Unverified Commit cdb93acd authored by Laurent Modolo's avatar Laurent Modolo
Browse files

change occurences of sge into psmn

parent fa486dc6
......@@ -78,7 +78,7 @@ src/nf_modules/Bowtie2/tests.sh
## Available tools
| tool | nf module | docker module | sge module |
| tool | nf module | docker module | psmn module |
|------|:---------:|:-------------:|:----------:|
BEDtools | ok | ok | ok
BFCtools |**no** | ok | ok
......
......@@ -95,14 +95,14 @@ total 16
-rwxr-xr-x 1 laurent users 627 Jun 18 17:14 tests.sh*
```
The [`kallisto.config`](./src/nf_modules/Kallisto/kallisto.config) file contains instructions for two profiles : `sge` and `docker`.
The [`kallisto.config`](./src/nf_modules/Kallisto/kallisto.config) file contains instructions for two profiles : `psmn` and `docker`.
The [`kallisto.nf`](./src/nf_modules/Kallisto/kallisto.nf) file contains nextflow processes to use `Kallisto`.
The [`tests/tests.sh`](./src/nf_modules/Kallisto/tests/tests.sh) script (with executable rights), contains a series of nextflow calls on the other `.nf` files of the [`tests/`](./src/nf_modules/kallisto/tests/) folder. Those tests correspond to execution of the processes present in the [`kallisto.nf`](./src/nf_modules/Kallisto/kallisto.nf) file on the [LBMC/tiny_dataset](https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset) dataset with the `docker` profile. You can read the *Running the tests* section of the [README.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md).
## [`kallisto.config`](./src/nf_modules/Kallisto/kallisto.config)
The `.config` file defines the configuration to apply to your process conditionally to the value of the `-profile` option. You must define configuration for at least the `sge` and `docker` profile.
The `.config` file defines the configuration to apply to your process conditionally to the value of the `-profile` option. You must define configuration for at least the `psmn` and `docker` profile.
```Groovy
profiles {
......@@ -112,7 +112,7 @@ profiles {
process {
}
}
sge {
psmn {
process{
}
}
......@@ -134,16 +134,16 @@ process {
}
```
### `sge` profile
### `psmn` profile
The `sge` profile defines for each process all the informations necessary to launch your process on a given queue with SGE at the [PSMN](http://www.ens-lyon.fr/PSMN/doku.php).
The `psmn` profile defines for each process all the informations necessary to launch your process on a given queue with SGE at the [PSMN](http://www.ens-lyon.fr/PSMN/doku.php).
For example, for `Kallisto`, we have:
```Groovy
process{
$index_fasta {
beforeScript = "module purge; module load Kallisto/0.44.0"
executor = "sge"
executor = "psmn"
cpus = 1
memory = "5GB"
time = "6h"
......@@ -154,7 +154,7 @@ process{
}
$mapping_fastq {
beforeScript = "module purge; module load Kallisto/0.44.0"
executor = "sge"
executor = "psmn"
cpus = 4
memory = "5GB"
time = "6h"
......
......@@ -38,11 +38,11 @@ profiles {
}
}
}
sge {
psmn {
process{
$build_synthetic_bed {
beforeScript = "module purge; module load BEDtools/2.25.0"
executor = "sge"
executor = "psmn"
cpus = 1
memory = "5GB"
time = "6h"
......@@ -53,7 +53,7 @@ profiles {
}
$fasta_from_bed {
beforeScript = "module purge; module load BEDtools/2.25.0"
executor = "sge"
executor = "psmn"
cpus = 1
memory = "5GB"
time = "6h"
......
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