From efbf549975aea11f580454f8ccacf14705e8ddb0 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 6 Jun 2018 10:14:05 +0200
Subject: [PATCH] TP.md: add Kallisto section

---
 doc/TP_experimental_biologists.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/doc/TP_experimental_biologists.md b/doc/TP_experimental_biologists.md
index 9099748..60fb239 100644
--- a/doc/TP_experimental_biologists.md
+++ b/doc/TP_experimental_biologists.md
@@ -344,7 +344,13 @@ Commit your work and test your pipeline with the following command :
 
 ## Kallisto
 
+Kallisto run in two step: the indexation of the reference and the quantification on this index.
 
+You can copy to your `src/RNASeq.nf` file the relevant content of [src/nf_modules/Kallisto/kallisto.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/Kallisto/kallisto.nf) and to your `src/RNASeq.config` file the content of [src/nf_modules/Kallisto/kallisto.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/Kallisto/kallisto.config).
+
+We are going to work with paired-end so only copy the relevant processes. The `index_fasta` process need to take as input the output of your `fasta_from_bed` process. The `fastq` input of your `mapping_fastq` process need to take as input the output of your `index_fasta` process and the `trimming` process.
+
+Commit your work and test your pipeline.
 
 
 
-- 
GitLab