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Merge branch 'nf-core:master' into master

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James A. Fellows Yates 2022-03-19 21:41:23 +01:00 committed by GitHub
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2
.editorconfig
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@ -8,5 +8,5 @@ trim_trailing_whitespace = true
indent_size = 4
indent_style = space
[*.{yml,yaml}]
[*.{md,yml,yaml}]
indent_size = 2

5
.github/CONTRIBUTING.md vendored
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@ -16,7 +16,9 @@ Contributions to the code are even more welcome ;)
If you'd like to write some code for nf-core/modules, the standard workflow is as follows:
1. Check that there isn't already an issue about your idea in the [nf-core/modules issues](https://github.com/nf-core/modules/issues) to avoid duplicating work
* If there isn't one already, please create one so that others know you're working on this
- If there isn't one already, please create one so that others know you're working on this
2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/modules repository](https://github.com/nf-core/modules) to your GitHub account
3. When adding a module file, follow the [guidelines](https://github.com/nf-core/modules#adding-a-new-module-file)
4. Ensure that [tests are working locally](https://github.com/nf-core/modules#running-tests-locally)
@ -40,7 +42,6 @@ These tests are run both with the latest available version of `Nextflow` and als
For further information/help, please consult the [nf-core/modules README](https://github.com/nf-core/modules) and don't hesitate to get in touch on the nf-core Slack [#modules](https://nfcore.slack.com/channels/modules) channel ([join our Slack here](https://nf-co.re/join/slack)).
### Images and figures
For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).

6
.github/PULL_REQUEST_TEMPLATE.md vendored
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@ -27,6 +27,6 @@ Closes #XXX <!-- If this PR fixes an issue, please link it here! -->
- [ ] Add a resource `label`
- [ ] Use BioConda and BioContainers if possible to fulfil software requirements.
- Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
- [ ] `PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware`
- [ ] `PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware`
- [ ] `PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware`
- [ ] `PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware`
- [ ] `PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware`
- [ ] `PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware`

32
.github/workflows/code-linting.yml vendored
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@ -5,20 +5,21 @@ on:
pull_request:
branches: [master]
jobs:
Markdown:
Prettier:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Check out repository
uses: actions/checkout@v2
- uses: actions/setup-node@v2
- name: Install NodeJS
uses: actions/setup-node@v2
- name: Install markdownlint
run: npm install -g markdownlint-cli
- name: Install Prettier
run: npm install -g prettier
- name: Run Markdownlint
run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.markdownlint.yml
- name: Run Prettier --check
run: prettier --check .
EditorConfig:
runs-on: ubuntu-latest
@ -32,18 +33,3 @@ jobs:
- name: Run ECLint check
run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
YAML:
runs-on: ubuntu-latest
steps:
- name: Check out repository
uses: actions/checkout@v2
- name: Install NodeJS
uses: actions/setup-node@v2
- name: Install yaml-lint
run: npm install -g yaml-lint
- name: Run yaml-lint
run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yaml" -or -name "*.yml")

18
.gitpod.yml
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@ -1,14 +1,14 @@
image: nfcore/gitpod:latest
vscode:
extensions: # based on nf-core.nf-core-extensionpack
- codezombiech.gitignore # Language support for .gitignore files
extensions: # based on nf-core.nf-core-extensionpack
- codezombiech.gitignore # Language support for .gitignore files
# - cssho.vscode-svgviewer # SVG viewer
- davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code
- eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
- EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
- Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
- mechatroner.rainbow-csv # Highlight columns in csv files in different colors
- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
- eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
- EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
- Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
- mechatroner.rainbow-csv # Highlight columns in csv files in different colors
# - nextflow.nextflow # Nextflow syntax highlighting
- oderwat.indent-rainbow # Highlight indentation level
- streetsidesoftware.code-spell-checker # Spelling checker for source code
- oderwat.indent-rainbow # Highlight indentation level
- streetsidesoftware.code-spell-checker # Spelling checker for source code

11
.markdownlint.yml
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@ -1,11 +0,0 @@
# Markdownlint configuration file
default: true
line-length: false
no-multiple-blanks: 0
blanks-around-headers: false
blanks-around-lists: false
header-increment: false
no-duplicate-header:
siblings_only: true
ul-indent:
indent: 4

16
.prettierignore Normal file
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@ -0,0 +1,16 @@
includes/Maven_Pro/
# gitignore
.nextflow*
work/
results/
test_output/
output/
.DS_Store
*.code-workspace
tests/data/
.screenrc
.*.sw?
__pycache__
*.pyo
*.pyc

1
.prettierrc.yml Normal file
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@ -0,0 +1 @@
printWidth: 120

5
.yamllint.yml
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@ -1,5 +0,0 @@
extends: default
rules:
document-start: disable
line-length: disable

142
README.md
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@ -31,105 +31,105 @@ We have written a helper command in the `nf-core/tools` package that uses the Gi
1. Install the latest version of [`nf-core/tools`](https://github.com/nf-core/tools#installation) (`>=2.0`)
2. List the available modules:
```console
$ nf-core modules list remote
```console
$ nf-core modules list remote
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.0
nf-core/tools version 2.0
INFO Modules available from nf-core/modules (master): pipeline_modules.py:164
INFO Modules available from nf-core/modules (master): pipeline_modules.py:164
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Module Name ┃
┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ bandage/image │
│ bcftools/consensus │
│ bcftools/filter │
│ bcftools/isec │
..truncated..
```
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Module Name ┃
┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ bandage/image │
│ bcftools/consensus │
│ bcftools/filter │
│ bcftools/isec │
..truncated..
```
3. Install the module in your pipeline directory:
```console
$ nf-core modules install fastqc
```console
$ nf-core modules install fastqc
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.0
nf-core/tools version 2.0
INFO Installing fastqc pipeline_modules.py:213
INFO Downloaded 3 files to ./modules/nf-core/modules/fastqc pipeline_modules.py:236
```
INFO Installing fastqc pipeline_modules.py:213
INFO Downloaded 3 files to ./modules/nf-core/modules/fastqc pipeline_modules.py:236
```
4. Import the module in your Nextflow script:
```nextflow
#!/usr/bin/env nextflow
```nextflow
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
nextflow.enable.dsl = 2
include { FASTQC } from './modules/nf-core/modules/fastqc/main'
```
include { FASTQC } from './modules/nf-core/modules/fastqc/main'
```
5. Remove the module from the pipeline repository if required:
```console
$ nf-core modules remove fastqc
```console
$ nf-core modules remove fastqc
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.0
nf-core/tools version 2.0
INFO Removing fastqc pipeline_modules.py:271
INFO Successfully removed fastqc pipeline_modules.py:285
```
INFO Removing fastqc pipeline_modules.py:271
INFO Successfully removed fastqc pipeline_modules.py:285
```
6. Check that a locally installed nf-core module is up-to-date compared to the one hosted in this repo:
```console
$ nf-core modules lint fastqc
```console
$ nf-core modules lint fastqc
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.0
nf-core/tools version 2.0
INFO Linting pipeline: . lint.py:104
INFO Linting module: fastqc lint.py:106
INFO Linting pipeline: . lint.py:104
INFO Linting module: fastqc lint.py:106
╭─────────────────────────────────────────────────────────────────────────────────╮
│ [!] 1 Test Warning │
╰─────────────────────────────────────────────────────────────────────────────────╯
╭──────────────┬───────────────────────────────┬──────────────────────────────────╮
│ Module name │ Test message │ File path │
├──────────────┼───────────────────────────────┼──────────────────────────────────┤
│ fastqc │ Local copy of module outdated │ modules/nf-core/modules/fastqc/ │
╰──────────────┴────────────────────────────── ┴──────────────────────────────────╯
╭──────────────────────╮
│ LINT RESULTS SUMMARY │
├──────────────────────┤
│ [✔] 15 Tests Passed │
│ [!] 1 Test Warning │
│ [✗] 0 Test Failed │
╰──────────────────────╯
```
╭─────────────────────────────────────────────────────────────────────────────────╮
│ [!] 1 Test Warning │
╰─────────────────────────────────────────────────────────────────────────────────╯
╭──────────────┬───────────────────────────────┬──────────────────────────────────╮
│ Module name │ Test message │ File path │
├──────────────┼───────────────────────────────┼──────────────────────────────────┤
│ fastqc │ Local copy of module outdated │ modules/nf-core/modules/fastqc/ │
╰──────────────┴────────────────────────────── ┴──────────────────────────────────╯
╭──────────────────────╮
│ LINT RESULTS SUMMARY │
├──────────────────────┤
│ [✔] 15 Tests Passed │
│ [!] 1 Test Warning │
│ [✗] 0 Test Failed │
╰──────────────────────╯
```
## Adding new modules

2
modules/abricate/run/meta.yml
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@ -11,7 +11,7 @@ tools:
documentation: https://github.com/tseemann/abricate
tool_dev_url: https://github.com/tseemann/abricate
doi: ""
licence: ['GPL v2', 'GPL v2']
licence: ["GPL v2", "GPL v2"]
input:
- meta:

2
modules/abricate/summary/meta.yml
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@ -11,7 +11,7 @@ tools:
documentation: https://github.com/tseemann/abricate
tool_dev_url: https://github.com/tseemann/abricate
doi: ""
licence: ['GPL v2', 'GPL v2']
licence: ["GPL v2", "GPL v2"]
input:
- meta:

3
modules/adapterremoval/meta.yml
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@ -26,8 +26,7 @@ input:
pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
- adapterlist:
type: file
description:
Optional text file containing list of adapters to look for for removal
description: Optional text file containing list of adapters to look for for removal
with one adapter per line. Otherwise will look for default adapters (see
AdapterRemoval man page), or can be modified to remove user-specified
adapters via ext.args.

2
modules/amrfinderplus/run/meta.yml
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@ -11,7 +11,7 @@ tools:
documentation: https://github.com/ncbi/amr/wiki
tool_dev_url: https://github.com/ncbi/amr
doi: "10.1038/s41598-021-91456-0"
licence: ['Public Domain']
licence: ["Public Domain"]
input:
- meta:

2
modules/amrfinderplus/update/meta.yml
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@ -11,7 +11,7 @@ tools:
documentation: https://github.com/ncbi/amr/wiki
tool_dev_url: https://github.com/ncbi/amr
doi: "10.1038/s41598-021-91456-0"
licence: ['Public Domain']
licence: ["Public Domain"]
input:
- input_not_required:

2
modules/ascat/meta.yml
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@ -9,7 +9,7 @@ tools:
documentation: None
tool_dev_url: https://github.com/Crick-CancerGenomics/ascat
doi: "10.1093/bioinformatics/btaa538"
licence: ['GPL v3']
licence: ["GPL v3"]
input:
- args:

2
modules/bcftools/annotate/meta.yml
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@ -12,7 +12,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: https://samtools.github.io/bcftools/bcftools.html#annotate
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

12
modules/biscuit/pileup/meta.yml
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@ -27,9 +27,9 @@ input:
- normal_bams:
type: file(s)
description: |
BAM files to be analyzed. If no tumor_bam file is provided, any number of "normal" BAMs may be provided
("normal" here is just a semantic issue, these BAMs could be from tumor or any other kind of tissue). If a
tumor BAM file is provided, exactly one normal (germline) BAM must be provided.
BAM files to be analyzed. If no tumor_bam file is provided, any number of "normal" BAMs may be provided
("normal" here is just a semantic issue, these BAMs could be from tumor or any other kind of tissue). If a
tumor BAM file is provided, exactly one normal (germline) BAM must be provided.
pattern: "*.{bam}"
- normal_bais:
type: file(s)
@ -38,9 +38,9 @@ input:
- tumor_bam:
type: file(s)
description: |
Optional. If a tumor BAM file is provided, pileup will run in "somatic" mode and will annotate variants with
their somatic state (present in tumor only, present in normal only, present in both, etc). Note that if a
tumor BAM file is provided, exactly one normal BAM must be provided.
Optional. If a tumor BAM file is provided, pileup will run in "somatic" mode and will annotate variants with
their somatic state (present in tumor only, present in normal only, present in both, etc). Note that if a
tumor BAM file is provided, exactly one normal BAM must be provided.
pattern: "*.{bam}"
- tumor_bai:
type: file(s)

21
modules/cellranger/README.md
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@ -2,23 +2,22 @@
Cell Ranger is a commercial tool from 10X Genomics. The container provided for the cellranger nf-core module is not provided nor supported by 10x Genomics. Updating the Cell Ranger versions in the container and pushing the update to Dockerhub needs to be done manually.
1. Navigate to the appropriate download page.
- [Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest): download the tar ball of the desired Cell Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
1. Navigate to the appropriate download page. - [Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest): download the tar ball of the desired Cell Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
2. Edit the Dockerfile. Update the Cell Ranger versions in this line:
```bash
ENV CELLRANGER_VER=<VERSION>
```
```bash
ENV CELLRANGER_VER=<VERSION>
```
3. Create and test the container:
```bash
docker build . -t nfcore/cellranger:<VERSION>
```
```bash
docker build . -t nfcore/cellranger:<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/cellranger:<VERSION>
```
```bash
docker push nfcore/cellranger:<VERSION>
```

24
modules/cellranger/mkfastq/README.md
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@ -2,25 +2,23 @@
Bcl2fastq2 and Cell Ranger are commercial tools from Illumina and 10X Genomics, respectively. The container provided for the cellranger nf-core module is not provided nor supported by either Illumina or 10x Genomics. Updating the bcl2fastq2 or Cell Ranger versions in the container and pushing the update to Dockerhub needs to be done manually.
1. Navigate to the appropriate download pages.
- [bcl2fastq2](https://emea.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html): download the linux rpm installer of the desired bcl2fastq2 version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
- [Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest): download the tar ball of the desired Cell Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
1. Navigate to the appropriate download pages. - [bcl2fastq2](https://emea.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html): download the linux rpm installer of the desired bcl2fastq2 version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies. - [Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest): download the tar ball of the desired Cell Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
2. Edit the Dockerfile. Update the bcl2fastq2 and Cell Ranger versions in this line:
```bash
ENV BCL2FASTQ2_VER=<VERSION> \
CELLRANGER_VER=<VERSION>
```
```bash
ENV BCL2FASTQ2_VER=<VERSION> \
CELLRANGER_VER=<VERSION>
```
3. Create and test the container:
```bash
docker build . -t nfcore/cellrangermkfastq:<CELLRANGER_VERSION>
```
```bash
docker build . -t nfcore/cellrangermkfastq:<CELLRANGER_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/cellrangermkfastq:<CELLRANGER_VERSION>
```
```bash
docker push nfcore/cellrangermkfastq:<CELLRANGER_VERSION>
```

63
modules/centrifuge/main.nf Normal file
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@ -0,0 +1,63 @@
process CENTRIFUGE {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' :
'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
input:
tuple val(meta), path(reads)
path db
val save_unaligned
val save_aligned
val sam_format
output:
tuple val(meta), path('*report.txt') , emit: report
tuple val(meta), path('*results.txt') , emit: results
tuple val(meta), path('*kreport.txt') , emit: kreport
tuple val(meta), path('*.sam') , optional: true, emit: sam
tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_mapped
tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
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 paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
def db_name = db.toString().replace(".tar.gz","")
def unaligned = ''
def aligned = ''
if (meta.single_end) {
unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
} else {
unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
}
def sam_output = sam_format ? "--out-fmt 'sam'" : ''
"""
tar -xf $db
centrifuge \\
-x $db_name \\
-p $task.cpus \\
$paired \\
--report-file ${prefix}.report.txt \\
-S ${prefix}.results.txt \\
$unaligned \\
$aligned \\
$sam_output \\
$args
centrifuge-kreport -x $db_name ${prefix}.results.txt > ${prefix}.kreport.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
centrifuge: \$( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //')
END_VERSIONS
"""
}

73
modules/centrifuge/meta.yml Normal file
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@ -0,0 +1,73 @@
name: centrifuge
description: Classifies metagenomic sequence data
keywords:
- classify
- metagenomics
- fastq
- db
tools:
- centrifuge:
description: Centrifuge is a classifier for metagenomic sequences.
homepage: https://ccb.jhu.edu/software/centrifuge/
documentation: https://ccb.jhu.edu/software/centrifuge/manual.shtml
doi: 10.1101/gr.210641.116
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- db:
type: directory
description: Centrifuge database in .tar.gz format
pattern: "*.tar.gz"
- save_unaligned:
type: value
description: If true unmapped fastq files are saved
- save_aligned:
type: value
description: If true mapped fastq files are saved
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- report:
type: file
description: |
File containing a classification summary
pattern: "*.{report.txt}"
- results:
type: file
description: |
File containing classification results
pattern: "*.{results.txt}"
- kreport:
type: file
description: |
File containing kraken-style report from centrifuge
out files.
pattern: "*.{kreport.txt}"
- fastq_unmapped:
type: file
description: Unmapped fastq files
pattern: "*.unmapped.fastq.gz"
- fastq_mapped:
type: file
description: Mapped fastq files
pattern: "*.mapped.fastq.gz"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@sofstam"
- "@jfy133"
- "@sateeshperi"

3
modules/cnvpytor/callcnvs/meta.yml
View file

@ -8,7 +8,7 @@ tools:
documentation: https://github.com/abyzovlab/CNVpytor
tool_dev_url: https://github.com/abyzovlab/CNVpytor
doi: "10.1101/2021.01.27.428472v1"
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map
@ -35,6 +35,5 @@ output:
description: File containing software versions
pattern: "versions.yml"
authors:
- "@sima-r"

2
modules/cnvpytor/histogram/meta.yml
View file

@ -10,7 +10,7 @@ tools:
documentation: https://github.com/abyzovlab/CNVpytor
tool_dev_url: https://github.com/abyzovlab/CNVpytor
doi: "10.1101/2021.01.27.428472v1"
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

3
modules/cnvpytor/importreaddepth/meta.yml
View file

@ -10,7 +10,7 @@ tools:
documentation: https://github.com/abyzovlab/CNVpytor
tool_dev_url: https://github.com/abyzovlab/CNVpytor
doi: "10.1101/2021.01.27.428472v1"
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
@ -35,7 +35,6 @@ input:
description: Index of reference fasta file
pattern: "*.fai"
output:
- meta:
type: map

2
modules/cnvpytor/partition/meta.yml
View file

@ -10,7 +10,7 @@ tools:
documentation: https://github.com/abyzovlab/CNVpytor
tool_dev_url: https://github.com/abyzovlab/CNVpytor
doi: "10.1101/2021.01.27.428472v1"
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

3
modules/controlfreec/meta.yml
View file

@ -13,7 +13,7 @@ tools:
documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html
tool_dev_url: https://github.com/BoevaLab/FREEC/
doi: "10.1093/bioinformatics/btq635"
licence: ['GPL >=2']
licence: ["GPL >=2"]
input:
- args:
@ -131,7 +131,6 @@ input:
description: Sorted bed file containing capture regions (optional)
pattern: "*.bed"
output:
- meta:
type: map

3
modules/csvtk/split/meta.yml
View file

@ -6,8 +6,7 @@ keywords:
- tsv
tools:
- csvtk:
description:
CSVTK is a cross-platform, efficient and practical CSV/TSV toolkit
description: CSVTK is a cross-platform, efficient and practical CSV/TSV toolkit
that allows rapid data investigation and manipulation.
homepage: https://bioinf.shenwei.me/csvtk/
documentation: https://bioinf.shenwei.me/csvtk/

6
modules/deeparg/downloaddata/main.nf
View file

@ -8,10 +8,10 @@ process DEEPARG_DOWNLOADDATA {
'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' :
'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }"
/*
We have to force singularity to run with --fakeroot to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
This flag may not be available on all systems and may be considered a security problem. so please document and /or warn for this in your pipeline!
We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
Original report: https://github.com/nf-core/funcscan/issues/23
*/
containerOptions { "${workflow.containerEngine}" == 'singularity' ? '--fakeroot' : '' }
containerOptions { "${workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : '' }
input:

2
modules/deeparg/downloaddata/meta.yml
View file

@ -17,7 +17,7 @@ tools:
licence: ["MIT"]
input:
- none: There is no input. This module downloads a pre-built database for use with deepARG.
- none: No input required for download module.
output:
- versions:

8
modules/deeparg/predict/main.nf
View file

@ -6,13 +6,13 @@ process DEEPARG_PREDICT {
conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity//deeparg:1.0.2--pyhdfd78af_1' :
'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' :
'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }"
/*
We have to force singularity to run with --fakeroot to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
This flag may not be available on all systems and may be considered a security problem. so please document and /or warn for this in your pipeline!
We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
Original report: https://github.com/nf-core/funcscan/issues/23
*/
containerOptions { "${workflow.containerEngine}" == 'singularity' ? '--fakeroot' : '' }
containerOptions { "${workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : '' }
input:
tuple val(meta), path(fasta), val(model)

2
modules/deeptools/bamcoverage/meta.yml
View file

@ -9,7 +9,7 @@ tools:
documentation: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
tool_dev_url: https://github.com/deeptools/deepTools/
doi: "https://doi.org/10.1093/nar/gkw257"
licence: ['GPL v3']
licence: ["GPL v3"]
input:
- meta:

2
modules/faqcs/meta.yml
View file

@ -13,7 +13,7 @@ tools:
documentation: https://github.com/LANL-Bioinformatics/FaQCs
tool_dev_url: https://github.com/LANL-Bioinformatics/FaQCs
doi: "https://doi.org/10.1186/s12859-014-0366-2"
licence: ['GPLv3 License']
licence: ["GPLv3 License"]
## TODO nf-core: Add a description of all of the variables used as input
input:

5
modules/gatk4/combinegvcfs/meta.yml
View file

@ -8,14 +8,15 @@ keywords:
- Short_Variant_Discovery
tools:
- gatk4:
description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
description:
Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
with a primary focus on variant discovery and genotyping. Its powerful processing engine
and high-performance computing features make it capable of taking on projects of any size.
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037593911-CombineGVCFs
tool_dev_url: https://github.com/broadinstitute/gatk
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
licence: ["Apache-2.0"]
input:
- fasta:

3
modules/gatk4/fastqtosam/meta.yml
View file

@ -24,8 +24,7 @@ input:
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description:
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
description: List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
pattern: "*.fastq.gz"

2
modules/gatk4/gatherpileupsummaries/meta.yml
View file

@ -9,7 +9,7 @@ tools:
documentation: https://gatk.broadinstitute.org/hc/en-us
tool_dev_url: https://github.com/broadinstitute/gatk
doi: "10.1158/1538-7445.AM2017-3590"
licence: ['BSD-3-clause']
licence: ["BSD-3-clause"]
input:
- meta:

1
modules/gatk4/getpileupsummaries/meta.yml
View file

@ -56,7 +56,6 @@ input:
description: Index file for the germline resource.
pattern: "*.vcf.gz.tbi"
output:
- pileup:
type: file

4
modules/gatk4/variantrecalibrator/meta.yml
View file

@ -52,11 +52,11 @@ input:
- resvcfs:
type: list
description: resource files to be used as truth, training and known sites resources, this imports the files into the module, file names are specified again in the resource_labels to be called via the command.
pattern: '*/hapmap_3.3.hg38_chr21.vcf.gz'
pattern: "*/hapmap_3.3.hg38_chr21.vcf.gz"
- restbis:
type: list
description: tbis for the corresponding vcfs files to be used as truth, training and known resources.
pattern: '*/hapmap_3.3.hg38_chr21.vcf.gz.tbi'
pattern: "*/hapmap_3.3.hg38_chr21.vcf.gz.tbi"
- reslabels:
type: list
description: labels for the resource files to be used as truth, training and known sites resources, label should include an identifier,which kind of resource(s) it is, prior value and name of the file.

2
modules/hamronization/deeparg/meta.yml
View file

@ -12,7 +12,7 @@ tools:
documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md
tool_dev_url: https://github.com/pha4ge/hAMRonization
doi: ""
licence: ['GNU Lesser General Public v3 (LGPL v3)']
licence: ["GNU Lesser General Public v3 (LGPL v3)"]
input:
- meta:

2
modules/hamronization/summarize/meta.yml
View file

@ -11,7 +11,7 @@ tools:
documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md
tool_dev_url: https://github.com/pha4ge/hAMRonization
doi: ""
licence: ['GNU Lesser General Public v3 (LGPL v3)']
licence: ["GNU Lesser General Public v3 (LGPL v3)"]
input:
- reports:

2
modules/hmmer/hmmsearch/meta.yml
View file

@ -12,7 +12,7 @@ tools:
documentation: http://hmmer.org/documentation.html
tool_dev_url: https://github.com/EddyRivasLab/hmmer
doi: "10.1371/journal.pcbi.1002195"
licence: ['BSD']
licence: ["BSD"]
input:
- meta:

2
modules/hpsuissero/meta.yml
View file

@ -11,7 +11,7 @@ tools:
documentation: https://github.com/jimmyliu1326/HpsuisSero
tool_dev_url: https://github.com/jimmyliu1326/HpsuisSero
doi: ""
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

2
modules/ichorcna/createpon/meta.yml
View file

@ -14,7 +14,7 @@ tools:
documentation: https://github.com/broadinstitute/ichorCNA/wiki
tool_dev_url: https://github.com/broadinstitute/ichorCNA
doi: "10.1038/s41467-017-00965-y"
licence: ['GPL v3']
licence: ["GPL v3"]
input:
- wigs:

2
modules/ichorcna/run/meta.yml
View file

@ -13,7 +13,7 @@ tools:
documentation: https://github.com/broadinstitute/ichorCNA/wiki
tool_dev_url: https://github.com/broadinstitute/ichorCNA
doi: "10.1038/s41467-017-00965-y"
licence: ['GPL v3']
licence: ["GPL v3"]
input:
- meta:

2
modules/legsta/meta.yml
View file

@ -10,7 +10,7 @@ tools:
documentation: https://github.com/tseemann/legsta
tool_dev_url: https://github.com/tseemann/legsta
doi: ""
licence: ['GPL v3']
licence: ["GPL v3"]
input:
- meta:

3
modules/macs2/callpeak/meta.yml
View file

@ -28,8 +28,7 @@ input:
description: The control file
- macs2_gsize:
type: string
description:
Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9),
description: Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9),
'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8)
output:

2
modules/mafft/meta.yml
View file

@ -10,7 +10,7 @@ tools:
documentation: https://mafft.cbrc.jp/alignment/software/manual/manual.html
tool_dev_url: https://mafft.cbrc.jp/alignment/software/source.html
doi: "10.1093/nar/gkf436"
licence: ['BSD']
licence: ["BSD"]
input:
- meta:

3
modules/manta/germline/main.nf
View file

@ -8,10 +8,9 @@ process MANTA_GERMLINE {
'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }"
input:
tuple val(meta), path(input), path(index)
tuple val(meta), path(input), path(index), path(target_bed), path(target_bed_tbi)
path fasta
path fasta_fai
tuple path(target_bed), path(target_bed_tbi)
output:

16
modules/manta/germline/meta.yml
View file

@ -31,14 +31,6 @@ input:
type: file
description: BAM/CRAM/SAM index file. For joint calling use a list of files.
pattern: "*.{bai,crai,sai}"
- fasta:
type: file
description: Genome reference FASTA file
pattern: "*.{fa,fasta}"
- fasta_fai:
type: file
description: Genome reference FASTA index file
pattern: "*.{fa.fai,fasta.fai}"
- target_bed:
type: file
description: BED file containing target regions for variant calling
@ -47,6 +39,14 @@ input:
type: file
description: Index for BED file containing target regions for variant calling
pattern: "*.{bed.tbi}"
- fasta:
type: file
description: Genome reference FASTA file
pattern: "*.{fa,fasta}"
- fasta_fai:
type: file
description: Genome reference FASTA index file
pattern: "*.{fa.fai,fasta.fai}"
output:
- meta:

4
modules/manta/somatic/main.nf
View file

@ -8,11 +8,9 @@ process MANTA_SOMATIC {
'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }"
input:
tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor)
tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(target_bed), path(target_bed_tbi)
path fasta
path fai
path target_bed
path target_bed_tbi
output:
tuple val(meta), path("*.candidate_small_indels.vcf.gz") , emit: candidate_small_indels_vcf

16
modules/manta/somatic/meta.yml
View file

@ -39,14 +39,6 @@ input:
type: file
description: BAM/CRAM/SAM index file
pattern: "*.{bai,crai,sai}"
- fasta:
type: file
description: Genome reference FASTA file
pattern: "*.{fa,fasta}"
- fai:
type: file
description: Genome reference FASTA index file
pattern: "*.{fa.fai,fasta.fai}"
- target_bed:
type: file
description: BED file containing target regions for variant calling
@ -55,6 +47,14 @@ input:
type: file
description: Index for BED file containing target regions for variant calling
pattern: "*.{bed.tbi}"
- fasta:
type: file
description: Genome reference FASTA file
pattern: "*.{fa,fasta}"
- fai:
type: file
description: Genome reference FASTA index file
pattern: "*.{fa.fai,fasta.fai}"
output:
- meta:

4
modules/manta/tumoronly/main.nf
View file

@ -8,11 +8,9 @@ process MANTA_TUMORONLY {
'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }"
input:
tuple val(meta), path(input), path(input_index)
tuple val(meta), path(input), path(input_index), path(target_bed), path(target_bed_tbi)
path fasta
path fai
path target_bed
path target_bed_tbi
output:
tuple val(meta), path("*candidate_small_indels.vcf.gz") , emit: candidate_small_indels_vcf

16
modules/manta/tumoronly/meta.yml
View file

@ -31,14 +31,6 @@ input:
type: file
description: BAM/CRAM/SAM index file
pattern: "*.{bai,crai,sai}"
- fasta:
type: file
description: Genome reference FASTA file
pattern: "*.{fa,fasta}"
- fai:
type: file
description: Genome reference FASTA index file
pattern: "*.{fa.fai,fasta.fai}"
- target_bed:
type: file
description: BED file containing target regions for variant calling
@ -47,6 +39,14 @@ input:
type: file
description: Index for BED file containing target regions for variant calling
pattern: "*.{bed.tbi}"
- fasta:
type: file
description: Genome reference FASTA file
pattern: "*.{fa,fasta}"
- fai:
type: file
description: Genome reference FASTA index file
pattern: "*.{fa.fai,fasta.fai}"
output:
- meta:

2
modules/mobsuite/recon/meta.yml
View file

@ -10,7 +10,7 @@ tools:
documentation: https://github.com/phac-nml/mob-suite
tool_dev_url: https://github.com/phac-nml/mob-suite
doi: "10.1099/mgen.0.000435"
licence: ['Apache License, Version 2.0']
licence: ["Apache License, Version 2.0"]
input:
- meta:

2
modules/msisensorpro/msi_somatic/meta.yml
View file

@ -12,7 +12,7 @@ tools:
documentation: https://github.com/xjtu-omics/msisensor-pro/wiki
tool_dev_url: https://github.com/xjtu-omics/msisensor-pro
doi: "doi.org/10.1016/j.gpb.2020.02.001"
licence: ['Custom Licence']
licence: ["Custom Licence"]
input:
- meta:

2
modules/msisensorpro/scan/meta.yml
View file

@ -11,7 +11,7 @@ tools:
documentation: https://github.com/xjtu-omics/msisensor-pro/wiki
tool_dev_url: https://github.com/xjtu-omics/msisensor-pro
doi: "doi.org/10.1016/j.gpb.2020.02.001"
licence: ['Custom Licence']
licence: ["Custom Licence"]
input:
- meta:

2
modules/ngscheckmate/ncm/meta.yml
View file

@ -11,7 +11,7 @@ tools:
documentation: https://github.com/parklab/NGSCheckMate
tool_dev_url: https://github.com/parklab/NGSCheckMate
doi: "doi:/10.1093/nar/gkx193"
licence: ['MIT']
licence: ["MIT"]
input:
- files:

2
modules/picard/addorreplacereadgroups/meta.yml
View file

@ -12,7 +12,7 @@ tools:
homepage: https://broadinstitute.github.io/picard/
documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037226472-AddOrReplaceReadGroups-Picard-
tool_dev_url: https://github.com/broadinstitute/picard
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

4
modules/picard/createsequencedictionary/meta.yml
View file

@ -7,11 +7,11 @@ keywords:
tools:
- picard:
description: |
Creates a sequence dictionary file (with ".dict" extension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools. The output file contains a header but no SAMRecords, and the header contains only sequence records.
Creates a sequence dictionary file (with ".dict" extension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools. The output file contains a header but no SAMRecords, and the header contains only sequence records.
homepage: https://broadinstitute.github.io/picard/
documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036712531-CreateSequenceDictionary-Picard-
tool_dev_url: https://github.com/broadinstitute/picard
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

2
modules/picard/fixmateinformation/meta.yml
View file

@ -10,7 +10,7 @@ tools:
homepage: https://broadinstitute.github.io/picard/
documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036713471-FixMateInformation-Picard-
tool_dev_url: https://github.com/broadinstitute/picard
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

2
modules/picard/sortvcf/meta.yml
View file

@ -8,7 +8,7 @@ tools:
description: Java tools for working with NGS data in the BAM/CRAM/SAM and VCF format
homepage: https://broadinstitute.github.io/picard/
documentation: https://broadinstitute.github.io/picard/command-line-overview.html#SortVcf
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

6
modules/plink2/score/meta.yml
View file

@ -6,13 +6,13 @@ keywords:
tools:
- plink2:
description: |
Whole genome association analysis toolset, designed to perform a range
of basic, large-scale analyses in a computationally efficient manner
Whole genome association analysis toolset, designed to perform a range
of basic, large-scale analyses in a computationally efficient manner
homepage: http://www.cog-genomics.org/plink/2.0/
documentation: http://www.cog-genomics.org/plink/2.0/general_usage
tool_dev_url: None
doi: "10.1186/s13742-015-0047-8"
licence: ['GPL v3']
licence: ["GPL v3"]
input:
- meta:

2
modules/rgi/main/meta.yml
View file

@ -11,7 +11,7 @@ tools:
documentation: https://github.com/arpcard/rgi
tool_dev_url: https://github.com/arpcard/rgi
doi: "10.1093/nar/gkz935"
licence: ['https://card.mcmaster.ca/about']
licence: ["https://card.mcmaster.ca/about"]
input:
- meta:

2
modules/rsem/calculateexpression/meta.yml
View file

@ -11,7 +11,7 @@ tools:
homepage: https://github.com/deweylab/RSEM
documentation: https://github.com/deweylab/RSEM
doi: https://doi.org/10.1186/1471-2105-12-323
licence: ['GPL-3.0-or-later']
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map

2
modules/seqkit/pair/meta.yml
View file

@ -10,7 +10,7 @@ tools:
documentation: https://bioinf.shenwei.me/seqkit/usage/
tool_dev_url: https://github.com/shenwei356/seqkit/
doi: "10.1371/journal.pone.0163962"
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

2
modules/seqtk/rename/meta.yml
View file

@ -8,7 +8,7 @@ tools:
homepage: https://github.com/lh3/seqtk
documentation: https://docs.csc.fi/apps/seqtk/
tool_dev_url: https://github.com/lh3/seqtk
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

2
modules/seqtk/seq/meta.yml
View file

@ -8,7 +8,7 @@ tools:
homepage: https://github.com/lh3/seqtk
documentation: https://docs.csc.fi/apps/seqtk/
tool_dev_url: https://github.com/lh3/seqtk
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

2
modules/sistr/meta.yml
View file

@ -11,7 +11,7 @@ tools:
documentation: https://github.com/phac-nml/sistr_cmd
tool_dev_url: https://github.com/phac-nml/sistr_cmd
doi: "10.1371/journal.pone.0147101"
licence: ['Apache-2.0']
licence: ["Apache-2.0"]
input:
- meta:

2
modules/sourmash/sketch/meta.yml
View file

@ -10,7 +10,7 @@ tools:
documentation: https://sourmash.readthedocs.io/
tool_dev_url: https://github.com/dib-lab/sourmash
doi: "10.1186/s13059-016-0997-x"
licence: ['BSD-3-clause']
licence: ["BSD-3-clause"]
input:
- meta:

2
modules/ssuissero/meta.yml
View file

@ -11,7 +11,7 @@ tools:
documentation: https://github.com/jimmyliu1326/SsuisSero
tool_dev_url: https://github.com/jimmyliu1326/SsuisSero
doi: ""
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

2
modules/stranger/meta.yml
View file

@ -12,7 +12,7 @@ tools:
documentation: https://github.com/moonso/stranger
tool_dev_url: https://github.com/moonso/stranger
doi: "10.5281/zenodo.4548873"
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

13
modules/umitools/dedup/main.nf
View file

@ -11,8 +11,11 @@ process UMITOOLS_DEDUP {
tuple val(meta), path(bam), path(bai)
output:
tuple val(meta), path("*.bam"), emit: bam
path "versions.yml" , emit: versions
tuple val(meta), path("*.bam") , emit: bam
tuple val(meta), path("*edit_distance.tsv"), emit: tsv_edit_distance
tuple val(meta), path("*per_umi.tsv") , emit: tsv_per_umi
tuple val(meta), path("*per_position.tsv") , emit: tsv_umi_per_position
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
@ -20,11 +23,13 @@ process UMITOOLS_DEDUP {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def paired = meta.single_end ? "" : "--paired"
def paired = meta.single_end ? "" : "--paired"
"""
umi_tools dedup \\
umi_tools \\
dedup \\
-I $bam \\
-S ${prefix}.bam \\
--output-stats $prefix \\
$paired \\
$args

12
modules/umitools/dedup/meta.yml
View file

@ -36,6 +36,18 @@ output:
type: file
description: BAM file with deduplicated UMIs.
pattern: "*.{bam}"
- tsv_edit_distance:
type: file
description: Reports the (binned) average edit distance between the UMIs at each position.
pattern: "*edit_distance.tsv"
- tsv_per_umi:
type: file
description: UMI-level summary statistics.
pattern: "*per_umi.tsv"
- tsv_umi_per_position:
type: file
description: Tabulates the counts for unique combinations of UMI and position.
pattern: "*per_position.tsv"
- versions:
type: file
description: File containing software versions

5
modules/yara/index/meta.yml
View file

@ -13,10 +13,7 @@ tools:
documentation: https://github.com/seqan/seqan
tool_dev_url: https://github.com/seqan/seqan
doi: ""
licence:
[
"https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE",
]
licence: ["https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE"]
input:
- fasta:

5
modules/yara/mapper/meta.yml
View file

@ -11,10 +11,7 @@ tools:
documentation: https://github.com/seqan/seqan
tool_dev_url: https://github.com/seqan/seqan
doi: ""
licence:
[
"https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE",
]
licence: ["https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE"]
input:
- meta:

3
pytest.ini Normal file
View file

@ -0,0 +1,3 @@
[pytest]
filterwarnings =
ignore::pytest.PytestRemovedIn8Warning:_pytest.nodes:140

12
tests/config/pytest_modules.yml
View file

@ -202,6 +202,10 @@ bedtools/subtract:
- modules/bedtools/subtract/**
- tests/modules/bedtools/subtract/**
biobambam/bammarkduplicates2:
- modules/biobambam/bammarkduplicates2/**
- tests/modules/biobambam/bammarkduplicates2/**
biscuit/align:
- modules/biscuit/index/**
- modules/biscuit/align/**
@ -245,10 +249,6 @@ biscuit/vcf2bed:
- modules/biscuit/vcf2bed/**
- tests/modules/biscuit/vcf2bed/**
biobambam/bammarkduplicates2:
- modules/biobambam/bammarkduplicates2/**
- tests/modules/biobambam/bammarkduplicates2/**
bismark/align:
- modules/bismark/align/**
- modules/bismark/genomepreparation/**
@ -379,6 +379,10 @@ cellranger/mkref:
- modules/cellranger/gtf/**
- tests/modules/cellranger/gtf/**
centrifuge:
- modules/centrifuge/**
- tests/modules/centrifuge/**
checkm/lineagewf:
- modules/checkm/lineagewf/**
- tests/modules/checkm/lineagewf/**

33
tests/modules/centrifuge/main.nf Normal file
View file

@ -0,0 +1,33 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { CENTRIFUGE } from '../../../modules/centrifuge/main.nf'
workflow test_centrifuge_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
]
db = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz", checkIfExists: true)
save_unaligned = true
save_aligned = false
sam_format = false
CENTRIFUGE ( input, db, save_unaligned, save_aligned, sam_format )
}
workflow test_centrifuge_paired_end {
input = [ [ id:'test', single_end:false ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
db = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz", checkIfExists: true)
save_unaligned = true
save_aligned = false
sam_format = false
CENTRIFUGE ( input, db, save_unaligned, save_aligned, sam_format )
}

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

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

22
tests/modules/centrifuge/test.yml Normal file
View file

@ -0,0 +1,22 @@
- name: centrifuge test_centrifuge_single_end
command: nextflow run tests/modules/centrifuge -entry test_centrifuge_single_end -c tests/config/nextflow.config
tags:
- centrifuge
files:
- path: output/centrifuge/test.kreport.txt
- path: output/centrifuge/test.report.txt
- path: output/centrifuge/test.results.txt
- path: output/centrifuge/test.unmapped.fastq.gz
- path: output/centrifuge/versions.yml
- name: centrifuge test_centrifuge_paired_end
command: nextflow run tests/modules/centrifuge -entry test_centrifuge_paired_end -c tests/config/nextflow.config
tags:
- centrifuge
files:
- path: output/centrifuge/test.kreport.txt
- path: output/centrifuge/test.report.txt
- path: output/centrifuge/test.results.txt
- path: output/centrifuge/test.unmapped.fastq.1.gz
- path: output/centrifuge/test.unmapped.fastq.2.gz
- path: output/centrifuge/versions.yml

2
tests/modules/deeparg/downloaddata/main.nf
View file

@ -5,5 +5,5 @@ nextflow.enable.dsl = 2
include { DEEPARG_DOWNLOADDATA } from '../../../../modules/deeparg/downloaddata/main.nf'
workflow test_deeparg_downloaddata {
DEEPARG_DOWNLOADDATA ()
DEEPARG_DOWNLOADDATA ( )
}

2
tests/modules/deeparg/predict/main.nf
View file

@ -13,7 +13,7 @@ workflow test_deeparg_predict {
'LS'
]
DEEPARG_DOWNLOADDATA()
DEEPARG_DOWNLOADDATA( )
DEEPARG_PREDICT ( input, DEEPARG_DOWNLOADDATA.out.db )
}

2
tests/modules/gatk4/combinegvcfs/test.yml
View file

@ -5,6 +5,6 @@
- gatk4/combinegvcfs
files:
- path: output/gatk4/test.combined.g.vcf.gz
contains: ['VCFv4.2']
contains: ["VCFv4.2"]
- path: output/gatk4/versions.yml
md5sum: 49d9c467f84b6a99a4da3ef161af26bd

10
tests/modules/gatk4/genotypegvcfs/test.yml
View file

@ -57,10 +57,7 @@
- gatk4/genotypegvcfs
files:
- path: output/gatk4/test.genotyped.vcf.gz
contains:
[
"AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=24.05;SOR=0.693",
]
contains: ["AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=24.05;SOR=0.693"]
- path: output/gatk4/test.genotyped.vcf.gz.tbi
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input
@ -109,8 +106,5 @@
- gatk4/genotypegvcfs
files:
- path: output/gatk4/test.genotyped.vcf.gz
contains:
[
"AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.66;SOR=0.693",
]
contains: ["AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.66;SOR=0.693"]
- path: output/gatk4/test.genotyped.vcf.gz.tbi

8
tests/modules/hmmer/hmmsearch/test.yml
View file

@ -6,7 +6,7 @@
files:
- path: output/hmmer/test.txt.gz
contains:
- '[ok]'
- "[ok]"
- path: output/hmmer/versions.yml
md5sum: ed0808c10abd205c6bd0fb01f45259bb
@ -20,12 +20,12 @@
md5sum: d3121aa33455074c566fb7f8fdcda7b0
- path: output/hmmer/test.domtbl.gz
contains:
- '# [ok]'
- "# [ok]"
- path: output/hmmer/test.tbl.gz
contains:
- '# [ok]'
- "# [ok]"
- path: output/hmmer/test.txt.gz
contains:
- '[ok]'
- "[ok]"
- path: output/hmmer/versions.yml
md5sum: ebdcb08ae540e840f7b5c4c75a3a2993

4
tests/modules/ichorcna/createpon/test.yml
View file

@ -5,7 +5,7 @@
- ichorcna
files:
- path: output/ichorcna/PoN_median.txt
contains: ['seqnames']
contains: ["seqnames"]
- path: output/ichorcna/versions.yml
md5sum: 59a2121301113cc013bfae65935e07f1
@ -16,6 +16,6 @@
- ichorcna
files:
- path: output/ichorcna/PoN_median.txt
contains: ['seqnames']
contains: ["seqnames"]
- path: output/ichorcna/versions.yml
md5sum: 31a5fcc0075dbe747f7736efbdb99644

4
tests/modules/ichorcna/run/test.yml
View file

@ -5,7 +5,7 @@
- ichorcna/run
files:
- path: output/ichorcna/test.cna.seg
contains: ['Corrected_Copy_Number']
contains: ["Corrected_Copy_Number"]
- path: output/ichorcna/test.params.txt
md5sum: e39a579cdcc9576679f06dc5c22605a7
- path: output/ichorcna/versions.yml
@ -18,7 +18,7 @@
- ichorcna/run
files:
- path: output/ichorcna/test.cna.seg
contains: ['Corrected_Copy_Number']
contains: ["Corrected_Copy_Number"]
- path: output/ichorcna/test.params.txt
md5sum: 0b97e0269cd0b571f5a85890f6ddb181
- path: output/ichorcna/versions.yml

30
tests/modules/manta/germline/main.nf
View file

@ -7,30 +7,28 @@ include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf'
workflow test_manta_germline {
input = [
[ id:'test'], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)],
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)]
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
[],[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
bed = [[],[]]
MANTA_GERMLINE ( input, fasta, fai, bed )
MANTA_GERMLINE ( input, fasta, fai )
}
workflow test_manta_germline_target_bed {
input = [
[ id:'test'], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)],
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)]
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
bed = [
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true),
]
MANTA_GERMLINE ( input, fasta, fai, bed )
MANTA_GERMLINE ( input, fasta, fai )
}
workflow test_manta_germline_target_bed_jointcalling {
@ -39,14 +37,12 @@ workflow test_manta_germline_target_bed_jointcalling {
[file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true)],
[file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),]
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),],
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
bed = [
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true),
]
MANTA_GERMLINE ( input, fasta, fai, bed )
MANTA_GERMLINE ( input, fasta, fai )
}

29
tests/modules/manta/somatic/main.nf
View file

@ -11,13 +11,30 @@ workflow test_manta_somatic {
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
[], []
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
MANTA_SOMATIC ( input, fasta, fai, bed, bed_tbi )
MANTA_SOMATIC ( input, fasta, fai )
}
workflow test_manta_somatic_target_bed {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true),
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
MANTA_SOMATIC ( input, fasta, fai )
}

23
tests/modules/manta/tumoronly/main.nf
View file

@ -8,28 +8,27 @@ workflow test_manta_tumoronly {
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
[], []
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
bed = []
bed_tbi = []
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
MANTA_TUMORONLY ( input, fasta, fai, bed, bed_tbi )
MANTA_TUMORONLY ( input, fasta, fai )
}
workflow test_manta_tumoronly_target_bed {
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
MANTA_TUMORONLY ( input, fasta, fai, bed, bed_tbi )
MANTA_TUMORONLY ( input, fasta, fai )
}

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

@ -5,6 +5,6 @@
- picard
files:
- path: output/picard/test.dict
contains: ['SN:MT192765.1']
contains: ["SN:MT192765.1"]
- path: output/picard/versions.yml
md5sum: b3d8c7ea65b8a6d3237b153d13fe2014

13
tests/modules/roary/test.yml
View file

@ -26,17 +26,14 @@
- path: output/roary/results/gene_presence_absence.Rtab
contains: ["Gene"]
- path: output/roary/results/gene_presence_absence.csv
contains:
[
'"Gene","Non-unique Gene name","Annotation","No. isolates","No. sequences"',
]
contains: ['"Gene","Non-unique Gene name","Annotation","No. isolates","No. sequences"']
- path: output/roary/results/number_of_conserved_genes.Rtab
contains: ["279"]
contains: ["2"]
- path: output/roary/results/number_of_genes_in_pan_genome.Rtab
contains: ["279"]
contains: ["2"]
- path: output/roary/results/number_of_new_genes.Rtab
contains: ["279"]
contains: ["2"]
- path: output/roary/results/number_of_unique_genes.Rtab
contains: ["279"]
contains: ["2"]
- path: output/roary/results/summary_statistics.txt
md5sum: 3921b5445df6a7ed59408119b8860a58