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Merge pull request #153 from tkchafin/anaconda_purge
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Anaconda purge
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@tkchafin
tkchafin authored Nov 25, 2024
2 parents c4f45a0 + dd58ec1 commit 4a86006
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4 changes: 2 additions & 2 deletions CITATIONS.md
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## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)
- [Conda](https://conda.org/)

> Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
> conda contributors. conda: A system-level, binary package and environment manager running on all major operating systems and platforms. Computer software. https://github.com/conda/conda
- [Bioconda](https://bioconda.github.io)

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2 changes: 1 addition & 1 deletion README.md
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[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7949384-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7949384)

[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=conda)](https://docs.conda.io/en/latest/)
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/sanger-tol/genomenote)
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4 changes: 2 additions & 2 deletions conf/modules.config
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Expand Up @@ -55,8 +55,8 @@ process {
ext.args = { 'test' in workflow.profile.tokenize(',') ?
// Additional configuration to speed processes up during testing.
// Note: BUSCO *must* see the double-quotes around the parameters
'--tar --metaeuk_parameters \'"-s=2"\' --metaeuk_rerun_parameters \'"-s=2"\''
: '--tar' }
'--tar --metaeuk --metaeuk_parameters \'"-s=2"\' --metaeuk_rerun_parameters \'"-s=2"\''
: '--tar --metaeuk ' }
}

withName: "RESTRUCTUREBUSCODIR" {
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94 changes: 62 additions & 32 deletions modules.json
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Expand Up @@ -7,84 +7,114 @@
"nf-core": {
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"multiqc": {
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"samtools/view": {
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}
}
}
}
}
}
2 changes: 0 additions & 2 deletions modules/nf-core/agat/spstatistics/environment.yml
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40 changes: 24 additions & 16 deletions modules/nf-core/agat/spstatistics/meta.yml
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2 changes: 0 additions & 2 deletions modules/nf-core/agat/sqstatbasic/environment.yml
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40 changes: 24 additions & 16 deletions modules/nf-core/agat/sqstatbasic/meta.yml
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4 changes: 1 addition & 3 deletions modules/nf-core/busco/environment.yml → ...nf-core/bedtools/bamtobed/environment.yml
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17 changes: 14 additions & 3 deletions modules/nf-core/bedtools/bamtobed/main.nf
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