From c11c26f15ffa59d576acaa43a931a84b06120903 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?= <60298098+ashildv@users.noreply.github.com> Date: Wed, 20 Jan 2021 23:45:26 +0100 Subject: [PATCH 01/19] Create ceh.config --- conf/ceh.config | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 conf/ceh.config diff --git a/conf/ceh.config b/conf/ceh.config new file mode 100644 index 0000000..1c54682 --- /dev/null +++ b/conf/ceh.config @@ -0,0 +1,31 @@ +//Profile config names for nf-core/configs + params { + config_profile_description = 'Centre for Evolutionary Hologenomics - CEH profile provided by nf-core/configs.' + config_profile_contact = 'Aashild Vaagene (@ashildv)' + } + +profiles { +ceh { + singularity { + enabled = true + autoMounts = true + cacheDir = '/shared/volume/hologenomics/data/cache/nf-eager/singularity' + } + process { + executor = 'slurm' + queue = { task.time < 24.h ? 'hologenomics-short' : task.time < 168.h ? 'hologenomics' : 'hologenomics-long' } + } + + cleanup = true + + executor { + queueSize = 8 + } + params { + max_memory = 250.GB + max_cpus = 35 + max_time = 720.h + } + } + } + From 8a8f95e364e8d0585053c927c1d596a9ca11862b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?= <60298098+ashildv@users.noreply.github.com> Date: Wed, 20 Jan 2021 23:47:58 +0100 Subject: [PATCH 02/19] Update nfcore_custom.config --- nfcore_custom.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nfcore_custom.config b/nfcore_custom.config index e31c38e..2519ee5 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -18,6 +18,7 @@ profiles { cbe { includeConfig "${params.custom_config_base}/conf/cbe.config" } ccga_dx { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" } ccga_med { includeConfig "${params.custom_config_base}/conf/ccga_med.config" } + ceh { includeConfig "${params.custom_config_base}/conf/ceh.config"} cfc { includeConfig "${params.custom_config_base}/conf/cfc.config" } cfc_dev { includeConfig "${params.custom_config_base}/conf/cfc_dev.config" } crick { includeConfig "${params.custom_config_base}/conf/crick.config" } From 65831b73ef4c7e1257350810777f98ef46000d82 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?= <60298098+ashildv@users.noreply.github.com> Date: Thu, 21 Jan 2021 00:17:08 +0100 Subject: [PATCH 03/19] Create ceh.md --- docs/ceh.md | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 docs/ceh.md diff --git a/docs/ceh.md b/docs/ceh.md new file mode 100644 index 0000000..b9c8b4f --- /dev/null +++ b/docs/ceh.md @@ -0,0 +1,21 @@ +# nf-core/configs: Centre for Evolutionary Hologenomics / EvoGenomics (hologenomics partition on HPC) Configuration + +The profile is configured to run with Singularity version 3.6.3-1.el7 which is part of the OS installtion and does not need to be loaded as a module. + +Before running the pipeline you will need to load Java, Miniconda and Nextflow. You can do this by including the commands below in your SLURM/sbatch script: + +```bash +## Load Java, Miniconda and Nextflow environment modules +module purge +module load lib +module load java/v1.8.0_202-jdk miniconda nextflow/v20.07.1.5412 +``` + +All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway. +The config contains a `cleanup` command that removes the `work/` directory automatically once the pipeline has completeed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space. + +This configuration will automatically choose the correct SLURM queue (short,medium,long) depending on the time and memory required by each process. + +>NB: You will need an account to use the HPC cluster to run the pipeline. If in doubt contact IT. + +>NB: Nextflow will need to submit the jobs via SLURM to the HPC cluster and as such the commands above will have to be submitted from one of the login nodes. From a6f316b58b6c83cee74a6f62572c2a9ce590805a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?= <60298098+ashildv@users.noreply.github.com> Date: Thu, 21 Jan 2021 00:21:13 +0100 Subject: [PATCH 04/19] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index a967049..42d2b91 100644 --- a/README.md +++ b/README.md @@ -102,6 +102,7 @@ Currently documentation is available for the following systems: * [CBE](docs/cbe.md) * [CCGA_DX](docs/ccga_dx.md) * [CCGA_MED](docs/ccga_med.md) +* [CEH] (docs/ceh.md) * [CFC](docs/cfc.md) * [CRICK](docs/crick.md) * [CZBIOHUB_AWS](docs/czbiohub.md) From 22e6a60db10edf5b19c0036a5d6ba2fa1e14ecf9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?= <60298098+ashildv@users.noreply.github.com> Date: Thu, 21 Jan 2021 00:22:13 +0100 Subject: [PATCH 05/19] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 42d2b91..1c1bcc4 100644 --- a/README.md +++ b/README.md @@ -102,7 +102,7 @@ Currently documentation is available for the following systems: * [CBE](docs/cbe.md) * [CCGA_DX](docs/ccga_dx.md) * [CCGA_MED](docs/ccga_med.md) -* [CEH] (docs/ceh.md) +* [CEH](docs/ceh.md) * [CFC](docs/cfc.md) * [CRICK](docs/crick.md) * [CZBIOHUB_AWS](docs/czbiohub.md) From 91594dffeaf5f9eceeb22ccf1e011ab2767627a1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?= <60298098+ashildv@users.noreply.github.com> Date: Thu, 21 Jan 2021 00:29:43 +0100 Subject: [PATCH 06/19] Update ceh.config --- conf/ceh.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/ceh.config b/conf/ceh.config index 1c54682..ff81cfb 100644 --- a/conf/ceh.config +++ b/conf/ceh.config @@ -1,6 +1,6 @@ //Profile config names for nf-core/configs params { - config_profile_description = 'Centre for Evolutionary Hologenomics - CEH profile provided by nf-core/configs.' + config_profile_description = 'Center for Evolutionary Hologenomics / Section for Evolutionary Genomics @ GLOBE - CEH profile provided by nf-core/configs.' config_profile_contact = 'Aashild Vaagene (@ashildv)' } From d108666950703a521518535c38eddad32de372f3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?= <60298098+ashildv@users.noreply.github.com> Date: Thu, 21 Jan 2021 00:30:54 +0100 Subject: [PATCH 07/19] Update ceh.md --- docs/ceh.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/ceh.md b/docs/ceh.md index b9c8b4f..fff2921 100644 --- a/docs/ceh.md +++ b/docs/ceh.md @@ -1,4 +1,4 @@ -# nf-core/configs: Centre for Evolutionary Hologenomics / EvoGenomics (hologenomics partition on HPC) Configuration +# nf-core/configs: Center for Evolutionary Hologenomics & Section for Evolutionary Genomics (hologenomics partition on HPC) Configuration The profile is configured to run with Singularity version 3.6.3-1.el7 which is part of the OS installtion and does not need to be loaded as a module. From f8973f153a59833ff727c1caac7ed7f5667e52db Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?= <60298098+ashildv@users.noreply.github.com> Date: Thu, 21 Jan 2021 00:31:49 +0100 Subject: [PATCH 08/19] Update ceh.config --- conf/ceh.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/ceh.config b/conf/ceh.config index ff81cfb..ee15f32 100644 --- a/conf/ceh.config +++ b/conf/ceh.config @@ -1,6 +1,6 @@ //Profile config names for nf-core/configs params { - config_profile_description = 'Center for Evolutionary Hologenomics / Section for Evolutionary Genomics @ GLOBE - CEH profile provided by nf-core/configs.' + config_profile_description = 'Center for Evolutionary Hologenomics & Section for Evolutionary Genomics @ GLOBE - CEH profile provided by nf-core/configs.' config_profile_contact = 'Aashild Vaagene (@ashildv)' } From 964cae4ac79cab4a1e209f826d9897a37d8d0d48 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 21 Jan 2021 06:22:37 +0100 Subject: [PATCH 09/19] Add CEH to CI --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index e78bddd..f9ffee0 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: matrix: - profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'imperial', 'imperial_mb', 'kraken', 'mpcdf', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] + profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ceh', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'imperial', 'imperial_mb', 'kraken', 'mpcdf', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] steps: - uses: actions/checkout@v1 - name: Install Nextflow From 2fd475c3398305e3377cc2e8af18cc5cb2c68180 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 21 Jan 2021 06:30:43 +0100 Subject: [PATCH 10/19] Fix some linting errors --- docs/ceh.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/ceh.md b/docs/ceh.md index fff2921..11fe720 100644 --- a/docs/ceh.md +++ b/docs/ceh.md @@ -1,6 +1,8 @@ # nf-core/configs: Center for Evolutionary Hologenomics & Section for Evolutionary Genomics (hologenomics partition on HPC) Configuration -The profile is configured to run with Singularity version 3.6.3-1.el7 which is part of the OS installtion and does not need to be loaded as a module. +> **NB:** You will need an account to use the HPC cluster to run the pipeline. If in doubt contact IT. + +The profile is configured to run with Singularity version 3.6.3-1.el7 which is part of the OS installtion and does not need to be loaded as a module. Before running the pipeline you will need to load Java, Miniconda and Nextflow. You can do this by including the commands below in your SLURM/sbatch script: @@ -16,6 +18,4 @@ The config contains a `cleanup` command that removes the `work/` directory autom This configuration will automatically choose the correct SLURM queue (short,medium,long) depending on the time and memory required by each process. ->NB: You will need an account to use the HPC cluster to run the pipeline. If in doubt contact IT. - ->NB: Nextflow will need to submit the jobs via SLURM to the HPC cluster and as such the commands above will have to be submitted from one of the login nodes. +> **NB:** Nextflow will need to submit the jobs via SLURM to the HPC cluster and as such the commands above will have to be submitted from one of the login nodes. From 8fa720b9cc4afe6c38eb8bb44e00ad0a0e5074ca Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?= <60298098+ashildv@users.noreply.github.com> Date: Thu, 21 Jan 2021 11:15:06 +0100 Subject: [PATCH 11/19] Update conf/ceh.config Co-authored-by: James A. Fellows Yates --- conf/ceh.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/ceh.config b/conf/ceh.config index ee15f32..77389a7 100644 --- a/conf/ceh.config +++ b/conf/ceh.config @@ -2,6 +2,7 @@ params { config_profile_description = 'Center for Evolutionary Hologenomics & Section for Evolutionary Genomics @ GLOBE - CEH profile provided by nf-core/configs.' config_profile_contact = 'Aashild Vaagene (@ashildv)' + config_profile_url = 'https://ceh.ku.dk/ } profiles { From ef80452577b18aa40ed2e1e63eab62e0abe3c3c9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?= <60298098+ashildv@users.noreply.github.com> Date: Thu, 21 Jan 2021 11:16:46 +0100 Subject: [PATCH 12/19] Update docs/ceh.md Co-authored-by: James A. Fellows Yates --- docs/ceh.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/ceh.md b/docs/ceh.md index 11fe720..1381613 100644 --- a/docs/ceh.md +++ b/docs/ceh.md @@ -4,7 +4,7 @@ The profile is configured to run with Singularity version 3.6.3-1.el7 which is part of the OS installtion and does not need to be loaded as a module. -Before running the pipeline you will need to load Java, Miniconda and Nextflow. You can do this by including the commands below in your SLURM/sbatch script: +Before running the pipeline you will need to load Java, and Nextflow. You can do this by including the commands below in your SLURM/sbatch script: ```bash ## Load Java, Miniconda and Nextflow environment modules From 594985f1eeac1bbf0c9cd535fc6e60ce9faa466d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?= <60298098+ashildv@users.noreply.github.com> Date: Thu, 21 Jan 2021 11:43:34 +0100 Subject: [PATCH 13/19] Update and rename ceh.config to seg_globe.config --- conf/{ceh.config => seg_globe.config} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename conf/{ceh.config => seg_globe.config} (75%) diff --git a/conf/ceh.config b/conf/seg_globe.config similarity index 75% rename from conf/ceh.config rename to conf/seg_globe.config index 77389a7..390d0ef 100644 --- a/conf/ceh.config +++ b/conf/seg_globe.config @@ -1,8 +1,8 @@ //Profile config names for nf-core/configs params { - config_profile_description = 'Center for Evolutionary Hologenomics & Section for Evolutionary Genomics @ GLOBE - CEH profile provided by nf-core/configs.' + config_profile_description = 'Section for Evolutionary Genomics @ GLOBE, University of Copenhagen - seg_globe profile provided by nf-core/configs.' config_profile_contact = 'Aashild Vaagene (@ashildv)' - config_profile_url = 'https://ceh.ku.dk/ + config_profile_url = 'https://globe.ku.dk/research/evogenomics/' } profiles { From bcd137225e293a4cdc93a822f81c53f67e9ea3dd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?= <60298098+ashildv@users.noreply.github.com> Date: Thu, 21 Jan 2021 11:46:46 +0100 Subject: [PATCH 14/19] Update and rename ceh.md to seg_globe.md --- docs/{ceh.md => seg_globe.md} | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) rename docs/{ceh.md => seg_globe.md} (74%) diff --git a/docs/ceh.md b/docs/seg_globe.md similarity index 74% rename from docs/ceh.md rename to docs/seg_globe.md index 1381613..1fa832f 100644 --- a/docs/ceh.md +++ b/docs/seg_globe.md @@ -1,16 +1,16 @@ -# nf-core/configs: Center for Evolutionary Hologenomics & Section for Evolutionary Genomics (hologenomics partition on HPC) Configuration +# nf-core/configs: Section for Evolutionary Genomics at GLOBE, Univeristy of Copenhagen (hologenomics partition on HPC) Configuration > **NB:** You will need an account to use the HPC cluster to run the pipeline. If in doubt contact IT. The profile is configured to run with Singularity version 3.6.3-1.el7 which is part of the OS installtion and does not need to be loaded as a module. -Before running the pipeline you will need to load Java, and Nextflow. You can do this by including the commands below in your SLURM/sbatch script: +Before running the pipeline you will need to load Java and Nextflow. You can do this by including the commands below in your SLURM/sbatch script: ```bash -## Load Java, Miniconda and Nextflow environment modules +## Load Java and Nextflow environment modules module purge module load lib -module load java/v1.8.0_202-jdk miniconda nextflow/v20.07.1.5412 +module load java/v1.8.0_202-jdk nextflow/v20.07.1.5412 ``` All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway. From 8037b73ddd6a5a1fae3803c65915c4c27f1180ba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?= <60298098+ashildv@users.noreply.github.com> Date: Thu, 21 Jan 2021 11:52:58 +0100 Subject: [PATCH 15/19] Update nfcore_custom.config --- nfcore_custom.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nfcore_custom.config b/nfcore_custom.config index 2519ee5..7310de5 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -18,7 +18,6 @@ profiles { cbe { includeConfig "${params.custom_config_base}/conf/cbe.config" } ccga_dx { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" } ccga_med { includeConfig "${params.custom_config_base}/conf/ccga_med.config" } - ceh { includeConfig "${params.custom_config_base}/conf/ceh.config"} cfc { includeConfig "${params.custom_config_base}/conf/cfc.config" } cfc_dev { includeConfig "${params.custom_config_base}/conf/cfc_dev.config" } crick { includeConfig "${params.custom_config_base}/conf/crick.config" } @@ -39,6 +38,7 @@ profiles { pasteur { includeConfig "${params.custom_config_base}/conf/pasteur.config" } phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } prince { includeConfig "${params.custom_config_base}/conf/prince.config" } + seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"} shh { includeConfig "${params.custom_config_base}/conf/shh.config" } uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" } uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" } From 765a2e0b7ed6460df9f980cfee350f5b7a7884f4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?= <60298098+ashildv@users.noreply.github.com> Date: Thu, 21 Jan 2021 11:55:00 +0100 Subject: [PATCH 16/19] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 1c1bcc4..a590599 100644 --- a/README.md +++ b/README.md @@ -102,7 +102,6 @@ Currently documentation is available for the following systems: * [CBE](docs/cbe.md) * [CCGA_DX](docs/ccga_dx.md) * [CCGA_MED](docs/ccga_med.md) -* [CEH](docs/ceh.md) * [CFC](docs/cfc.md) * [CRICK](docs/crick.md) * [CZBIOHUB_AWS](docs/czbiohub.md) @@ -120,6 +119,7 @@ Currently documentation is available for the following systems: * [PASTEUR](docs/pasteur.md) * [PHOENIX](docs/phoenix.md) * [PRINCE](docs/prince.md) +* [SEG_GLOBE](docs/seg_globe.md) * [SHH](docs/shh.md) * [UCT_HPC](docs/uct_hpc.md) * [UPPMAX](docs/uppmax.md) From 7cffcf809bdd0070d317085923499bacc96c9068 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 21 Jan 2021 12:50:14 +0100 Subject: [PATCH 17/19] Update main.yml --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f9ffee0..ea2117d 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: matrix: - profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ceh', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'imperial', 'imperial_mb', 'kraken', 'mpcdf', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] + profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'imperial', 'imperial_mb', 'kraken', 'mpcdf', 'munin', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] steps: - uses: actions/checkout@v1 - name: Install Nextflow From c4604450d864392741e37867f622298bf2fc4626 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 21 Jan 2021 13:04:12 +0100 Subject: [PATCH 18/19] Update seg_globe.md --- docs/seg_globe.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/seg_globe.md b/docs/seg_globe.md index 1fa832f..da03737 100644 --- a/docs/seg_globe.md +++ b/docs/seg_globe.md @@ -4,13 +4,13 @@ The profile is configured to run with Singularity version 3.6.3-1.el7 which is part of the OS installtion and does not need to be loaded as a module. -Before running the pipeline you will need to load Java and Nextflow. You can do this by including the commands below in your SLURM/sbatch script: +Before running the pipeline you will need to load Java, miniconda and Nextflow. You can do this by including the commands below in your SLURM/sbatch script: ```bash ## Load Java and Nextflow environment modules module purge module load lib -module load java/v1.8.0_202-jdk nextflow/v20.07.1.5412 +module load java/v1.8.0_202-jdk miniconda nextflow/v20.07.1.5412 ``` All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway. From 26d164ca74ccc25ba7ee1e6e8fb9843ee7563f65 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 21 Jan 2021 13:15:08 +0100 Subject: [PATCH 19/19] Remove ceh profile for now --- conf/seg_globe.config | 53 ++++++++++++++++++++----------------------- 1 file changed, 24 insertions(+), 29 deletions(-) diff --git a/conf/seg_globe.config b/conf/seg_globe.config index 390d0ef..41a3d6e 100644 --- a/conf/seg_globe.config +++ b/conf/seg_globe.config @@ -1,32 +1,27 @@ //Profile config names for nf-core/configs - params { - config_profile_description = 'Section for Evolutionary Genomics @ GLOBE, University of Copenhagen - seg_globe profile provided by nf-core/configs.' - config_profile_contact = 'Aashild Vaagene (@ashildv)' - config_profile_url = 'https://globe.ku.dk/research/evogenomics/' - } +params { + config_profile_description = 'Section for Evolutionary Genomics @ GLOBE, University of Copenhagen - seg_globe profile provided by nf-core/configs.' + config_profile_contact = 'Aashild Vaagene (@ashildv)' + config_profile_url = 'https://globe.ku.dk/research/evogenomics/' + max_memory = 250.GB + max_cpus = 35 + max_time = 720.h +} -profiles { -ceh { - singularity { - enabled = true - autoMounts = true - cacheDir = '/shared/volume/hologenomics/data/cache/nf-eager/singularity' - } - process { - executor = 'slurm' - queue = { task.time < 24.h ? 'hologenomics-short' : task.time < 168.h ? 'hologenomics' : 'hologenomics-long' } - } +singularity { + enabled = true + autoMounts = true + cacheDir = '/shared/volume/hologenomics/data/cache/nf-eager/singularity' +} + +process { + executor = 'slurm' + queue = { task.time < 24.h ? 'hologenomics-short' : task.time < 168.h ? 'hologenomics' : 'hologenomics-long' } +} - cleanup = true - - executor { - queueSize = 8 - } - params { - max_memory = 250.GB - max_cpus = 35 - max_time = 720.h - } - } - } - +cleanup = true + +executor { + queueSize = 8 +} +