From 67b9e31d1464a35ac56531cde351338d173b4f65 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 23 Sep 2021 14:36:15 +0200
Subject: [PATCH] fix README url
---
README.md | 2 +-
doc/building_your_pipeline.md | 14 +++++++-------
2 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/README.md b/README.md
index df5e0ee8..cab03de4 100644
--- a/README.md
+++ b/README.md
@@ -9,7 +9,7 @@ To get the last commits from this repository into your fork use the following co
For the first time:
```sh
-git remote add upstream git@gitbio.ens-lyon.fr:pipelines/nextflow.git
+git remote add upstream git@gitbio.ens-lyon.fr:LBMC/nextflow.git
git pull upstream master
```
diff --git a/doc/building_your_pipeline.md b/doc/building_your_pipeline.md
index f6d05a94..3aa8196f 100644
--- a/doc/building_your_pipeline.md
+++ b/doc/building_your_pipeline.md
@@ -57,10 +57,10 @@ Here is an example of **process**:
```Groovy
process sample_fasta {
input:
- file fasta
+ path fasta
output:
- file "sample.fasta", emit: fasta_sample
+ path "sample.fasta", emit: fasta_sample
script:
"""
@@ -69,20 +69,20 @@ head ${fasta} > sample.fasta
}
```
-We have the process `sample_fasta` that takes fasta `file` input and as output a fasta `file`. The `process` task itself is defined in the `script:` block and within `"""`.
+We have the process `sample_fasta` that takes fasta `path` input and as output a fasta `path`. The `process` task itself is defined in the `script:` block and within `"""`.
```Groovy
input:
-file fasta
+path fasta
```
-When we zoom on the `input:` block, we see that we define a variable `fasta` of type `file`.
+When we zoom on the `input:` block, we see that we define a variable `fasta` of type `path`.
This means that the `sample_fasta` `process` is going to get a flux of fasta file(s).
Nextflow is going to write a file named as the content of the variable `fasta` in the root of the folder where `script:` is executed.
```Groovy
output:
-file "sample.fasta", emit: fasta_sample
+path "sample.fasta", emit: fasta_sample
```
At the end of the script, a file named `sample.fasta` is found in the root the folder where `script:` is executed and will be emitted as `fasta_sample`.
@@ -201,7 +201,7 @@ Every `fasta_sampler` process write a `sample.fasta` file. We need to make the n
```Groovy
output:
-file "*_sample.fasta", emit: fasta_sample
+path "*_sample.fasta", emit: fasta_sample
script:
"""
--
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