diff --git a/README.md b/README.md index 0dfba8fe623202146267404293bdad5968d74c33..d5568fa9f098214530874165eb6e671ad64e37ff 100644 --- a/README.md +++ b/README.md @@ -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 diff --git a/doc/TP_computational_biologists.md b/doc/TP_computational_biologists.md index 09b9574e5bb2171799e987225389ab4cb39f891b..dddbb7a121834ec8731b446bdc6528bd852cc806 100644 --- a/doc/TP_computational_biologists.md +++ b/doc/TP_computational_biologists.md @@ -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" diff --git a/src/training_dataset.config b/src/training_dataset.config index 00a471c6c4a356b9fd843e7185b6c440ea37bfcb..1fb6161075464de356df5fc0cc47d46cde22f164 100644 --- a/src/training_dataset.config +++ b/src/training_dataset.config @@ -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"