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Merge pull request #19 from nf-core/nf-core-template-merge-2.3

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Important! Template update for nf-core/tools v2.3
This commit is contained in:
James A. Fellows Yates 2022-03-17 13:18:29 +01:00 committed by GitHub
commit 9fac82d342
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GPG key ID: 4AEE18F83AFDEB23
25 changed files with 193 additions and 139 deletions
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1
.github/ISSUE_TEMPLATE/bug_report.yml vendored
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@ -1,4 +1,3 @@
name: Bug report
description: Report something that is broken or incorrect
labels: bug

2
.github/PULL_REQUEST_TEMPLATE.md vendored
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@ -19,7 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/taxp
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/taxprofiler/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/taxprofiler _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
- [ ] Make sure your code lints (`nf-core lint`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker` --outdir <OUTDIR>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
- [ ] Output Documentation in `docs/output.md` is updated.
- [ ] `CHANGELOG.md` is updated.

6
.github/workflows/awsfulltest.yml vendored
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@ -14,7 +14,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Launch workflow via tower
uses: nf-core/tower-action@v2
uses: nf-core/tower-action@v3
# TODO nf-core: You can customise AWS full pipeline tests as required
# Add full size test data (but still relatively small datasets for few samples)
# on the `test_full.config` test runs with only one set of parameters
@ -31,4 +31,6 @@ jobs:
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/taxprofiler/results-${{ github.sha }}"
}
profiles: test_full,aws_tower
pre_run_script: 'export NXF_VER=21.10.3'
nextflow_config: |
process.errorStrategy = 'retry'
process.maxRetries = 3

6
.github/workflows/awstest.yml vendored
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@ -11,7 +11,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Launch workflow via tower
uses: nf-core/tower-action@v2
uses: nf-core/tower-action@v3
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@ -25,4 +25,6 @@ jobs:
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/taxprofiler/results-test-${{ github.sha }}"
}
profiles: test,aws_tower
pre_run_script: 'export NXF_VER=21.10.3'
nextflow_config: |
process.errorStrategy = 'retry'
process.maxRetries = 3

4
.github/workflows/ci.yml vendored
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@ -14,7 +14,7 @@ env:
jobs:
test:
name: Run workflow tests
name: Run pipeline with test data
# Only run on push if this is the nf-core dev branch (merged PRs)
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
runs-on: ubuntu-latest
@ -47,4 +47,4 @@ jobs:
# For example: adding multiple test runs with different parameters
# Remember that you can parallelise this by using strategy.matrix
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results

28
.github/workflows/linting.yml vendored
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@ -12,9 +12,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-node@v1
with:
node-version: '10'
- uses: actions/setup-node@v2
- name: Install markdownlint
run: npm install -g markdownlint-cli
- name: Run Markdownlint
@ -51,9 +49,7 @@ jobs:
steps:
- uses: actions/checkout@v2
- uses: actions/setup-node@v1
with:
node-version: '10'
- uses: actions/setup-node@v2
- name: Install editorconfig-checker
run: npm install -g editorconfig-checker
@ -64,14 +60,13 @@ jobs:
YAML:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v1
- uses: actions/setup-node@v1
- name: Checkout
uses: actions/checkout@master
- name: 'Yamllint'
uses: karancode/yamllint-github-action@master
with:
node-version: '10'
- name: Install yaml-lint
run: npm install -g yaml-lint
- name: Run yaml-lint
run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml")
yamllint_file_or_dir: '.'
yamllint_config_filepath: '.yamllint.yml'
# If the above check failed, post a comment on the PR explaining the failure
- name: Post PR comment
@ -84,10 +79,11 @@ jobs:
To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:
* Install `yaml-lint`
* [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`)
* Install `yamllint`
* Install `yamllint` following [this](https://yamllint.readthedocs.io/en/stable/quickstart.html#installing-yamllint)
instructions or alternative install it in your [conda environment](https://anaconda.org/conda-forge/yamllint)
* Fix the markdown errors
* Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")`
* Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml") -c ./.yamllint.yml`
* Fix any reported errors in your YAML files
Once you push these changes the test should pass, and you can hide this comment :+1:

14
.gitpod.yml Normal file
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@ -0,0 +1,14 @@
image: nfcore/gitpod:latest
vscode:
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
# - nextflow.nextflow # Nextflow syntax highlighting
- oderwat.indent-rainbow # Highlight indentation level
- streetsidesoftware.code-spell-checker # Spelling checker for source code

1
.nf-core.yml Normal file
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@ -0,0 +1 @@
repository_type: pipeline

6
.yamllint.yml Normal file
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@ -0,0 +1,6 @@
extends: default
rules:
document-start: disable
line-length: disable
truthy: disable

12
README.md
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@ -56,22 +56,22 @@ On release, automated continuous integration tests run the pipeline on a full-si
3. Download the pipeline and test it on a minimal dataset with a single command:
```console
nextflow run nf-core/taxprofiler -profile test,YOURPROFILE
nextflow run nf-core/taxprofiler -profile test,YOURPROFILE --outdir <OUTDIR>
```
Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
> * The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
> * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
> * If you are using `singularity` and are persistently observing issues downloading Singularity images directly due to timeout or network issues, then you can use the `--singularity_pull_docker_container` parameter to pull and convert the Docker image instead. Alternatively, you can use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
> * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
> - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
> - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
> - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
> - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
4. Start running your own analysis!
<!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
```console
nextflow run nf-core/taxprofiler -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.csv --genome GRCh37
nextflow run nf-core/taxprofiler --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
```
## Documentation

2
bin/check_samplesheet.py
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@ -37,8 +37,6 @@ def print_error(error, context="Line", context_str=""):
print(error_str)
sys.exit(1)
# TODO nf-core: Update the check_samplesheet function
def check_samplesheet(file_in, file_out):
"""
This function checks that the samplesheet follows the following structure:

4
conf/base.config
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@ -1,7 +1,7 @@
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/taxprofiler Nextflow base config file
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
A 'blank slate' config file, appropriate for general use on most high performance
compute environments. Assumes that all software is installed and available on
the PATH. Runs in `local` mode - all jobs will be run on the logged in environment.

80
conf/igenomes.config
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@ -1,7 +1,7 @@
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for iGenomes paths
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Defines reference genomes using iGenome paths.
Can be used by any config that customises the base path using:
$params.igenomes_base / --igenomes_base
@ -13,7 +13,7 @@ params {
genomes {
'GRCh37' {
fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/"
@ -26,7 +26,7 @@ params {
}
'GRCh38' {
fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/"
@ -38,7 +38,7 @@ params {
}
'GRCm38' {
fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/"
@ -51,7 +51,7 @@ params {
}
'TAIR10' {
fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/"
@ -62,7 +62,7 @@ params {
}
'EB2' {
fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/"
@ -72,7 +72,7 @@ params {
}
'UMD3.1' {
fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/"
@ -83,7 +83,7 @@ params {
}
'WBcel235' {
fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/"
@ -94,7 +94,7 @@ params {
}
'CanFam3.1' {
fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/"
@ -105,7 +105,7 @@ params {
}
'GRCz10' {
fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/"
@ -115,7 +115,7 @@ params {
}
'BDGP6' {
fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/"
@ -126,7 +126,7 @@ params {
}
'EquCab2' {
fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/"
@ -137,7 +137,7 @@ params {
}
'EB1' {
fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/"
@ -147,7 +147,7 @@ params {
}
'Galgal4' {
fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/"
@ -157,7 +157,7 @@ params {
}
'Gm01' {
fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/"
@ -167,7 +167,7 @@ params {
}
'Mmul_1' {
fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/"
@ -178,7 +178,7 @@ params {
}
'IRGSP-1.0' {
fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/"
@ -188,7 +188,7 @@ params {
}
'CHIMP2.1.4' {
fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/"
@ -199,7 +199,7 @@ params {
}
'Rnor_5.0' {
fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/"
@ -209,7 +209,7 @@ params {
}
'Rnor_6.0' {
fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/"
@ -219,7 +219,7 @@ params {
}
'R64-1-1' {
fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/"
@ -230,7 +230,7 @@ params {
}
'EF2' {
fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/"
@ -242,7 +242,7 @@ params {
}
'Sbi1' {
fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/"
@ -252,7 +252,7 @@ params {
}
'Sscrofa10.2' {
fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/"
@ -263,7 +263,7 @@ params {
}
'AGPv3' {
fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/"
@ -273,7 +273,7 @@ params {
}
'hg38' {
fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/"
@ -285,7 +285,7 @@ params {
}
'hg19' {
fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/"
@ -298,7 +298,7 @@ params {
}
'mm10' {
fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/"
@ -311,7 +311,7 @@ params {
}
'bosTau8' {
fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/"
@ -321,7 +321,7 @@ params {
}
'ce10' {
fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/"
@ -333,7 +333,7 @@ params {
}
'canFam3' {
fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/"
@ -344,7 +344,7 @@ params {
}
'danRer10' {
fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/"
@ -355,7 +355,7 @@ params {
}
'dm6' {
fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/"
@ -366,7 +366,7 @@ params {
}
'equCab2' {
fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/"
@ -377,7 +377,7 @@ params {
}
'galGal4' {
fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/"
@ -388,7 +388,7 @@ params {
}
'panTro4' {
fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/"
@ -399,7 +399,7 @@ params {
}
'rn6' {
fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/"
@ -409,7 +409,7 @@ params {
}
'sacCer3' {
fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/"
@ -419,7 +419,7 @@ params {
}
'susScr3' {
fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/genome.fa"
bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/"
bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/"

18
conf/modules.config
View file

@ -1,12 +1,12 @@
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Config file for defining DSL2 per module options and publishing paths
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Available keys to override module options:
ext.args = Additional arguments appended to command in module.
ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
ext.prefix = File name prefix for output files.
ext.args = Additional arguments appended to command in module.
ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
ext.prefix = File name prefix for output files.
----------------------------------------------------------------------------------------
*/
@ -14,14 +14,14 @@ process {
publishDir = [
path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
mode: 'copy',
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
withName: SAMPLESHEET_CHECK {
publishDir = [
path: { "${params.outdir}/pipeline_info" },
mode: 'copy',
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
@ -92,7 +92,7 @@ process {
withName: CUSTOM_DUMPSOFTWAREVERSIONS {
publishDir = [
path: { "${params.outdir}/pipeline_info" },
mode: 'copy',
mode: params.publish_dir_mode,
pattern: '*_versions.yml'
]
}

6
conf/test.config
View file

@ -1,11 +1,11 @@
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running minimal tests
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Defines input files and everything required to run a fast and simple pipeline test.
Use as follows:
nextflow run nf-core/taxprofiler -profile test,<docker/singularity>
nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
----------------------------------------------------------------------------------------
*/

6
conf/test_full.config
View file

@ -1,11 +1,11 @@
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running full-size tests
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Defines input files and everything required to run a full size pipeline test.
Use as follows:
nextflow run nf-core/taxprofiler -profile test_full,<docker/singularity>
nextflow run nf-core/taxprofiler -profile test_full,<docker/singularity> --outdir <OUTDIR>
----------------------------------------------------------------------------------------
*/

21
docs/usage.md
View file

@ -57,7 +57,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
The typical command for running the pipeline is as follows:
```console
nextflow run nf-core/taxprofiler --input samplesheet.csv --genome GRCh37 -profile docker
nextflow run nf-core/taxprofiler --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile docker
```
This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
@ -141,11 +141,11 @@ Whilst the default requirements set within the pipeline will hopefully work for
For example, if the nf-core/rnaseq pipeline is failing after multiple re-submissions of the `STAR_ALIGN` process due to an exit code of `137` this would indicate that there is an out of memory issue:
```console
[62/149eb0] NOTE: Process `RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1)
Error executing process > 'RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)'
[62/149eb0] NOTE: Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1)
Error executing process > 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)'
Caused by:
Process `RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137)
Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137)
Command executed:
STAR \
@ -169,17 +169,24 @@ Work dir:
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
```
To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so based on the search results the file we want is `modules/nf-core/software/star/align/main.nf`. If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. Providing you haven't set any other standard nf-core parameters to __cap__ the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB. The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections.
To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN).
We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/software/star/align/main.nf`.
If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9).
The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements.
The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB.
Providing you haven't set any other standard nf-core parameters to **cap** the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB.
The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections.
```nextflow
process {
withName: STAR_ALIGN {
withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN' {
memory = 100.GB
}
}
```
> **NB:** We specify just the process name i.e. `STAR_ALIGN` in the config file and not the full task name string that is printed to screen in the error message or on the terminal whilst the pipeline is running i.e. `RNASEQ:ALIGN_STAR:STAR_ALIGN`. You may get a warning suggesting that the process selector isn't recognised but you can ignore that if the process name has been specified correctly. This is something that needs to be fixed upstream in core Nextflow.
> **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden.
> If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly.
### Updating containers

4
lib/NfcoreSchema.groovy
View file

@ -27,7 +27,7 @@ class NfcoreSchema {
/* groovylint-disable-next-line UnusedPrivateMethodParameter */
public static void validateParameters(workflow, params, log, schema_filename='nextflow_schema.json') {
def has_error = false
//=====================================================================//
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~//
// Check for nextflow core params and unexpected params
def json = new File(getSchemaPath(workflow, schema_filename=schema_filename)).text
def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions')
@ -135,7 +135,7 @@ class NfcoreSchema {
}
}
//=====================================================================//
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~//
// Validate parameters against the schema
InputStream input_stream = new File(getSchemaPath(workflow, schema_filename=schema_filename)).newInputStream()
JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream))

4
lib/Utils.groovy
View file

@ -29,12 +29,12 @@ class Utils {
conda_check_failed |= !(channels.indexOf('bioconda') < channels.indexOf('defaults'))
if (conda_check_failed) {
log.warn "=============================================================================\n" +
log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
" There is a problem with your Conda configuration!\n\n" +
" You will need to set-up the conda-forge and bioconda channels correctly.\n" +
" Please refer to https://bioconda.github.io/user/install.html#set-up-channels\n" +
" NB: The order of the channels matters!\n" +
"==================================================================================="
"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
}
}
}

4
lib/WorkflowTaxprofiler.groovy
View file

@ -49,11 +49,11 @@ class WorkflowTaxprofiler {
//
private static void genomeExistsError(params, log) {
if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
log.error "=============================================================================\n" +
log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
" Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
" Currently, the available genome keys are:\n" +
" ${params.genomes.keySet().join(", ")}\n" +
"==================================================================================="
"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
System.exit(1)
}
}

24
main.nf
View file

@ -1,8 +1,8 @@
#!/usr/bin/env nextflow
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/taxprofiler
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/taxprofiler
Website: https://nf-co.re/taxprofiler
Slack : https://nfcore.slack.com/channels/taxprofiler
@ -12,25 +12,25 @@
nextflow.enable.dsl = 2
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENOME PARAMETER VALUES
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
VALIDATE & PRINT PARAMETER SUMMARY
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
WorkflowMain.initialise(workflow, params, log)
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOW FOR PIPELINE
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { TAXPROFILER } from './workflows/taxprofiler'
@ -43,9 +43,9 @@ workflow NFCORE_TAXPROFILER {
}
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN ALL WORKFLOWS
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
@ -57,7 +57,7 @@ workflow {
}
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

16
nextflow.config
View file

@ -1,7 +1,7 @@
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/taxprofiler Nextflow config file
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
@ -24,8 +24,9 @@ params {
max_multiqc_email_size = '25.MB'
// Boilerplate options
outdir = './results'
outdir = null
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
@ -75,6 +76,15 @@ try {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/taxprofiler custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/taxprofiler.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/taxprofiler profiles: ${params.custom_config_base}/pipeline/taxprofiler.config")
// }
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {

23
nextflow_schema.json
View file

@ -11,7 +11,8 @@
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": [
"input"
"input",
"outdir"
],
"properties": {
"input": {
@ -26,8 +27,8 @@
},
"outdir": {
"type": "string",
"description": "Path to the output directory where the results will be saved.",
"default": "./results",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open"
},
"email": {
@ -169,6 +170,22 @@
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"publish_dir_mode": {
"type": "string",
"default": "copy",
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": [
"symlink",
"rellink",
"link",
"copy",
"copyNoFollow",
"move"
],
"hidden": true
},
"email_on_fail": {
"type": "string",
"description": "Email address for completion summary, only when pipeline fails.",

12
subworkflows/local/input_check.nf
View file

@ -35,26 +35,28 @@ workflow INPUT_CHECK {
}
// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
def create_fastq_channels(LinkedHashMap row) {
def create_fastq_channel(LinkedHashMap row) {
// create meta map
def meta = [:]
meta.id = row.sample
meta.run_accession = row.run_accession
meta.instrument_platform = row.instrument_platform
meta.single_end = row.single_end.toBoolean()
def array = []
// add path(s) of the fastq file(s) to the meta map
def fastq_meta = []
if (!file(row.fastq_1).exists()) {
exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}"
}
if (meta.single_end) {
array = [ meta, [ file(row.fastq_1) ] ]
fastq_meta = [ meta, [ file(row.fastq_1) ] ]
} else {
if (!file(row.fastq_2).exists()) {
exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
}
array = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
}
return array
return fastq_meta
}
// Function to get list of [ meta, fasta ]

28
workflows/taxprofiler.nf
View file

@ -1,7 +1,7 @@
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
VALIDATE INPUTS
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
@ -19,18 +19,18 @@ if (params.input ) { ch_input = file(params.input) } else { exit 1, '
if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CONFIG FILES
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
ch_multiqc_config = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true)
ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT LOCAL MODULES/SUBWORKFLOWS
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
@ -43,9 +43,9 @@ include { FASTQ_PREPROCESSING } from '../subworkflows/local/preprocessing'
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT NF-CORE MODULES/SUBWORKFLOWS
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
@ -61,9 +61,9 @@ include { KRAKEN2_KRAKEN2 } from '../modules/nf-core/modules/kraken2
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
// Info required for completion email and summary
@ -213,9 +213,9 @@ workflow TAXPROFILER {
}
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
COMPLETION EMAIL AND SUMMARY
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
workflow.onComplete {
@ -226,7 +226,7 @@ workflow.onComplete {
}
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/