Verified Commit 67b9e31d authored by Laurent Modolo's avatar Laurent Modolo
Browse files

fix README url

parent aaa243c8
......@@ -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
```
......
......@@ -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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