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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/sge_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: ...

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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, ...)

### Changed

- `sge` profile is now called `psmn` profile to prepare tests in the CCIN2P3

- every `psmn` config file has an update configuration for mono or 16 cpus queues

- update process naming to follow new nextflow format

## [0.2.6] - 2018-08-23

### Added

- Added `src/training_dataset.nf` to build a small training dataset from NGS data

## [0.1.0] - 2018-05-06

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

<!--

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

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

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# Contributing

When contributing to this repository, please first discuss the change you wish to make via issue,

email, or any other method with the owners of this repository before making a change. 

When contributing to this repository, please first discuss the change you wish to make via issues,

email, or on the [ENS-Bioinfo channel](https://matrix.to/#/#ens-bioinfo:matrix.org) before making a change. 

## Forking

In git, the [action of forking](https://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project) means that you are going to make your own private copy of a repository. You can then write modifications in your project, and if they are of interest for the source repository create a merge request (here [LBMC/nextflow](https://gitbio.ens-lyon.fr/LBMC/nextflow)). Merge requests are sent to the source repository to ask the maintainers to integrate modifications.

![merge request button](./doc/img/merge_request.png)

## Project organization

The `LBMC/nextflow` project is structured as follows:

- all the code is in the `src/` folder

- scripts downloading external tools should download them in the `bin/` folder

- all the documentation (including this file) can be found int he `doc/` folder

- the `data` and `results` folders contain the data and results of your pipelines and are ignored by `git`

## Code structure

The `src/` folder is where we want to save the pipeline (`.nf`) scripts. This folder also contains

- the `src/install_nextflow.sh` to install the nextflow executable at the root of the project.

- some pipelines examples (like the one build during the nf_pratical)

- the `src/nextflow.config` global configuration file which contains the `docker`, `singularity`, `psmn` and `ccin2p3` profiles.

- the `src/nf_modules` folder contains per tools `main.nf` modules with predefined process that users can import in their projects with the [DSL2](https://www.nextflow.io/docs/latest/dsl2.html)

But also some hidden folders that users don't need to see when building their pipeline:

- the `src/.docker_modules` contains the recipes for the `docker` containers used in the `src/nf_modules/<tool_names>/main.nf` files

- the `src/.singularity_in2p3` and `src/.singularity_psmn` are symbolic links to the shared folder where the singularity images are downloaded on the PSMN and CCIN2P3 

# Proposing a new tool

Each tool named `<tool_name>` must have two dedicated folders:

- [`src/nf_modules/<tool_name>`](./src/nf_modules/fastp/) where users can find `.nf` files to include

- [`src/.docker_modules/<tool_name>/<version_number>`](./src/.docker_modules/fastp/0.20.1/) where we have the [`Dockerfile`](./src/.docker_modules/fastp/0.20.1/Dockerfile) to construct the container used in the `main.nf` file

## `src/nf_module` guide lines

We are going to take the [`fastp`, `nf_module`](./src/nf_modules/fastp/) as an example.

The [`src/nf_modules/<tool_name>`](./src/nf_modules/fastp/) should contain a [`main.nf`](./src/nf_modules/fastp/main.nf) file that describe at least one process using `<tool_name>`

### container informations

The first two lines of [`main.nf`](./src/nf_modules/fastp/main.nf) should define two variables

```Groovy

version = "0.20.1"

container_url = "lbmc/fastp:${version}"

```

we can then use the `container_url` definition in each `process` in the `container` attribute.

In addition to the `container` directive, each `process` should have one of the following `label` attributes (defined in the `src/nextflow.config` file)

- `big_mem_mono_cpus`

- `big_mem_multi_cpus`

- `small_mem_mono_cpus`

- `small_mem_multi_cpus`

```Groovy

process fastp {

  container = "${container_url}"

  label = "big_mem_multi_cpus"

  ...

}

```

### process options

Before each process, you should declare at least two `params.` variables:

- A `params.<process_name>` defaulting to `""` (empty string) to allow user to add more command line option to your process without rewriting the process definition

- A `params.<process_name>_out` defaulting to `""` (empty string) that define the `results/` subfolder where the process output should be copied if the user wants to save the process output

```Groovy

params.fastp = ""

params.fastp_out = ""

process fastp {

  container = "${container_url}"

  label "big_mem_multi_cpus"

  if (params.fastp_out != "") {

    publishDir "results/${params.fastp_out}", mode: 'copy'

  }

  ...

  script:

"""

fastp --thread ${task.cpus} \

${params.fastp} \

...

"""

}

```

The user can then change the value of these variables:

- from the command line `--fastp "--trim_head1=10"``

- with the `include` command within their pipeline: `include { fastq } from "nf_modules/fastq/main" addParams(fastq_out: "QC/fastq/")

- by defining the variable within their pipeline: `params.fastq_out = "QC/fastq/"

### `input` and `output` format

You should always use `tuple` for input and output channel format with at least:

- a `val` containing variable(s) related to the item

- a `path` for the file(s) that you want to process

for example:

```Groovy

process fastp {

  container = "${container_url}"

  label "big_mem_multi_cpus"

  tag "$file_id"

  if (params.fastp_out != "") {

    publishDir "results/${params.fastp_out}", mode: 'copy'

  }

  input:

  tuple val(file_id), path(reads)

  output:

    tuple val(file_id), path("*.fastq.gz"), emit: fastq

    tuple val(file_id), path("*.html"), emit: html

    tuple val(file_id), path("*.json"), emit: report

...

```

Here `file_id` can be anything from a simple identifier to a list of several variables.

In which case the first item of the List should be usable as a file prefix.

So you have to keep that in mind if you want to use it to define output file names (you can test for that with `file_id instanceof List`).

In some case, the `file_id` may be a Map to have a cleaner access to the `file_id` content by explicit keywords.

If you want to use information within the `file_id` to name outputs in your `script` section, you can use the following snipet:

```Groovy

  script:

    switch(file_id) {

    case {it instanceof List}:

      file_prefix = file_id[0]

    break

    case {it instanceof Map}:

      file_prefix = file_id.values()[0]

    break

    default:

      file_prefix = file_id

    break

  }

```

and use the `file_prefix` variable.

This also means that channel emitting `path` item should be transformed with at least the following map function:

```Groovy

.map { it -> [it.simpleName, it]}

```

for example

```Groovy

channel

  .fromPath( params.fasta )

  .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }

  .map { it -> [it.simpleName, it]}

  .set { fasta_files }

```

The rationale behind taking a `file_id` and emitting the same `file_id` is to facilitate complex channel operations in pipelines without having to rewrite the `process` blocks.

### dealing with paired-end and single-end data

When oppening fastq files with `channel.fromFilePairs( params.fastq )`, item in the channel have the following shape:

```Groovy

[file_id, [read_1_file, read_2_file]]

```

To make this call more generic, we can use the `size: -1` option, and accept arbitrary number of associated fastq files:

```Groovy

channel.fromFilePairs( params.fastq, size: -1 )

```

Please note we have a code of conduct, please follow it in all your interactions with the project.

will thus give `[file_id, [read_1_file, read_2_file]]` for paired-end data and `[file_id, [read_1_file]]` for single-end data

## Pull Request Process

1. Ensure any install or build dependencies are removed before the end of the layer when doing a 

   build.

2. Update the README.md with details of changes to the interface, this includes new environment 

   variables, exposed ports, useful file locations and container parameters.

3. Increase the version numbers in any examples files and the README.md to the new version that this

   Pull Request would represent. The versioning scheme we use is [SemVer](http://semver.org/).

4. You may merge the Pull Request in once you have the sign-off of two other developers, or if you 

   do not have permission to do that, you may request the second reviewer to merge it for you.

You can the use tests on `read.size()` to define conditional `script` block:

## Code of Conduct

```Groovy

...

  script:

  if (file_id instanceof List){

    file_prefix = file_id[0]

  } else {

    file_prefix = file_id

  }

  if (reads.size() == 2)

  """

  fastp --thread ${task.cpus} \

    ${params.fastp} \

    --in1 ${reads[0]} \

    --in2 ${reads[1]} \

    --out1 ${file_prefix}_R1_trim.fastq.gz \

    --out2 ${file_prefix}_R2_trim.fastq.gz \

    --html ${file_prefix}.html \

    --json ${file_prefix}_fastp.json \

    --report_title ${file_prefix}

  """

  else

  """

  fastp --thread ${task.cpus} \

    ${params.fastp} \

    --in1 ${reads[0]} \

    --out1 ${file_prefix}_trim.fastq.gz \

    --html ${file_prefix}.html \

    --json ${file_prefix}_fastp.json \

    --report_title ${file_prefix}

  """

...

```

### Our Pledge

### Complex processes

In the interest of fostering an open and welcoming environment, we as

contributors and maintainers pledge to making participation in our project and

our community a harassment-free experience for everyone, regardless of age, body

size, disability, ethnicity, gender identity and expression, level of experience,

nationality, personal appearance, race, religion, or sexual identity and

orientation.

Sometime you want to do write complex processes, for example for `fastp` we want to have predefine `fastp` process for different protocols, order of adapter trimming and reads clipping.

We can then use the fact that `process` or named `workflow` can be interchangeably imported with th [DSL2](https://www.nextflow.io/docs/latest/dsl2.html#workflow-composition).

### Our Standards

With the following example, the user can simply include the `fastp` step without knowing that it's a named `workflow` instead of a `process`.

By specifying the `params.fastp_protocol`, the `fastp` step will transparently switch betwen the different `fastp` `process`es.

Here `fastp_default` or `fastp_accel_1splus`, and other protocols can be added later, pipeline will be able to handle these new protocols by simply updating from the `upstream` repository without changing their codes.

Examples of behavior that contributes to creating a positive environment

include:

```Groovy

params.fastp_protocol = ""

workflow fastp {

  take:

    fastq

* Using welcoming and inclusive language

* Being respectful of differing viewpoints and experiences

* Gracefully accepting constructive criticism

* Focusing on what is best for the community

* Showing empathy towards other community members

  main:

  switch(params.fastp_protocol) {

    case "accel_1splus":

      fastp_accel_1splus(fastq)

      fastp_accel_1splus.out.fastq.set{res_fastq}

      fastp_accel_1splus.out.report.set{res_report}

    break;

    default:

      fastp_default(fastq)

      fastp_default.out.fastq.set{res_fastq}

      fastp_default.out.report.set{res_report}

    break;

  }

  emit:

    fastq = res_fastq

    report = res_report

}

```

Examples of unacceptable behavior by participants include:

## `src/.docker_modules` guide lines

* The use of sexualized language or imagery and unwelcome sexual attention or

advances

* Trolling, insulting/derogatory comments, and personal or political attacks

* Public or private harassment

* Publishing others' private information, such as a physical or electronic

  address, without explicit permission

* Other conduct which could reasonably be considered inappropriate in a

  professional setting

We are going to take the [`fastp`, `.docker_modules`](./src/.docker_module/fastp/0.20.1/) as an example.

### Our Responsibilities

The [`src/.docker_modules/<tool_name>/<version_number>`](./src/nf_modules/fastp/0.20.1/) should contain a [`Dockerfile`](./src/.docker_module/fastp/0.20.1/Dockerfile) and a [`docker_init.sh`](./src/.docker_module/fastp/0.20.1/docker_init.sh).

Project maintainers are responsible for clarifying the standards of acceptable

behavior and are expected to take appropriate and fair corrective action in

response to any instances of unacceptable behavior.

### `Dockerfile`

Project maintainers have the right and responsibility to remove, edit, or

reject comments, commits, code, wiki edits, issues, and other contributions

that are not aligned to this Code of Conduct, or to ban temporarily or

permanently any contributor for other behaviors that they deem inappropriate,

threatening, offensive, or harmful.

The [`Dockerfile`](./src/.docker_module/fastp/0.20.1/Dockerfile) shoud contains a `docker` recipe to build a image with `<tool_name>` installed in a system-wide binary folder (`/bin`, `/usr/local/bin/`, etc).

Therefore, your scripts are easily accessible from within the container.

### Scope

This recipe should have:

This Code of Conduct applies both within project spaces and in public spaces

when an individual is representing the project or its community. Examples of

representing a project or community include using an official project e-mail

address, posting via an official social media account, or acting as an appointed

representative at an online or offline event. Representation of a project may be

further defined and clarified by project maintainers.

- an easily changeable `<version_number>` to be able to update the corresponding image to a newer version of the tool

- the `ps` executable (package `procps` in debian)

- a default `bash` command (`CMD ["bash"]`)

### Enforcement

### `docker_init.sh`

Instances of abusive, harassing, or otherwise unacceptable behavior may be

reported by contacting the project team at [INSERT EMAIL ADDRESS]. All

complaints will be reviewed and investigated and will result in a response that

is deemed necessary and appropriate to the circumstances. The project team is

obligated to maintain confidentiality with regard to the reporter of an incident.

Further details of specific enforcement policies may be posted separately.

The [`docker_init.sh`](./src/.docker_module/fastp/0.20.1/docker_init.sh) script is a small sh script with the following content:

Project maintainers who do not follow or enforce the Code of Conduct in good

faith may face temporary or permanent repercussions as determined by other

members of the project's leadership.

```sh

#!/bin/sh

docker pull lbmc/fastp:0.20.1

docker build src/.docker_modules/fastp/0.20.1 -t 'lbmc/fastp:0.20.1'

docker push lbmc/fastp:0.20.1

```

### Attribution

We want to be able to execute the `src/.docker_module/fastp/0.20.1/docker_init.sh` from the root of the project to :

This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,

available at [http://contributor-covenant.org/version/1/4][version]

- try to download the corresponding container if it exists on the [Docker Hub](https://hub.docker.com/repository/docker/lbmc/)

- if not build the container from the correspondig [`Dockerfile`](./src/.docker_module/fastp/0.20.1/Dockerfile) and with the same name as the name we would get from the `docker pull` command

- push the container on the [Docker Hub](https://hub.docker.com/repository/docker/lbmc/) (only [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr) can do this step for the group **lbmc**)

[homepage]: http://contributor-covenant.org

[version]: http://contributor-covenant.org/version/1/4/

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Where the Licensed Rights include Sui Generis Database Rights that apply to Your use of the Licensed Material:

     a.	for the avoidance of doubt, Section 2(a)(1) grants You the right to extract, reuse, reproduce, and Share all or a substantial portion of the contents of the database;

     b.	if You include all or a substantial portion of the database contents in a database in which You have Sui Generis Database Rights, then the database in which You have Sui Generis Database Rights (but not its individual contents) is Adapted Material, including for purposes of Section 3(b); and

     c.	You must comply with the conditions in Section 3(a) if You Share all or a substantial portion of the contents of the database.

For the avoidance of doubt, this Section 4 supplements and does not replace Your obligations under this Public License where the Licensed Rights include other Copyright and Similar Rights.

Section 5 – Disclaimer of Warranties and Limitation of Liability.

     a.	Unless otherwise separately undertaken by the Licensor, to the extent possible, the Licensor offers the Licensed Material as-is and as-available, and makes no representations or warranties of any kind concerning the Licensed Material, whether express, implied, statutory, or other. This includes, without limitation, warranties of title, merchantability, fitness for a particular purpose, non-infringement, absence of latent or other defects, accuracy, or the presence or absence of errors, whether or not known or discoverable. Where disclaimers of warranties are not allowed in full or in part, this disclaimer may not apply to You.

     b.	To the extent possible, in no event will the Licensor be liable to You on any legal theory (including, without limitation, negligence) or otherwise for any direct, special, indirect, incidental, consequential, punitive, exemplary, or other losses, costs, expenses, or damages arising out of this Public License or use of the Licensed Material, even if the Licensor has been advised of the possibility of such losses, costs, expenses, or damages. Where a limitation of liability is not allowed in full or in part, this limitation may not apply to You.

     c.	The disclaimer of warranties and limitation of liability provided above shall be interpreted in a manner that, to the extent possible, most closely approximates an absolute disclaimer and waiver of all liability.

Section 6 – Term and Termination.

     a.	This Public License applies for the term of the Copyright and Similar Rights licensed here. However, if You fail to comply with this Public License, then Your rights under this Public License terminate automatically.

     b.	Where Your right to use the Licensed Material has terminated under Section 6(a), it reinstates:

          1. automatically as of the date the violation is cured, provided it is cured within 30 days of Your discovery of the violation; or

          2. upon express reinstatement by the Licensor.

     c.	For the avoidance of doubt, this Section 6(b) does not affect any right the Licensor may have to seek remedies for Your violations of this Public License.

     d.	For the avoidance of doubt, the Licensor may also offer the Licensed Material under separate terms or conditions or stop distributing the Licensed Material at any time; however, doing so will not terminate this Public License.

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Section 7 – Other Terms and Conditions.

     a.	The Licensor shall not be bound by any additional or different terms or conditions communicated by You unless expressly agreed.

     b.	Any arrangements, understandings, or agreements regarding the Licensed Material not stated herein are separate from and independent of the terms and conditions of this Public License.

Section 8 – Interpretation.

     a.	For the avoidance of doubt, this Public License does not, and shall not be interpreted to, reduce, limit, restrict, or impose conditions on any use of the Licensed Material that could lawfully be made without permission under this Public License.

     b.	To the extent possible, if any provision of this Public License is deemed unenforceable, it shall be automatically reformed to the minimum extent necessary to make it enforceable. If the provision cannot be reformed, it shall be severed from this Public License without affecting the enforceability of the remaining terms and conditions.

     c.	No term or condition of this Public License will be waived and no failure to comply consented to unless expressly agreed to by the Licensor.

     d.	Nothing in this Public License constitutes or may be interpreted as a limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or You, including from the legal processes of any jurisdiction or authority.

Creative Commons is not a party to its public licenses. Notwithstanding, Creative Commons may elect to apply one of its public licenses to material it publishes and in those instances will be considered the “Licensor.” Except for the limited purpose of indicating that material is shared under a Creative Commons public license or as otherwise permitted by the Creative Commons policies published at creativecommons.org/policies, Creative Commons does not authorize the use of the trademark “Creative Commons” or any other trademark or logo of Creative Commons without its prior written consent including, without limitation, in connection with any unauthorized modifications to any of its public licenses or any other arrangements, understandings, or agreements concerning use of licensed material. For the avoidance of doubt, this paragraph does not form part of the public licenses.

Creative Commons may be contacted at creativecommons.org.

<!--

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

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

-->

# nextflow pipeline

This repository is a template and a library repository to help you build nextflow pipeline.

You can fork this repository to build your own pipeline.

To get the last commits from this repository into your fork use the following commands:

```sh

git remote add upstream gitlab_lbmc:pipelines/nextflow.git

git pull upstream master

```

## Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

### Prerequisites

To run nextflow on you computer you need to have java (>= 1.8) installed.

## Getting the last updates

```sh

java --version

```

To be able to easily test tools already implemented for nextflow on your computer (`src/nf_modules/` to see their list). You need to have docker installed.

```sh

docker run hello-world

```

### Installing

To install nextflow on you computer simply run the following command:

```sh

src/install_nextflow.sh

```

Then to initialize a given tools run the following command:

```sh

src/docker_modules/<tool_name>/<tool_version>/docker_init.sh

```

For example to initialize `file_handle` version `0.1.1`, run:

To get the last commits from this repository into your fork use the following commands:

For the first time:

```sh

src/docker_modules/file_handle/0.1.1/docker_init.sh

git remote add upstream git@gitbio.ens-lyon.fr:LBMC/nextflow.git

git pull upstream master

```

To initialize all the tools:

Then to make an update:

```sh

find src/docker_modules/ -name "docker_init.sh" | awk '{system($0)}'

git pull upstream master

git merge upstream/master

```

## Running the tests

To run tests we first need to get a training set

```sh

cd data

git clone -c http.sslVerify=false https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset.git

cp tiny_dataset/fastq/tiny_R1.fastq tiny_dataset/fastq/tiny2_R1.fastq

cp tiny_dataset/fastq/tiny_R2.fastq tiny_dataset/fastq/tiny2_R2.fastq

cp tiny_dataset/fastq/tiny_S.fastq tiny_dataset/fastq/tiny2_S.fastq

cd ..

```

## Getting Started

Then to run the tests for a given tools run the following command:

These instructions will get you a copy of the project as a template when you want to build your own pipeline.

```sh

src/nf_modules/<tool_name>/<tool_version>/tests.sh

```

[you can follow them here.](doc/getting_started.md)

For example to run the tests on `Bowtie2` run:

## Building your pipeline

```sh

src/nf_modules/Bowtie2/tests.sh

```

You can follow the [building your pipeline guide](./doc/building_your_pipeline.md) for a gentle introduction to `nextflow` and taking advantage of this template to build your pipelines.

## Available tools

| tool | nf module | docker module | sge module |

|------|:---------:|:-------------:|:----------:|

BEDtools | ok | ok | ok

Bowtie | ok | ok | **no**

Bowtie2 | ok | ok | ok

canu | ok | ok | ok

cutadapt | ok | ok | ok

deepTools | **no** | ok | ok

FastQC | ok | ok | ok

file_handle | **no** | ok | ok

HISAT2 | **no** | ok | **no**

HTSeq | ok | ok | ok

Kallisto | ok | ok | ok

MACS2 | **no** | ok | ok

MultiQC | ok | ok | ok

MUSIC | **no** | ok | ok

picard | **no** | ok | ok

pigz | **no** | ok | ok

RSEM | ok | ok | ok

SAMtools | ok | ok | ok

SRAtoolkit | ok | ok | ok

Salmon | **no** | ok | ok

TopHat | **no** | ok | ok

Trimmomatic | **no** | ok | ok

UrQt | ok | ok | ok

## Existing Nextflow pipeline

Before starting a new project, you can check if someone else didn’t already to the work !

- [on the nextflow project page](./doc/nf_projects.md)

- [on the nf-core project](https://nf-co.re/pipelines)

## Contributing

Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduct, and the process for submitting pull requests to us.

## Versioning

We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tags). 

If you want to add more tools to this project, please read the [CONTRIBUTING.md](CONTRIBUTING.md).

## Authors

* **Laurent Modolo** - *Initial work*

See also the list of [contributors](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/graphs/master) who participated in this project.

See also the list of [contributors](https://gitbio.ens-lyon.fr/pipelines/nextflow/graphs/master) who participated in this project.

## License

This project is licensed under the CeCiLL License- see the [LICENSE](LICENSE) file for details

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

#

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

*

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

#

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

*

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

#

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

*.pdf

all: TP_experimental_biologists.pdf TP_computational_biologists.pdf

TP_experimental_biologists.pdf: TP_experimental_biologists.md

	R -e 'require(rmarkdown); rmarkdown::render("TP_experimental_biologists.md")'

TP_computational_biologists.pdf: TP_computational_biologists.md

	R -e 'require(rmarkdown); rmarkdown::render("TP_computational_biologists.md")'

---

title: "TP for computational biologists"

author: Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr)

date: 20 Jun 2018

output:

pdf_document:

toc: true

toc_depth: 3

    number_sections: true

highlight: tango

    latex_engine: xelatex

---

The goal of this practical is to learn how to *wrap* tools in [Docker](https://www.docker.com/what-docker) or [Environment Module](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules) to make them available to nextflow on a personal computer or at the [PSMN](http://www.ens-lyon.fr/PSMN/doku.php).

Here we assume that you followed the [TP for experimental biologists](./TP_experimental_biologists.md), and that you know the basics of [Docker containers](https://www.docker.com/what-container) and [Environment Module](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules). We are also going to assume that you know how to build and use a nextflow pipeline from the template [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow).

For the practical you can either work with the WebIDE of Gitlab, or locally as described in the [git: basis formation](https://gitlab.biologie.ens-lyon.fr/formations/git_basis).

# Docker

To run a tool within a [Docker container](https://www.docker.com/what-container) you need to write a `Dockerfile`.

[`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile) are found in the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) project under `src/docker_modules/`. Each [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile) is paired with a [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh) file like following the example for `Kallisto` version `0.43.1`:

```sh

$ ls -l src/docker_modules/Kallisto/0.43.1/

total 16K                                                                        

drwxr-xr-x 2 laurent users 4.0K Jun 5 19:06 ./                                  

drwxr-xr-x 3 laurent users 4.0K Jun 6 09:49 ../                                 

-rw-r--r-- 1 laurent users  587 Jun  5 19:06 Dockerfile                          

-rwxr-xr-x 1 laurent users 79 Jun 5 19:06 docker_init.sh*                     

```

## [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh)

The [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh) is a simple sh script with executable rights (`chmod +x`). By executing this script, the user creates a [Docker container](https://www.docker.com/what-container) with the tool installed a specific version. You can check the [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh) file of any implemented tools as a template.

Remember that the name of the [container](https://www.docker.com/what-container) must be in lower case and in the format `<tool_name>:<version>`.

For tools without a version number you can use a commit hash instead.

## [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile)

The recipe to wrap your tool in a [Docker container](https://www.docker.com/what-container) is written in a [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile) file.

For `Kallisto` version `0.44.0` the header of the `Dockerfile` is :

```Docker

FROM ubuntu:18.04

MAINTAINER Laurent Modolo

ENV KALLISTO_VERSION=0.44.0

```

The `FROM` instruction means that the [container](https://www.docker.com/what-container) is initialized from a bare installation of Ubuntu 18.04. You can check the versions of Ubuntu available [here](https://hub.docker.com/_/ubuntu/) or others operating systems like [debian](https://hub.docker.com/_/debian/) or [worst](https://hub.docker.com/r/microsoft/windowsservercore/).

Then we declare the *maintainer* of the container. Before declaring an environment variable for the container named `KALLISTO_VERSION`, which contains the version of the tool wrapped. This this bash variable will be declared for the user root within the [container](https://www.docker.com/what-container).

You should always declare a variable `TOOLSNAME_VERSION` that contains the version number of commit number of the tools you wrap. In simple cases you just have to modify this line to create a new `Dockerfile` for another version of the tool.

The following lines of the [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile) are a succession of `bash` commands executed as the **root** user within the container.

Each `RUN` block is run sequentially by `Docker`. If there is an error or modifications in a `RUN` block, only this block and the following `RUN` will be executed.

You can learn more about the building of Docker containers [here](https://docs.docker.com/engine/reference/builder/#usage).

When you build your [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile), instead of launching many times the [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh) script to tests your [container](https://www.docker.com/what-container), you can connect to a base container in interactive mode to launch tests your commands.

```sh

docker run -it ubuntu:18.04 bash

KALLISTO_VERSION=0.44.0

```

# SGE / [PSMN](http://www.ens-lyon.fr/PSMN/doku.php)

To run easily tools on the [PSMN](http://www.ens-lyon.fr/PSMN/doku.php), you need to build your own [Environment Module](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules).

You can read the Contributing guide for the [PMSN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) project [here](https://gitlab.biologie.ens-lyon.fr/PSMN/modules/blob/master/CONTRIBUTING.md)

# Nextflow

The last step to wrap your tool is to make it available in nextflow. For this you need to create at least 4 files, like the following for Kallisto version `0.44.0`:

```sh

ls -lR src/nf_modules/Kallisto

src/nf_modules/Kallisto/:

total 12

-rw-r--r-- 1 laurent users 866 Jun 18 17:13 kallisto.config

-rw-r--r-- 1 laurent users 2711 Jun 18 17:13 kallisto.nf

drwxr-xr-x 2 laurent users 4096 Jun 18 17:14 tests/

src/nf_modules/Kallisto/tests:

total 16

-rw-r--r-- 1 laurent users 551 Jun 18 17:14 index.nf

-rw-r--r-- 1 laurent users 901 Jun 18 17:14 mapping_paired.nf