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# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>

#

# SPDX-License-Identifier: AGPL-3.0-or-later

nextflow

.nextflow.log*

.nextflow/

work/

results

workspace.code-workspace

[submodule "src/sge_modules"]

	path = src/psmn_modules

	url = gitlab_lbmc:PSMN/modules.git

# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>

#

# SPDX-License-Identifier: AGPL-3.0-or-later

[submodule "src/.docker_modules/hicstuff/3.1.3/hicstuff"]

	path = src/.docker_modules/hicstuff/3.1.3/hicstuff

	url = git@github.com:koszullab/hicstuff.git

Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/

Upstream-Name: nextflow

Upstream-Contact: Laurent Modolo <laurent.modolo@ens-lyon.fr>

Source: https://gitbio.ens-lyon.fr/LBMC/nextflow

# Sample paragraph, commented out:

#

# Files: src/*

# Copyright: $YEAR $NAME <$CONTACT>

# License: ...

<!--

SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>

SPDX-License-Identifier: CC-BY-SA-4.0

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# Changelog

All notable changes to this project will be documented in this file.

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),

and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [0.4.0] - 2019-11-18

### Added

- Add new tools (star,...)

- conda support at the psmn

## Changed

- configuration simplification

- docker and singularity image download instead of local build

- hidden directories in `src` for project clarity (only `nf_modules` is visible)

## Removed

- conda support at in2p3 with `-profile in2p3_conda`

## [0.3.0] - 2019-05-23

### Added

- Add new tools (umi_tools, fastp,...)

- singularity support at in2p3 with `-profile in2p3`

- conda support at in2p3 with `-profile in2p3_conda`

## [0.2.9] - 2019-03-26

### Added

- Add new tools (fastq, macs2, umitools, ...)

- singularity support

### Changed

- every tool name is now in lowercase in each module section

## [0.2.7] - 2018-10-23

### Added

- Add new tools (BWA, GATK, sambamba, ...)

## [0.1.0] - 2018-05-06

This is the first working version of the repository as a nextflow module repository