; break
case "xml": outfmt = 5; break
case "txt": outfmt = 6; break
case "daa": outfmt = 100; break
case "sam": outfmt = 101; break
case "tsv": outfmt = 102; break
case "paf": outfmt = 103; break
default:
outfmt = '6';
out_ext = 'txt';
log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)");
break
}
"""
DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
@ -31,8 +52,9 @@ process DIAMOND_BLASTP {
--threads $task.cpus \\
--db \$DB \\
--query $fasta \\
--outfmt ${outfmt} ${columns} \\
$args \\
--out ${prefix}.txt
--out ${prefix}.${out_ext}
cat <<-END_VERSIONS > versions.yml
"${task.process}":

43
modules/diamond/blastp/meta.yml
View file

@ -28,12 +28,50 @@ input:
type: directory
description: Directory containing the protein blast database
pattern: "*"
- out_ext:
type: string
description: |
Specify the type of output file to be generated. `blast` corresponds to
BLAST pairwise format. `xml` corresponds to BLAST xml format.
`txt` corresponds to to BLAST tabular format. `tsv` corresponds to
taxonomic classification format.
pattern: "blast|xml|txt|daa|sam|tsv|paf"
- blast_columns:
type: string
description: |
Optional space separated list of DIAMOND tabular BLAST output keywords
used for in conjunction with the 'txt' out_ext option (--outfmt 6). See
DIAMOND documnetation for more information.
output:
- txt:
- blast:
type: file
description: File containing blastp hits
pattern: "*.{blastp.txt}"
pattern: "*.{blast}"
- xml:
type: file
description: File containing blastp hits
pattern: "*.{xml}"
- txt:
type: file
description: File containing hits in tabular BLAST format.
pattern: "*.{txt}"
- daa:
type: file
description: File containing hits DAA format
pattern: "*.{daa}"
- sam:
type: file
description: File containing aligned reads in SAM format
pattern: "*.{sam}"
- tsv:
type: file
description: Tab separated file containing taxonomic classification of hits
pattern: "*.{tsv}"
- paf:
type: file
description: File containing aligned reads in pairwise mapping format format
pattern: "*.{paf}"
- versions:
type: file
description: File containing software versions
@ -41,3 +79,4 @@ output:
authors:
- "@spficklin"
- "@jfy133"

40
modules/diamond/blastx/main.nf
View file

@ -2,20 +2,26 @@ process DIAMOND_BLASTX {
tag "$meta.id"
label 'process_medium'
// Dimaond is limited to v2.0.9 because there is not a
// singularity version higher than this at the current time.
conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null)
conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' :
'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }"
'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
input:
tuple val(meta), path(fasta)
path db
path db
val out_ext
val blast_columns
output:
tuple val(meta), path('*.txt'), emit: txt
path "versions.yml" , emit: versions
tuple val(meta), path('*.blast'), optional: true, emit: blast
tuple val(meta), path('*.xml') , optional: true, emit: xml
tuple val(meta), path('*.txt') , optional: true, emit: txt
tuple val(meta), path('*.daa') , optional: true, emit: daa
tuple val(meta), path('*.sam') , optional: true, emit: sam
tuple val(meta), path('*.tsv') , optional: true, emit: tsv
tuple val(meta), path('*.paf') , optional: true, emit: paf
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
@ -23,6 +29,21 @@ process DIAMOND_BLASTX {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def columns = blast_columns ? "${blast_columns}" : ''
switch ( out_ext ) {
case "blast": outfmt = 0; break
case "xml": outfmt = 5; break
case "txt": outfmt = 6; break
case "daa": outfmt = 100; break
case "sam": outfmt = 101; break
case "tsv": outfmt = 102; break
case "paf": outfmt = 103; break
default:
outfmt = '6';
out_ext = 'txt';
log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)");
break
}
"""
DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
@ -31,8 +52,9 @@ process DIAMOND_BLASTX {
--threads $task.cpus \\
--db \$DB \\
--query $fasta \\
--outfmt ${outfmt} ${columns} \\
$args \\
--out ${prefix}.txt
--out ${prefix}.${out_ext}
cat <<-END_VERSIONS > versions.yml
"${task.process}":

37
modules/diamond/blastx/meta.yml
View file

@ -28,12 +28,44 @@ input:
type: directory
description: Directory containing the nucelotide blast database
pattern: "*"
- out_ext:
type: string
description: |
Specify the type of output file to be generated. `blast` corresponds to
BLAST pairwise format. `xml` corresponds to BLAST xml format.
`txt` corresponds to to BLAST tabular format. `tsv` corresponds to
taxonomic classification format.
pattern: "blast|xml|txt|daa|sam|tsv|paf"
output:
- blast:
type: file
description: File containing blastp hits
pattern: "*.{blast}"
- xml:
type: file
description: File containing blastp hits
pattern: "*.{xml}"
- txt:
type: file
description: File containing blastx hits
pattern: "*.{blastx.txt}"
description: File containing hits in tabular BLAST format.
pattern: "*.{txt}"
- daa:
type: file
description: File containing hits DAA format
pattern: "*.{daa}"
- sam:
type: file
description: File containing aligned reads in SAM format
pattern: "*.{sam}"
- tsv:
type: file
description: Tab separated file containing taxonomic classification of hits
pattern: "*.{tsv}"
- paf:
type: file
description: File containing aligned reads in pairwise mapping format format
pattern: "*.{paf}"
- versions:
type: file
description: File containing software versions
@ -41,3 +73,4 @@ output:
authors:
- "@spficklin"
- "@jfy133"

8
modules/diamond/makedb/main.nf
View file

@ -2,12 +2,10 @@ process DIAMOND_MAKEDB {
tag "$fasta"
label 'process_medium'
// Dimaond is limited to v2.0.9 because there is not a
// singularity version higher than this at the current time.
conda (params.enable_conda ? 'bioconda::diamond=2.0.9' : null)
conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' :
'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }"
'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
input:
path fasta

43
modules/elprep/merge/main.nf Normal file
View file

@ -0,0 +1,43 @@
process ELPREP_MERGE {
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 suffix = args.contains("--output-type sam") ? "sam" : "bam"
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 ${bam} input/
elprep merge \\
input/ \\
output/${prefix}.${suffix} \\
$args \\
${single_end} \\
--nr-of-threads $task.cpus
cat <<-END_VERSIONS > versions.yml
"${task.process}":
elprep: \$(elprep 2>&1 | head -n2 | tail -n1 |sed 's/^.*version //;s/ compiled.*\$//')
END_VERSIONS
"""
}

44
modules/elprep/merge/meta.yml Normal file
View file

@ -0,0 +1,44 @@
name: "elprep_merge"
description: Merge split bam/sam chunks in one file
keywords:
- bam
- sam
- merge
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: List of BAM/SAM chunks to merge
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: Merged BAM/SAM file
pattern: "*.{bam,sam}"
authors:
- "@matthdsm"

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

@ -12,7 +12,7 @@ process GATK4_MARKDUPLICATES {
output:
tuple val(meta), path("*.bam") , emit: bam
tuple val(meta), path("*.bai") , emit: bai
tuple val(meta), path("*.bai") , optional:true, emit: bai
tuple val(meta), path("*.metrics"), emit: metrics
path "versions.yml" , emit: versions

4
modules/minimap2/align/main.nf
View file

@ -27,8 +27,8 @@ process MINIMAP2_ALIGN {
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" : ''
def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
"""
minimap2 \\
$args \\

18
modules/picard/addorreplacereadgroups/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_ADDORREPLACEREADGROUPS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
@ -38,12 +38,12 @@ process PICARD_ADDORREPLACEREADGROUPS {
-Xmx${avail_mem}g \\
--INPUT ${bam} \\
--OUTPUT ${prefix}.bam \\
-ID ${ID} \\
-LB ${LIBRARY} \\
-PL ${PLATFORM} \\
-PU ${BARCODE} \\
-SM ${SAMPLE} \\
-CREATE_INDEX true
--RGID ${ID} \\
--RGLB ${LIBRARY} \\
--RGPL ${PLATFORM} \\
--RGPU ${BARCODE} \\
--RGSM ${SAMPLE} \\
--CREATE_INDEX true
cat <<-END_VERSIONS > versions.yml
"${task.process}":

10
modules/picard/cleansam/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_CLEANSAM {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
@ -31,8 +31,8 @@ process PICARD_CLEANSAM {
-Xmx${avail_mem}g \\
CleanSam \\
${args} \\
-I ${bam} \\
-O ${prefix}.bam
--INPUT ${bam} \\
--OUTPUT ${prefix}.bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":

14
modules/picard/collecthsmetrics/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
@ -38,10 +38,10 @@ process PICARD_COLLECTHSMETRICS {
CollectHsMetrics \\
$args \\
$reference \\
-BAIT_INTERVALS $bait_intervals \\
-TARGET_INTERVALS $target_intervals \\
-INPUT $bam \\
-OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics
--BAIT_INTERVALS $bait_intervals \\
--TARGET_INTERVALS $target_intervals \\
--INPUT $bam \\
--OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics
cat <<-END_VERSIONS > versions.yml

12
modules/picard/collectmultiplemetrics/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
@ -33,9 +33,9 @@ process PICARD_COLLECTMULTIPLEMETRICS {
-Xmx${avail_mem}g \\
CollectMultipleMetrics \\
$args \\
INPUT=$bam \\
OUTPUT=${prefix}.CollectMultipleMetrics \\
REFERENCE_SEQUENCE=$fasta
--INPUT $bam \\
--OUTPUT ${prefix}.CollectMultipleMetrics \\
--REFERENCE_SEQUENCE $fasta
cat <<-END_VERSIONS > versions.yml
"${task.process}":

15
modules/picard/collectwgsmetrics/main.nf
View file

@ -2,13 +2,13 @@ process PICARD_COLLECTWGSMETRICS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam), path(bai)
tuple val(meta), path(bam)
path fasta
output:
@ -32,9 +32,10 @@ process PICARD_COLLECTWGSMETRICS {
-Xmx${avail_mem}g \\
CollectWgsMetrics \\
$args \\
INPUT=$bam \\
OUTPUT=${prefix}.CollectWgsMetrics.coverage_metrics \\
REFERENCE_SEQUENCE=$fasta
--INPUT $bam \\
--OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
--REFERENCE_SEQUENCE $fasta
cat <<-END_VERSIONS > versions.yml
"${task.process}":

10
modules/picard/createsequencedictionary/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_CREATESEQUENCEDICTIONARY {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input:
tuple val(meta), path(fasta)
@ -31,8 +31,8 @@ process PICARD_CREATESEQUENCEDICTIONARY {
-Xmx${avail_mem}g \\
CreateSequenceDictionary \\
$args \\
R=$fasta \\
O=${prefix}.dict
--REFERENCE $fasta \\
--OUTPUT ${prefix}.dict
cat <<-END_VERSIONS > versions.yml
"${task.process}":

6
modules/picard/crosscheckfingerprints/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_CROSSCHECKFINGERPRINTS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input:
tuple val(meta), path(input1)

6
modules/picard/filtersamreads/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam), path(readlist)

10
modules/picard/fixmateinformation/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_FIXMATEINFORMATION {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
@ -31,8 +31,8 @@ process PICARD_FIXMATEINFORMATION {
picard \\
FixMateInformation \\
-Xmx${avail_mem}g \\
-I ${bam} \\
-O ${prefix}.bam \\
--INPUT ${bam} \\
--OUTPUT ${prefix}.bam \\
--VALIDATION_STRINGENCY ${STRINGENCY}
cat <<-END_VERSIONS > versions.yml

16
modules/picard/liftovervcf/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_LIFTOVERVCF {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input:
tuple val(meta), path(input_vcf)
@ -35,11 +35,11 @@ process PICARD_LIFTOVERVCF {
-Xmx${avail_mem}g \\
LiftoverVcf \\
$args \\
I=$input_vcf \\
O=${prefix}.lifted.vcf.gz \\
CHAIN=$chain \\
REJECT=${prefix}.unlifted.vcf.gz \\
R=$fasta
--INPUT $input_vcf \\
--OUTPUT ${prefix}.lifted.vcf.gz \\
--CHAIN $chain \\
--REJECT ${prefix}.unlifted.vcf.gz \\
--REFERENCE_SEQUENCE $fasta
cat <<-END_VERSIONS > versions.yml
"${task.process}":

12
modules/picard/markduplicates/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
@ -33,9 +33,9 @@ process PICARD_MARKDUPLICATES {
-Xmx${avail_mem}g \\
MarkDuplicates \\
$args \\
I=$bam \\
O=${prefix}.bam \\
M=${prefix}.MarkDuplicates.metrics.txt
--INPUT $bam \\
--OUTPUT ${prefix}.bam \\
--METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":

10
modules/picard/mergesamfiles/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input:
tuple val(meta), path(bams)
@ -33,8 +33,8 @@ process PICARD_MERGESAMFILES {
-Xmx${avail_mem}g \\
MergeSamFiles \\
$args \\
${'INPUT='+bam_files.join(' INPUT=')} \\
OUTPUT=${prefix}.bam
${'--INPUT '+bam_files.join(' --INPUT ')} \\
--OUTPUT ${prefix}.bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
picard: \$( echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)

6
modules/picard/sortsam/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_SORTSAM {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam)

10
modules/picard/sortvcf/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_SORTVCF {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input:
tuple val(meta), path(vcf)
@ -22,8 +22,8 @@ process PICARD_SORTVCF {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def seq_dict = sequence_dict ? "-SEQUENCE_DICTIONARY $sequence_dict" : ""
def reference = reference ? "-REFERENCE_SEQUENCE $reference" : ""
def seq_dict = sequence_dict ? "--SEQUENCE_DICTIONARY $sequence_dict" : ""
def reference = reference ? "--REFERENCE_SEQUENCE $reference" : ""
def avail_mem = 3
if (!task.memory) {
log.info '[Picard SortVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'

41
subworkflows/nf-core/bam_qc_picard/main.nf Normal file
View file

@ -0,0 +1,41 @@
//
// Run QC steps on BAM/CRAM files using Picard
//
include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/picard/collectmultiplemetrics/main'
include { PICARD_COLLECTWGSMETRICS } from '../../../modules/picard/collectwgsmetrics/main'
include { PICARD_COLLECTHSMETRICS } from '../../../modules/picard/collecthsmetrics/main'
workflow BAM_QC_PICARD {
take:
ch_bam // channel: [ val(meta), [ bam ]]
ch_fasta // channel: [ fasta ]
ch_fasta_fai // channel: [ fasta_fai ]
ch_bait_interval // channel: [ bait_interval ]
ch_target_interval // channel: [ target_interval ]
main:
ch_versions = Channel.empty()
ch_coverage_metrics = Channel.empty()
PICARD_COLLECTMULTIPLEMETRICS( ch_bam, ch_fasta )
ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
if (ch_bait_interval || ch_target_interval) {
if (!ch_bait_interval) log.error("Bait interval channel is empty")
if (!ch_target_interval) log.error("Target interval channel is empty")
PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, ch_fasta_fai, ch_bait_interval, ch_target_interval )
ch_coverage_metrics = ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.metrics)
ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
} else {
PICARD_COLLECTWGSMETRICS( ch_bam, ch_fasta )
ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions.first())
ch_coverage_metrics = ch_coverage_metrics.mix(PICARD_COLLECTWGSMETRICS.out.metrics)
}
emit:
coverage_metrics = ch_coverage_metrics // channel: [ val(meta), [ coverage_metrics ] ]
multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), [ multiple_metrics ] ]
versions = ch_versions // channel: [ versions.yml ]
}

60
subworkflows/nf-core/bam_qc_picard/meta.yml Normal file
View file

@ -0,0 +1,60 @@
name: bam_qc
description: Produces comprehensive statistics from BAM file
keywords:
- statistics
- counts
- hs_metrics
- wgs_metrics
- bam
- sam
- cram
modules:
- picard/collectmultiplemetrics
- picard/collectwgsmetrics
- picard/collecthsmetrics
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- fasta:
type: optional file
description: Reference fasta file
pattern: "*.{fasta,fa}"
- fasta_fai:
type: optional file
description: Reference fasta file index
pattern: "*.{fasta,fa}.fai"
- bait_intervals:
type: optional file
description: An interval list file that contains the locations of the baits used.
pattern: "baits.interval_list"
- target_intervals:
type: optional file
description: An interval list file that contains the locations of the targets.
pattern: "targets.interval_list"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- coverage_metrics:
type: file
description: Alignment metrics files generated by picard CollectHsMetrics or CollectWgsMetrics
pattern: "*_metrics.txt"
- multiple_metrics:
type: file
description: Alignment metrics files generated by picard CollectMultipleMetrics
pattern: "*_{metrics}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@matthdsm"

4
tests/config/pytest_modules.yml
View file

@ -603,6 +603,10 @@ elprep/filter:
- modules/elprep/filter/**
- tests/modules/elprep/filter/**
elprep/merge:
- modules/elprep/merge/**
- tests/modules/elprep/merge/**
elprep/split:
- modules/elprep/split/**
- tests/modules/elprep/split/**

1
tests/config/test_data.config
View file

@ -14,6 +14,7 @@ params {
genome_paf = "${test_data_dir}/genomics/sarscov2/genome/genome.paf"
genome_sizes = "${test_data_dir}/genomics/sarscov2/genome/genome.sizes"
transcriptome_fasta = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.fasta"
proteome_fasta = "${test_data_dir}/genomics/sarscov2/genome/proteome.fasta"
transcriptome_paf = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.paf"
test_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed"

7
tests/modules/antismash/antismashlitedownloaddatabases/test.yml
View file

@ -1,8 +1,8 @@
- 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
- antismash
files:
- path: output/antismash/versions.yml
md5sum: 24859c67023abab99de295d3675a24b6
@ -12,6 +12,5 @@
- 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
- path: output/antismash/antismash_dir
- path: output/antismash/antismash_dir/detection/hmm_detection/data/bgc_seeds.hmm

24
tests/modules/bamtools/split/main.nf
View file

@ -2,13 +2,29 @@
nextflow.enable.dsl = 2
include { BAMTOOLS_SPLIT } from '../../../../modules/bamtools/split/main.nf'
include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_SINGLE } from '../../../../modules/bamtools/split/main.nf'
include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_MULTIPLE } from '../../../../modules/bamtools/split/main.nf'
workflow test_bamtools_split {
workflow test_bamtools_split_single_input {
input = [
[ id:'test', single_end:false ], // 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'], checkIfExists: true)
]
BAMTOOLS_SPLIT ( input )
BAMTOOLS_SPLIT_SINGLE ( input )
}
workflow test_bamtools_split_multiple {
input = [
[ id:'test', single_end:false ], // meta map
[
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
]
]
BAMTOOLS_SPLIT_MULTIPLE ( input )
}

23
tests/modules/bamtools/split/test.yml
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@ -1,10 +1,23 @@
- name: bamtools split test_bamtools_split
command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
- name: bamtools split test_bamtools_split_single_input
command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split_single_input -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
tags:
- bamtools/split
- bamtools
- bamtools/split
files:
- path: output/bamtools/test.paired_end.sorted.REF_chr22.bam
- path: output/bamtools/test.REF_chr22.bam
md5sum: b7dc50e0edf9c6bfc2e3b0e6d074dc07
- path: output/bamtools/test.paired_end.sorted.REF_unmapped.bam
- path: output/bamtools/test.REF_unmapped.bam
md5sum: e0754bf72c51543b2d745d96537035fb
- path: output/bamtools/versions.yml
- name: bamtools split test_bamtools_split_multiple
command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split_multiple -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
tags:
- bamtools
- bamtools/split
files:
- path: output/bamtools/test.REF_chr22.bam
md5sum: 585675bea34c48ebe9db06a561d4b4fa
- path: output/bamtools/test.REF_unmapped.bam
md5sum: 16ad644c87b9471f3026bc87c98b4963
- path: output/bamtools/versions.yml

19
tests/modules/diamond/blastp/main.nf
View file

@ -7,9 +7,22 @@ include { DIAMOND_BLASTP } from '../../../../modules/diamond/blastp/main.nf'
workflow test_diamond_blastp {
db = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
out_ext = 'txt'
blast_columns = 'qseqid qlen'
DIAMOND_MAKEDB ( db )
DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db )
DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
}
workflow test_diamond_blastp_daa {
db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
out_ext = 'daa'
blast_columns = []
DIAMOND_MAKEDB ( db )
DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
}

19
tests/modules/diamond/blastp/test.yml
View file

@ -1,8 +1,17 @@
- name: diamond blastp
command: nextflow run ./tests/modules/diamond/blastp -entry test_diamond_blastp -c ./tests/config/nextflow.config -c ./tests/modules/diamond/blastp/nextflow.config
- name: diamond blastp test_diamond_blastp
command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp -c tests/config/nextflow.config
tags:
- diamond
- diamond/blastp
- diamond
files:
- path: ./output/diamond/test.diamond_blastp.txt
md5sum: 3ca7f6290c1d8741c573370e6f8b4db0
- path: output/diamond/test.diamond_blastp.txt
- path: output/diamond/versions.yml
- name: diamond blastp test_diamond_blastp_daa
command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp_daa -c tests/config/nextflow.config
tags:
- diamond/blastp
- diamond
files:
- path: output/diamond/test.diamond_blastp.daa
- path: output/diamond/versions.yml

17
tests/modules/diamond/blastx/main.nf
View file

@ -7,9 +7,22 @@ include { DIAMOND_BLASTX } from '../../../../modules/diamond/blastx/main.nf'
workflow test_diamond_blastx {
db = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
out_ext = 'tfdfdt' // Nonsense file extension to check default case.
blast_columns = 'qseqid qlen'
DIAMOND_MAKEDB ( db )
DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db )
DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
}
workflow test_diamond_blastx_daa {
db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
out_ext = 'daa'
blast_columns = []
DIAMOND_MAKEDB ( db )
DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
}

18
tests/modules/diamond/blastx/test.yml
View file

@ -1,8 +1,18 @@
- name: diamond blastx
command: nextflow run ./tests/modules/diamond/blastx -entry test_diamond_blastx -c ./tests/config/nextflow.config -c ./tests/modules/diamond/blastx/nextflow.config
- name: diamond blastx test_diamond_blastx
command: nextflow run tests/modules/diamond/blastx -entry test_diamond_blastx -c tests/config/nextflow.config
tags:
- diamond
- diamond/blastx
files:
- path: ./output/diamond/test.diamond_blastx.txt
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/diamond/test.diamond_blastx.txt
- path: output/diamond/versions.yml
- name: diamond blastx test_diamond_blastx_daa
command: nextflow run tests/modules/diamond/blastx -entry test_diamond_blastx_daa -c tests/config/nextflow.config
tags:
- diamond
- diamond/blastx
files:
- path: output/diamond/test.diamond_blastx.daa
md5sum: 0df4a833408416f32981415873facc11
- path: output/diamond/versions.yml

2
tests/modules/diamond/makedb/main.nf
View file

@ -6,7 +6,7 @@ include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf'
workflow test_diamond_makedb {
input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
input = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
DIAMOND_MAKEDB ( input )
}

9
tests/modules/diamond/makedb/test.yml
View file

@ -1,8 +1,9 @@
- name: diamond makedb test_diamond_makedb
command: nextflow run ./tests/modules/diamond/makedb -entry test_diamond_makedb -c ./tests/config/nextflow.config -c ./tests/modules/diamond/makedb/nextflow.config
command: nextflow run tests/modules/diamond/makedb -entry test_diamond_makedb -c tests/config/nextflow.config
tags:
- diamond
- diamond/makedb
- diamond
files:
- path: output/diamond/genome.fasta.dmnd
md5sum: 2447fb376394c20d43ea3aad2aa5d15d
- path: output/diamond/proteome.fasta.dmnd
md5sum: fc28c50b202dd7a7c5451cddff2ba1f4
- path: output/diamond/versions.yml

17
tests/modules/elprep/merge/main.nf Normal file
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@ -0,0 +1,17 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { ELPREP_SPLIT } from '../../../../modules/elprep/split/main.nf'
include { ELPREP_MERGE } from '../../../../modules/elprep/merge/main.nf'
workflow test_elprep_merge {
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 )
ELPREP_MERGE ( ELPREP_SPLIT.out.bam )
}

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

8
tests/modules/elprep/merge/test.yml Normal file
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@ -0,0 +1,8 @@
- name: elprep merge test_elprep_merge
command: nextflow run tests/modules/elprep/merge -entry test_elprep_merge -c tests/config/nextflow.config
tags:
- elprep
- elprep/merge
files:
- path: output/elprep/output/test.bam
- path: output/elprep/versions.yml

1
tests/modules/picard/addorreplacereadgroups/test.yml
View file

@ -7,4 +7,3 @@
- path: output/picard/test.bam
md5sum: 7b82f3461c2d80fc6a10385e78c9427f
- path: output/picard/versions.yml
md5sum: 8a2d176295e1343146ea433c79bb517f

1
tests/modules/picard/cleansam/test.yml
View file

@ -7,4 +7,3 @@
- path: output/picard/test.bam
md5sum: a48f8e77a1480445efc57570c3a38a68
- path: output/picard/versions.yml
md5sum: e6457d7c6de51bf6f4b577eda65e57ac

3
tests/modules/picard/collectwgsmetrics/main.nf
View file

@ -6,8 +6,7 @@ include { PICARD_COLLECTWGSMETRICS } from '../../../../modules/picard/collectwgs
workflow test_picard_collectwgsmetrics {
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)
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)

1
tests/modules/picard/createsequencedictionary/test.yml
View file

@ -7,4 +7,3 @@
- path: output/picard/test.dict
contains: ["SN:MT192765.1"]
- path: output/picard/versions.yml
md5sum: b3d8c7ea65b8a6d3237b153d13fe2014

1
tests/modules/picard/fixmateinformation/test.yml
View file

@ -7,4 +7,3 @@
- path: output/picard/test.bam
md5sum: 746102e8c242c0ef42e045c49d320030
- path: output/picard/versions.yml
md5sum: 4329ba7cdca8f4f6018dfd5c019ba2eb

2
tests/modules/picard/liftovervcf/nextflow.config
View file

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

2
tests/modules/picard/markduplicates/nextflow.config
View file

@ -3,7 +3,7 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: PICARD_MARKDUPLICATES_UNSORTED {
ext.args = 'ASSUME_SORT_ORDER=queryname'
ext.args = '--ASSUME_SORT_ORDER queryname'
}
}

27
tests/subworkflows/nf-core/bam_qc_picard/main.nf Normal file
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@ -0,0 +1,27 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BAM_QC_PICARD } from '../../../../subworkflows/nf-core/bam_qc_picard/main' addParams([:])
workflow test_bam_qc_picard_wgs {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fasta_fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
BAM_QC_PICARD ( input, fasta, fasta_fai, [], [] )
}
workflow test_bam_qc_picard_targetted {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fasta_fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
bait = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
target = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
BAM_QC_PICARD ( input, fasta, fasta_fai, bait, target )
}

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

33
tests/subworkflows/nf-core/bam_qc_picard/test.yml Normal file
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@ -0,0 +1,33 @@
- name: bam qc picard wgs
command: nextflow run ./tests/subworkflows/nf-core/bam_qc_picard -entry test_bam_qc_picard_wgs -c tests/config/nextflow.config
tags:
- subworkflows
# - subworkflows/bam_qc_picard
# Modules
# - picard
# - picard/collectmultiplemetrics
# - picard/collectwgsmetrics
files:
- path: ./output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
- path: ./output/picard/test.CollectMultipleMetrics.insert_size_metrics
- path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
- path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
- path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
- path: ./output/picard/test.CollectWgsMetrics.coverage_metrics
- name: bam qc picard targetted
command: nextflow run ./tests/subworkflows/nf-core/bam_qc_picard -entry test_bam_qc_picard_targetted -c tests/config/nextflow.config
tags:
- subworkflows
# - subworkflows/bam_qc_picard
# Modules
# - picard
# - picard/collectmultiplemetrics
# - picard/collecthsmetrics
files:
- path: ./output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
- path: ./output/picard/test.CollectMultipleMetrics.insert_size_metrics
- path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
- path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
- path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
- path: ./output/picard/test.CollectHsMetrics.coverage_metrics