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IARC bioinformatics pipelines and tools (updated on 29/07/2024)

This page lists all the pipelines and tools developed at IARC (mostly nextflow pipelines which are suffixed with -nf). It includes also some useful ressources like courses or data notes and tips/tricks. Finally at the bottom of the page you will also find explanations on how to use nextflow pipelines.

<ins>Table of Content:</ins>

1. IARC pipelines/tools list

• 1a. Raw NGS data processing

• 1b. RNA Seq

• 1c. Single-cell RNA seq

• 1d. QC

• 1e. Variant calling

• 1f. Deep learning pipelines and tools for digital pathology

  • 1f1. Whole slide images (WSI) pre-processing

  • 1f2. Tumor segmentation

  • 1f3. Supervised learning on immunohistochemistry slides

  • 1f4. Self-suprevised feature extractor for WSIs

  • 1f5. Additional tools

• 1g. Other tools/pipelines

2. Courses and data notes

3. Tips & Tricks

4. Coming soon... (only dev branches yet)

5. Nextflow, Docker and Singularity installation and use

• 5a. Nextflow

• 5b. Docker

• 5c. Singularity

• 5d. Usage

• 5e. Updates

• 5f. Help

6. Outdated and unmaintained pipelines and tools

<a name="head1"></a>1. IARC pipelines/tools list

<a name="head1a"></a>1a. Raw NGS data processing

<a name="head1b">1b. RNA Seq

<a name="head1c">1c. Single-cell RNA seq

<a name="head1d">1d. QC

<a name="head1e">1e. Variant calling

<a name="head1f">1f. Deep learning pipelines and tools for digital pathology

<a name="head1f1">1f1. Whole slide images (WSI) pre-processing

<a name="head1f2">1f2. Tumor segmentation with CFlow AD

<a name="head1f3">1f3. Supervised learning on immunohistochemistry slides

<a name="head1f4">1f4. Self-suprevised feature extractor for WSIs

<a name="head1f5">1f5. Additional tools

<a name="head1g">1g. Other tools/pipelines

<a name="head2">2. Courses and data notes

<a name="head3">3.Tips & Tricks

<a name="head4">4. Coming soon... (only dev branches yet)

<a name="head5">5. Nextflow, Docker and Singularity installation and use

<a name="head5a">5a. Nextflow

1. Install java JRE if you don't already have it (7 or higher).

2. Install nextflow.

   curl -fsSL get.nextflow.io | bash
   

   And move it to a location in your $PATH (/usr/local/bin for example here):

   sudo mv nextflow /usr/local/bin
   

<a name="head5b">5b. Docker

To avoid having to installing all dependencies each time you use a pipeline, you can instead install docker and let nextflow dealing with it. Installing docker is system specific (but quite easy in most cases), follow  docker documentation (docker CE is sufficient). Also follow the post-installation step to manage Docker as a non-root user (here for Linux), otherwise you will need to change the sudo option in nextflow docker config scope as described in the nextflow documentation here.

To run nextflow pipeline with Docker, simply add the -with-docker option in the nextflow run command.

<a name="head5c">5c. Singularity

To avoid having to installing all dependencies each time you use a pipeline, you can also install singularity and let nextflow dealing with it.

See documentation here.

In case you want to use the same singularity container - with the exactly same versions of pipeline and tools - on several data over time you may want to pull the container and archive it somewhere :

singularity pull shub://IARCbioinfo/pipeline-nf:v2.2

where "pipeline-nf" should be replaced by the name of the pipeline you want to use (example: RNAseq-nf) and 2.2 by the version of the pipeline you want to use (example: 2.4) This will create a singularity container file: pipeline-nf_v2.2.sif (example: RNAseq-nf_v2.4.sif) that you can then use by specifying it in the nextflow command (see usage)

=> example:

singularity pull shub://IARCbioinfo/RNAseq-nf:v2.4

<a name="head5d">5d. Usage

nextflow run iarcbioinfo/pipeline_name -r X --input_folder xxx --output_folder xxx -params-file xxx.yml -w /scratch/work

OR USING SINGULARITY

nextflow run iarcbioinfo/pipeline_name -r X -profile singularity --input_folder xxx --output_folder xxx -params-file xxx.yml -w /scratch/work

OR USING SINGULARITY WITH SPECIFIC CONTAINER

nextflow run iarcbioinfo/pipeline_name -r X -with-singularity XXX.sif --input_folder xxx --output_folder xxx -params-file xxx.yml -w /scratch/work

<a name="head5e">5e. Updates

You can update the nextflow sofware and the pipeline itself simply using:

nextflow -self-update
nextflow pull iarcbioinfo/pipeline_name

You can also automatically update the pipeline when you run it by adding the option -latest in the nextflow run command. Doing so you will always run the latest version from Github.

<a name="head5f">5f. Help

nextflow run iarcbioinfo/pipeline_name --help

<a name="head6">6. Outdated and unmaintained pipelines and tools