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Merge pull request #13 from UMCUGenetics/feature/nf-core_clean
NF core base to develop
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‎.gitignore

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# Nextflow
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.nextflow*
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work/
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#JetBrains
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.idea/
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# MacOS
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.DS_Store

‎.nf-core.yml

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lint:
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files_exist:
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- .gitattributes
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- .editorconfig
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- .prettierignore
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- .prettierrc.yml
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- .github/CONTRIBUTING.md
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- .github/ISSUE_TEMPLATE/bug_report.yml
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- .github/ISSUE_TEMPLATE/config.yml
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- .github/ISSUE_TEMPLATE/feature_request.yml
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- .github/PULL_REQUEST_TEMPLATE.md
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- .github/.dockstore.yml
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- .github/workflows/ci.yml
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- .github/workflows/awstest.yml
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- .github/workflows/awsfulltest.yml
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- .github/workflows/branch.yml
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- .github/workflows/linting_comment.yml
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- .github/workflows/linting.yml
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- CODE_OF_CONDUCT.md
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- CHANGELOG.md
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- CITATIONS.md
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- assets/email_template.html
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- assets/email_template.txt
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- assets/sendmail_template.txt
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- assets/nf-core-DxNextflowRNA_logo_light.png
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- assets/nf-core-dxnextflowrna_logo_light.png
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- conf/igenomes.config
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- conf/modules.config
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- conf/test.config
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- conf/test_full.config
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- docs/images/nf-core-DxNextflowRNA_logo_light.png
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- docs/images/nf-core-DxNextflowRNA_logo_dark.png
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- docs/output.md
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- docs/README.md
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- docs/README.md
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- docs/usage.md
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- lib/nfcore_external_java_deps.jar
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- lib/NfcoreTemplate.groovy
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- lib/Utils.groovy
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- lib/WorkflowMain.groovy
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- lib/WorkflowDxNextflowRNA.groovy
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- pyproject.toml
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files_unchanged:
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- .github/ISSUE_TEMPLATE/bug_report.yml
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- .github/workflows/linting.yml
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- .gitignore
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- CODE_OF_CONDUCT.md
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- assets/nf-core-dxnextflowrna_logo_light.png
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- docs/images/nf-core-dxnextflowrna_logo_light.png
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- docs/images/nf-core-dxnextflowrna_logo_dark.png
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multiqc_config:
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- report_comment
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nextflow_config:
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- dag.enabled
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- dag.file
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- manifest.name
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- manifest.homePage
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- params.outdir
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- params.input
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- params.validationShowHiddenParams
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- params.validationSchemaIgnoreParams
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- process.cpus
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- process.memory
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- process.time
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- custom_config
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repository_type: pipeline

‎LICENSE

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MIT License
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Copyright (c) UMCU Genetics
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎README.md

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# UMCUGenetics-DxNextflowRNA
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To run the workflow please use the following command (there will be bash script for the next version):
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[![GitHub Actions CI Status](https://github.com/UMCUGenetics/dxnextflowrna/workflows/nf-core%20CI/badge.svg)](https://github.com/UMCUGenetics/dxnextflowrna/actions?query=workflow%3A%22nf-core+CI%22)
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[![GitHub Actions Linting Status](https://github.com/UMCUGenetics/dxnextflowrna/workflows/nf-core%20linting/badge.svg)](https://github.com/UMCUGenetics/dxnextflowrna/actions?query=workflow%3A%22nf-core+linting%22)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
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nextflow run -ansi-log false main.nf
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[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
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[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
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# DxNextflowRNA
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UMCU Genetics Nextflow RNA workflow
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## Usage
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```bash
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export NXF_JAVA_HOME='/hpc/diaggen/projects/woc/rna/tools/jdk-18.0.2.1'
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/hpc/diaggen/projects/woc/rna/tools/nextflow run DxNextflowRNA --input /hpc/diaggen/projects/woc/rna/testdata/fastq --outdir ...
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```
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## Citations
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<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
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<!-- If you use DxNextflowRNA for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
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This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
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> **The nf-core framework for community-curated bioinformatics pipelines.**
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>
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> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
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>
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> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).

‎assets/multiqc_config.yml

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top_modules:
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- 'fastqc'

‎conf/base.config

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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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UMCUGenetics/DxNextflowRNA Nextflow base config file
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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process {
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// Defaults for all processes, based on HPC defaults
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cpus = { 2 * task.attempt }
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memory = { 10.GB * task.attempt }
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time = { 1.h * task.attempt }
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errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
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maxRetries = 1
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maxErrors = '-1'
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executor = 'slurm'
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queue = 'cpu'
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// clusterOptions = "$params.cluster_options"
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// Process-specific resource requirements
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// See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
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withLabel:process_single {
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cpus = { 2 }
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memory = { 8.GB * task.attempt }
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time = { 4.h * task.attempt }
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}
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withLabel:process_low {
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cpus = { 2 * task.attempt }
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memory = { 16.GB * task.attempt }
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time = { 4.h * task.attempt }
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}
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withLabel:process_medium {
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cpus = { 6 * task.attempt }
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memory = { 32.GB * task.attempt }
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time = { 8.h * task.attempt }
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}
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withLabel:process_high {
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cpus = { 12 * task.attempt }
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memory = { 64.GB * task.attempt }
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time = { 16.h * task.attempt }
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}
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withLabel:process_long {
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time = { 20.h * task.attempt }
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}
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withLabel:process_high_memory {
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memory = { 128.GB * task.attempt }
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}
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withLabel:error_ignore {
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errorStrategy = 'ignore'
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}
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withLabel:error_retry {
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errorStrategy = 'retry'
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maxRetries = 2
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}
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}
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singularity {
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enabled = true
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runOptions = '-B /hpc:/hpc -B $TMPDIR:$TMPDIR'
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autoMounts = true
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cacheDir = '/hpc/diaggen/projects/woc/rna/container'
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}
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executor {
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queueSize = 1000
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pollInterval = '1min'
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queueStatInterval = '5min'
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submitRatelimit = '10sec'
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}
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mail {
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smtp.host = 'localhost'
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}

‎conf/modules.config

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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Config file for defining DSL2 per module options and publishing paths
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Available keys to override module options:
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ext.args = Additional arguments appended to command in module.
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ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
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ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
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ext.prefix = File name prefix for output files.
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----------------------------------------------------------------------------------------
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*/
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process {
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withName: FASTQC {
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ext.args = '--quiet'
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publishDir = [
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[path: "$params.outdir/QC/", mode: params.publish_dir_mode, pattern: '*_{fastqc.html}']
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]
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cpus = 2
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memory = { 8.GB * task.attempt }
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time = { 15.m * task.attempt }
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}
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withName: SAMTOOLS_MERGE {
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cpus = { 8 * task.attempt }
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memory = { 8.GB * task.attempt }
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time = { 1.h * task.attempt }
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}
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withName: STAR_ALIGN {
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cpus = { 12 * task.attempt }
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memory = { 40.GB * task.attempt }
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time = { 1.h * task.attempt }
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ext.args = '--readFilesCommand zcat --outSAMtype BAM SortedByCoordinate'
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}
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withName: MULTIQC {
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publishDir = [
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path: { "${params.outdir}/QC" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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}
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withName: UMITOOLS_DEDUP {
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ext.args = "--umi-separator=:"
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ext.prefix = { "${meta.id}.markdup" }
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publishDir = [
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[path: "$params.outdir/bam_files/", mode: params.publish_dir_mode, pattern: '*.ba*']
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]
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clusterOptions = "--gres=tmpspace:50G"
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}
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withName: SUBREAD_FEATURECOUNTS {
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publishDir = [
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[path: "$params.outdir/feature_counts/", mode: params.publish_dir_mode, pattern: '*featureCounts.txt*'],
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]
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}
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}

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