From ce39096f32d94071a9fdd2aab6e93c3bfaecbe7a Mon Sep 17 00:00:00 2001 From: Giuseppe Martone <46596039+giusmar@users.noreply.github.com> Date: Tue, 4 Oct 2022 10:44:19 +0200 Subject: [PATCH 1/9] Create tigem.config --- conf/tigem.config | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 conf/tigem.config diff --git a/conf/tigem.config b/conf/tigem.config new file mode 100644 index 0000000..1e5adea --- /dev/null +++ b/conf/tigem.config @@ -0,0 +1,31 @@ +params { + config_profile_description = 'Telethon Institute of Genetic and Medicine (TIGEM) provided by nf-core/configs.' + config_profile_contact = 'Giuseppe Martone (@giusmar)' + config_profile_url = 'https://github.com/giusmar' +} + +process.executor = 'slurm' +google.zone = 'europe-west1' + +singularity { + enabled = true + autoMounts = true + cacheDir = 'work/singularity' +} + +timeline { + enabled = true + file = "${params.outdir}/execution/timeline.html" +} +report { + enabled = true + file = "${params.outdir}/execution/report.html" +} +trace { + enabled = true + file = "${params.outdir}/execution/trace.txt" +} +dag { + enabled = true + file = "${params.outdir}/execution/pipeline.svg" +} From da0482a904fb3ec4d9d6f92a942db89f79ecc7a4 Mon Sep 17 00:00:00 2001 From: Giuseppe Martone <46596039+giusmar@users.noreply.github.com> Date: Tue, 4 Oct 2022 10:52:50 +0200 Subject: [PATCH 2/9] Create tigem.md --- docs/tigem.md | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 docs/tigem.md diff --git a/docs/tigem.md b/docs/tigem.md new file mode 100644 index 0000000..6997e82 --- /dev/null +++ b/docs/tigem.md @@ -0,0 +1,7 @@ +# nf-core/configs: TIGEM configuration + +To use, run the pipeline with -profile tigem. This will download and launch the tigem.config which has been pre-configured with a setup suitable for the TIGEM personal biocluster. + +--- + +For this pipeline you need a docker container containing the tools needed for the specific pipeline. You can find the docker containers on giusmar docker hub profile. A docker image containing the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. From 2479c1e7e8af9c512d11ea5023d940eb71d18337 Mon Sep 17 00:00:00 2001 From: Giuseppe Martone <46596039+giusmar@users.noreply.github.com> Date: Tue, 4 Oct 2022 10:53:27 +0200 Subject: [PATCH 3/9] Update tigem.md --- docs/tigem.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tigem.md b/docs/tigem.md index 6997e82..31e42de 100644 --- a/docs/tigem.md +++ b/docs/tigem.md @@ -1,6 +1,6 @@ # nf-core/configs: TIGEM configuration -To use, run the pipeline with -profile tigem. This will download and launch the tigem.config which has been pre-configured with a setup suitable for the TIGEM personal biocluster. +To use, run the pipeline with `-profile tigem`. This will download and launch the tigem.config which has been pre-configured with a setup suitable for the TIGEM personal biocluster. --- From bde7502ed278e90a3c0b8071ace5f65b0b30d330 Mon Sep 17 00:00:00 2001 From: Giuseppe Martone <46596039+giusmar@users.noreply.github.com> Date: Tue, 4 Oct 2022 10:54:13 +0200 Subject: [PATCH 4/9] Update nfcore_custom.config --- nfcore_custom.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nfcore_custom.config b/nfcore_custom.config index aba5349..97b66f2 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -69,6 +69,7 @@ profiles { sanger { includeConfig "${params.custom_config_base}/conf/sanger.config"} sbc_sharc { includeConfig "${params.custom_config_base}/conf/sbc_sharc.config"} seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"} + tigem { includeConfig "${params.custom_config_base}/conf/tigem.config"} uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" } unibe_ibu { includeConfig "${params.custom_config_base}/conf/unibe_ibu.config" } uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" } From a4244eb3462475bd90109f06a2cdb8cb03ee1600 Mon Sep 17 00:00:00 2001 From: Giuseppe Martone <46596039+giusmar@users.noreply.github.com> Date: Tue, 4 Oct 2022 11:06:26 +0200 Subject: [PATCH 5/9] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 838d288..da1d6f1 100644 --- a/README.md +++ b/README.md @@ -141,6 +141,7 @@ Currently documentation is available for the following systems: - [SANGER](docs/sanger.md) - [SBC_SHARC](docs/sbc_sharc.md) - [SEG_GLOBE](docs/seg_globe.md) +- [TIGEM](docs/tigem.md) - [UCT_HPC](docs/uct_hpc.md) - [UNIBE_IBU](docs/unibe_ibu.md) - [UPPMAX](docs/uppmax.md) From 5758687a091d40271ccda8716e5a2be3743d0afc Mon Sep 17 00:00:00 2001 From: Giuseppe Martone <46596039+giusmar@users.noreply.github.com> Date: Tue, 4 Oct 2022 11:07:36 +0200 Subject: [PATCH 6/9] Update main.yml --- .github/workflows/main.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index e4d68ca..61af682 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -87,6 +87,7 @@ jobs: - "sanger" - "sbc_sharc" - "seg_globe" + - "tigem" - "uct_hpc" - "unibe_ibu" - "uppmax" From baf857654c60d2fc42dde1601907022a21870047 Mon Sep 17 00:00:00 2001 From: Giuseppe Martone <46596039+giusmar@users.noreply.github.com> Date: Tue, 4 Oct 2022 22:28:38 +0200 Subject: [PATCH 7/9] Update tigem.md --- docs/tigem.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tigem.md b/docs/tigem.md index 31e42de..95d5415 100644 --- a/docs/tigem.md +++ b/docs/tigem.md @@ -4,4 +4,4 @@ To use, run the pipeline with `-profile tigem`. This will download and launch th --- -For this pipeline you need a docker container containing the tools needed for the specific pipeline. You can find the docker containers on giusmar docker hub profile. A docker image containing the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. +This pipeline can be used on TIGEM clusters, in which is installed slurm as job scheduling system, so you can use this config if you have the same tool installed. An additional parameter is google.zone to allow downloading data from GCP for a specific time zone. It should not interfere with a local or an AWS configuration. From e37bccc9d8dff9beff40ae8512b48a0224cd6a00 Mon Sep 17 00:00:00 2001 From: Giuseppe Martone <46596039+giusmar@users.noreply.github.com> Date: Tue, 4 Oct 2022 22:58:50 +0200 Subject: [PATCH 8/9] Update tigem.config --- conf/tigem.config | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/conf/tigem.config b/conf/tigem.config index 1e5adea..b89a4ed 100644 --- a/conf/tigem.config +++ b/conf/tigem.config @@ -12,20 +12,3 @@ singularity { autoMounts = true cacheDir = 'work/singularity' } - -timeline { - enabled = true - file = "${params.outdir}/execution/timeline.html" -} -report { - enabled = true - file = "${params.outdir}/execution/report.html" -} -trace { - enabled = true - file = "${params.outdir}/execution/trace.txt" -} -dag { - enabled = true - file = "${params.outdir}/execution/pipeline.svg" -} From e2146b5905a7b2bf44da160c052c944a6d80055b Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 5 Oct 2022 09:59:07 +0200 Subject: [PATCH 9/9] Update docs/tigem.md --- docs/tigem.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tigem.md b/docs/tigem.md index 95d5415..e562fe4 100644 --- a/docs/tigem.md +++ b/docs/tigem.md @@ -4,4 +4,4 @@ To use, run the pipeline with `-profile tigem`. This will download and launch th --- -This pipeline can be used on TIGEM clusters, in which is installed slurm as job scheduling system, so you can use this config if you have the same tool installed. An additional parameter is google.zone to allow downloading data from GCP for a specific time zone. It should not interfere with a local or an AWS configuration. +This configuration profile can be used on TIGEM clusters, with the pre-installed SLURM job scheduling system. An additional parameter is `google.zone` to allow downloading data from GCP for a specific time zone. It should not interfere with any local or other AWS configuration.