From 2af0f4a7741e365bb017711a8a578bb07be9517f Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Wed, 28 Jul 2021 13:03:59 -0500 Subject: [PATCH 01/33] Added link to NU Genomics markdown --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 29fbce2..64a530c 100644 --- a/README.md +++ b/README.md @@ -121,6 +121,7 @@ Currently documentation is available for the following systems: * [LUGH](docs/lugh.md) * [MPCDF](docs/mpcdf.md) * [MUNIN](docs/munin.md) +* [NU_GENOMICS](docs/nu_genomics.md) * [OIST](docs/oist.md) * [PASTEUR](docs/pasteur.md) * [PHOENIX](docs/phoenix.md) From 40170632aa132a3a4cc2c662702e0b2b8fef2efa Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Wed, 28 Jul 2021 13:04:32 -0500 Subject: [PATCH 02/33] First draft of markdown file, with instructions for installing nextflow and getting access --- docs/nu_genomics.md | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 docs/nu_genomics.md diff --git a/docs/nu_genomics.md b/docs/nu_genomics.md new file mode 100644 index 0000000..0d7ecda --- /dev/null +++ b/docs/nu_genomics.md @@ -0,0 +1,28 @@ +# nf-core/configs: NU_Genomics Configuration + +All nf-core pipelines have been successfully configured for use on the Quest Genomics Nodes at Northwestern University. + +To use, run the pipeline with `-profile nu_genomics`. This will download and launch the [`nu_genomics.config`](../conf/nu_genomics.config) which has been pre-configured with a setup suitable for the Quest Genomics Nodes. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. + +## Before running the pipeline + +There are several important steps to take before this pipeline will run successfully on Quest. First, you must have an active Quest allocation. If you do not, please apply [here](https://www.it.northwestern.edu/secure/forms/research/allocation-request.html). You will also need access to the Genomics Nodes. If you do not already have access, please apply [here](https://app.smartsheet.com/b/form?EQBCT=9b3647a8cb2145929737ab4a0540cb46). Finally, you will need to perform a local installation of Nextflow and add it to your path. Please follow the basic installation instructions shown [here](https://www.nextflow.io/), or install in your home directory as shown. If you already have a bin directory in your path, you will not need to create the directory or append to your path. + +```bash +cd ~ +mkdir bin +cd bin +curl -s https://get.nextflow.io | bash +export PATH=~/bin:$PATH +``` + +Note that you may need to install an "edge" version of Nextflow, depending on which pipeline you use. Please read the documentation carefully to see if this is the case, or you may see an error when running the pipeline. If this is the case, you need to explicitly set the version when installing, e.g.: + +```bash +curl -s https://github.com/nextflow-io/nextflow/releases/download/v20.11.0-edge/nextflow-20.11.0-edge-all | bash +``` + +## Use of iGenomes + +A local copy of the iGenomes resource with all commonly used genomes has been made available for all of Quest so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. +You can do this by simply using the `--genome ` parameter. While you can technically "stream" genomes from iGenomes directly using the pipeline, this is a substantial use of bandwidth and resources on both ends, and potentially poses reproducibility issues later on. Please use the local copies unless absolutely necessary, and save your own to your personal allocation where necessary. \ No newline at end of file From e28a83670267bc5ad1dd98f1ffd551dec28fab87 Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Wed, 28 Jul 2021 13:10:18 -0500 Subject: [PATCH 03/33] Added nu_genomics to list --- .github/workflows/main.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index c5e6a57..a73e3ca 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -48,6 +48,7 @@ jobs: - 'lugh' - 'mpcdf' - 'munin' + - 'nu_genomics' - 'oist' - 'pasteur' - 'phoenix' From 30ca5550608c4894a3aba07b9ceb703e09874409 Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Wed, 28 Jul 2021 13:10:35 -0500 Subject: [PATCH 04/33] Added nu_genomics to list --- nfcore_custom.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nfcore_custom.config b/nfcore_custom.config index 74d25b9..a74178b 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -42,6 +42,7 @@ profiles { lugh { includeConfig "${params.custom_config_base}/conf/lugh.config" } mpcdf { includeConfig "${params.custom_config_base}/conf/mpcdf.config" } munin { includeConfig "${params.custom_config_base}/conf/munin.config" } + nu_genomics { includeConfig "${params.custom_config_base}/conf/nu_genomics.config" } oist { includeConfig "${params.custom_config_base}/conf/oist.config" } pasteur { includeConfig "${params.custom_config_base}/conf/pasteur.config" } phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } From 9957e9eea1d77d6f1a07a4c443e5520a8923f36e Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Wed, 28 Jul 2021 13:11:02 -0500 Subject: [PATCH 05/33] Version 1 of custom config with queue-switching for long jobs and module loading --- conf/nu_genomics.config | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 conf/nu_genomics.config diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config new file mode 100644 index 0000000..67465cb --- /dev/null +++ b/conf/nu_genomics.config @@ -0,0 +1,31 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'Northwestern University Quest HPC (Genomics Nodes) config provided by nf-core/configs' + config_profile_contact = 'Rogan Grant / Janna Nugent (@RoganGrant, @NUjon)' + config_profile_url = 'https://www.it.northwestern.edu/research/user-services/quest/' +} + +singularity { + enabled = true + autoMounts = true + queue = {task.time < 48.h ? 'genomics' : 'genomicslong'} + clusterOptions = '-A b1042' + cacheDir = "/projects/b1042/singularity_cache" +} + +process { + beforeScript = 'module load singularity/latest graphviz/2.40.1' + executor = 'slurm' +} + +executor { + submitRateLimit = '1sec' +} + +params { + max_memory = 190.GB + max_cpus = 40 + max_time = 240.h + igenomes_base = "/projects/genomicsshare/igenomes" #pending + +} \ No newline at end of file From ff6823ec1d96800ce621c1038cc12828dbb83839 Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Wed, 28 Jul 2021 13:22:52 -0500 Subject: [PATCH 06/33] removed unnecessary space --- conf/nu_genomics.config | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config index 67465cb..71f28f6 100644 --- a/conf/nu_genomics.config +++ b/conf/nu_genomics.config @@ -27,5 +27,4 @@ params { max_cpus = 40 max_time = 240.h igenomes_base = "/projects/genomicsshare/igenomes" #pending - } \ No newline at end of file From 9df267a1922dfa78dc1ec8dd9363a11f3f20bd23 Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Wed, 28 Jul 2021 13:27:17 -0500 Subject: [PATCH 07/33] Merged duplicate params --- conf/nu_genomics.config | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config index 71f28f6..fbd023d 100644 --- a/conf/nu_genomics.config +++ b/conf/nu_genomics.config @@ -3,6 +3,10 @@ params { config_profile_description = 'Northwestern University Quest HPC (Genomics Nodes) config provided by nf-core/configs' config_profile_contact = 'Rogan Grant / Janna Nugent (@RoganGrant, @NUjon)' config_profile_url = 'https://www.it.northwestern.edu/research/user-services/quest/' + max_memory = 190.GB + max_cpus = 40 + max_time = 240.h + igenomes_base = "/projects/genomicsshare/igenomes" #pending } singularity { @@ -20,11 +24,4 @@ process { executor { submitRateLimit = '1sec' -} - -params { - max_memory = 190.GB - max_cpus = 40 - max_time = 240.h - igenomes_base = "/projects/genomicsshare/igenomes" #pending } \ No newline at end of file From f104250ff4025c94a9971a0e179640cb10e386e7 Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Wed, 28 Jul 2021 13:34:49 -0500 Subject: [PATCH 08/33] Removed comment --- conf/nu_genomics.config | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config index fbd023d..2f313bd 100644 --- a/conf/nu_genomics.config +++ b/conf/nu_genomics.config @@ -1,15 +1,17 @@ //Profile config names for nf-core/configs -params { +params +{ config_profile_description = 'Northwestern University Quest HPC (Genomics Nodes) config provided by nf-core/configs' config_profile_contact = 'Rogan Grant / Janna Nugent (@RoganGrant, @NUjon)' config_profile_url = 'https://www.it.northwestern.edu/research/user-services/quest/' max_memory = 190.GB max_cpus = 40 max_time = 240.h - igenomes_base = "/projects/genomicsshare/igenomes" #pending + igenomes_base = "/projects/genomicsshare/igenomes" } -singularity { +singularity +{ enabled = true autoMounts = true queue = {task.time < 48.h ? 'genomics' : 'genomicslong'} @@ -17,11 +19,13 @@ singularity { cacheDir = "/projects/b1042/singularity_cache" } -process { +process +{ beforeScript = 'module load singularity/latest graphviz/2.40.1' executor = 'slurm' } -executor { +executor +{ submitRateLimit = '1sec' } \ No newline at end of file From e2c566ed13aaf4a858049537eb42e90bbbe4e9d0 Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Wed, 28 Jul 2021 13:38:06 -0500 Subject: [PATCH 09/33] Testing "automounts" --- conf/nu_genomics.config | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config index 2f313bd..6da5642 100644 --- a/conf/nu_genomics.config +++ b/conf/nu_genomics.config @@ -13,7 +13,6 @@ params singularity { enabled = true - autoMounts = true queue = {task.time < 48.h ? 'genomics' : 'genomicslong'} clusterOptions = '-A b1042' cacheDir = "/projects/b1042/singularity_cache" From e1e0810d1b7fcd3be7593c6a11df359aaa472f6c Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Wed, 28 Jul 2021 13:44:48 -0500 Subject: [PATCH 10/33] Clean up module loading script --- conf/nu_genomics.config | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config index 6da5642..b5bb27c 100644 --- a/conf/nu_genomics.config +++ b/conf/nu_genomics.config @@ -20,7 +20,12 @@ singularity process { - beforeScript = 'module load singularity/latest graphviz/2.40.1' + beforeScript = "" + module purge + module load singularity/latest + module load graphviz/2.40.1s + "" + .stripIndent() executor = 'slurm' } From 09e0ea2674916450c1acf8e5139e8951072ab92d Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Wed, 28 Jul 2021 13:46:40 -0500 Subject: [PATCH 11/33] typo --- conf/nu_genomics.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config index b5bb27c..1df0d92 100644 --- a/conf/nu_genomics.config +++ b/conf/nu_genomics.config @@ -23,7 +23,7 @@ process beforeScript = "" module purge module load singularity/latest - module load graphviz/2.40.1s + module load graphviz/2.40.1 "" .stripIndent() executor = 'slurm' From 09ed4d54b981c2632e479c76f954629887381fde Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Wed, 28 Jul 2021 13:52:26 -0500 Subject: [PATCH 12/33] Just make command a single line for simplicity --- conf/nu_genomics.config | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config index 1df0d92..48a102f 100644 --- a/conf/nu_genomics.config +++ b/conf/nu_genomics.config @@ -20,12 +20,7 @@ singularity process { - beforeScript = "" - module purge - module load singularity/latest - module load graphviz/2.40.1 - "" - .stripIndent() + beforeScript = 'module purge; module load singularity/latest; module load graphviz/2.40.1' executor = 'slurm' } From 3dd4f16d09c04b0118abd543458cde1fcccfa895 Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Wed, 28 Jul 2021 14:01:12 -0500 Subject: [PATCH 13/33] Added indicator for testing --- conf/nu_genomics.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config index 48a102f..119aeb7 100644 --- a/conf/nu_genomics.config +++ b/conf/nu_genomics.config @@ -20,7 +20,7 @@ singularity process { - beforeScript = 'module purge; module load singularity/latest; module load graphviz/2.40.1' + beforeScript = 'echo "loading modules"; module purge; module load singularity/latest; module load graphviz/2.40.1' executor = 'slurm' } From ac11ca5568ef4048d5a595c929ef034766a402eb Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Wed, 28 Jul 2021 16:48:08 -0500 Subject: [PATCH 14/33] Remove echo used for testing --- conf/nu_genomics.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config index 119aeb7..48a102f 100644 --- a/conf/nu_genomics.config +++ b/conf/nu_genomics.config @@ -20,7 +20,7 @@ singularity process { - beforeScript = 'echo "loading modules"; module purge; module load singularity/latest; module load graphviz/2.40.1' + beforeScript = 'module purge; module load singularity/latest; module load graphviz/2.40.1' executor = 'slurm' } From bcc69fe83cac3bc5e23418e693dcdc3af74c3bf9 Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Wed, 28 Jul 2021 17:54:51 -0500 Subject: [PATCH 15/33] Enable use of himem nodes --- conf/nu_genomics.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config index 48a102f..1bb6dd8 100644 --- a/conf/nu_genomics.config +++ b/conf/nu_genomics.config @@ -13,7 +13,7 @@ params singularity { enabled = true - queue = {task.time < 48.h ? 'genomics' : 'genomicslong'} + queue = {task.memory >= 190.GB ? 'genomics-himem' : task.time >= 48.h ? 'genomicslong' : 'genomics'} clusterOptions = '-A b1042' cacheDir = "/projects/b1042/singularity_cache" } From 6862fb8bfdefd9f3e2e65b5cc368b01f7e8bd236 Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Wed, 28 Jul 2021 18:01:03 -0500 Subject: [PATCH 16/33] testing ternary operatory --- conf/nu_genomics.config | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config index 1bb6dd8..880810b 100644 --- a/conf/nu_genomics.config +++ b/conf/nu_genomics.config @@ -13,7 +13,8 @@ params singularity { enabled = true - queue = {task.memory >= 190.GB ? 'genomics-himem' : task.time >= 48.h ? 'genomicslong' : 'genomics'} + //queue = {task.memory >= 190.GB ? 'genomics-himem' : task.time >= 48.h ? 'genomicslong' : 'genomics'} + queue = 'genomics' clusterOptions = '-A b1042' cacheDir = "/projects/b1042/singularity_cache" } From 24a2949fe24e41e52116494bb1c3c7807a42bf76 Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Wed, 28 Jul 2021 18:05:45 -0500 Subject: [PATCH 17/33] Had executor options in wrong spot :( --- conf/nu_genomics.config | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config index 880810b..690c22e 100644 --- a/conf/nu_genomics.config +++ b/conf/nu_genomics.config @@ -13,9 +13,6 @@ params singularity { enabled = true - //queue = {task.memory >= 190.GB ? 'genomics-himem' : task.time >= 48.h ? 'genomicslong' : 'genomics'} - queue = 'genomics' - clusterOptions = '-A b1042' cacheDir = "/projects/b1042/singularity_cache" } @@ -23,6 +20,8 @@ process { beforeScript = 'module purge; module load singularity/latest; module load graphviz/2.40.1' executor = 'slurm' + queue = {task.memory >= 190.GB ? 'genomics-himem' : task.time >= 48.h ? 'genomicslong' : 'genomics'} + clusterOptions = '-A b1042' } executor From 482478878dd5999f99da0ea2c706088836bf4470 Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Wed, 28 Jul 2021 18:11:10 -0500 Subject: [PATCH 18/33] Added instructions for module loading --- docs/nu_genomics.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/nu_genomics.md b/docs/nu_genomics.md index 0d7ecda..901bcd0 100644 --- a/docs/nu_genomics.md +++ b/docs/nu_genomics.md @@ -1,6 +1,6 @@ # nf-core/configs: NU_Genomics Configuration -All nf-core pipelines have been successfully configured for use on the Quest Genomics Nodes at Northwestern University. +All nf-core pipelines have been successfully configured for use on the Quest Genomics Nodes at Northwestern University. Note that, at present, this config has only been tested with nf-core/RNA-seq, but should function similarly for other nf-core pipelines. If you would like to test other pipelines and share on the genomics-rcs Slack, we would be very much obliged. To use, run the pipeline with `-profile nu_genomics`. This will download and launch the [`nu_genomics.config`](../conf/nu_genomics.config) which has been pre-configured with a setup suitable for the Quest Genomics Nodes. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. @@ -22,6 +22,14 @@ Note that you may need to install an "edge" version of Nextflow, depending on wh curl -s https://github.com/nextflow-io/nextflow/releases/download/v20.11.0-edge/nextflow-20.11.0-edge-all | bash ``` +Note that while the config does explicitly load the necessary modules, you will often need to load them manually anyway. Please do so before each run as follows, or you may run into errors: + +```bash +module purge +module load singularity/latest +module load graphviz/2.40.1 +``` + ## Use of iGenomes A local copy of the iGenomes resource with all commonly used genomes has been made available for all of Quest so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. From 079258ebbbd6112c67a07ebfb3b35fd5c3fe4bf1 Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Thu, 29 Jul 2021 11:38:40 -0500 Subject: [PATCH 19/33] Minor text edits --- docs/nu_genomics.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/nu_genomics.md b/docs/nu_genomics.md index 901bcd0..4c2034f 100644 --- a/docs/nu_genomics.md +++ b/docs/nu_genomics.md @@ -33,4 +33,4 @@ module load graphviz/2.40.1 ## Use of iGenomes A local copy of the iGenomes resource with all commonly used genomes has been made available for all of Quest so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. -You can do this by simply using the `--genome ` parameter. While you can technically "stream" genomes from iGenomes directly using the pipeline, this is a substantial use of bandwidth and resources on both ends, and potentially poses reproducibility issues later on. Please use the local copies unless absolutely necessary, and save your own to your personal allocation where necessary. \ No newline at end of file +You can do this by simply using the `--genome ` parameter. While you can technically "stream" genomes from iGenomes directly using the pipeline, this is a substantial use of bandwidth and resources on both ends, and potentially poses reproducibility issues later on. Please use the local copies unless absolutely necessary, and save your custom genomes to your personal allocation where necessary. From f793ffaace6d86460f2b515912d958f1c293b77b Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Tue, 3 Aug 2021 15:10:54 -0500 Subject: [PATCH 20/33] Updated iGenomes location --- conf/nu_genomics.config | 2 +- docs/nu_genomics.md | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config index 690c22e..3598a31 100644 --- a/conf/nu_genomics.config +++ b/conf/nu_genomics.config @@ -7,7 +7,7 @@ params max_memory = 190.GB max_cpus = 40 max_time = 240.h - igenomes_base = "/projects/genomicsshare/igenomes" + igenomes_base = "/projects/genomicsshare/AWS_iGenomes" } singularity diff --git a/docs/nu_genomics.md b/docs/nu_genomics.md index 4c2034f..21fc2b4 100644 --- a/docs/nu_genomics.md +++ b/docs/nu_genomics.md @@ -32,5 +32,4 @@ module load graphviz/2.40.1 ## Use of iGenomes -A local copy of the iGenomes resource with all commonly used genomes has been made available for all of Quest so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. -You can do this by simply using the `--genome ` parameter. While you can technically "stream" genomes from iGenomes directly using the pipeline, this is a substantial use of bandwidth and resources on both ends, and potentially poses reproducibility issues later on. Please use the local copies unless absolutely necessary, and save your custom genomes to your personal allocation where necessary. +A local copy of the iGenomes resource with all commonly used genomes has been made available for all of Quest so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. These files can be found at `/projects/genomicsshare/AWS_iGenomes`. You can do this by simply using the `--genome ` parameter. While you can technically "stream" genomes from iGenomes directly using the pipeline, this is a substantial use of bandwidth and resources on both ends, and potentially poses reproducibility issues later on. Please use the local copies unless absolutely necessary, and save your custom genomes to your personal allocation where necessary. From 5fbd938bc12bc2f7b78c8d2929b4624c2a235453 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 27 Aug 2021 10:08:20 +0200 Subject: [PATCH 21/33] Export user env too --- conf/pipeline/eager/eva.config | 108 ++++++++++++++++----------------- 1 file changed, 54 insertions(+), 54 deletions(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 880df27..f1caff6 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -14,7 +14,7 @@ process { maxRetries = 2 // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion - clusterOptions = { "-S /bin/bash -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" } + clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" } withLabel:'sc_tiny'{ cpus = { check_max( 1, 'cpus' ) } @@ -61,72 +61,72 @@ process { // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use withName: makeSeqDict { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: fastqc { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: adapter_removal { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: dedup { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: markduplicates { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: library_merge { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: malt { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: maltextract { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: multivcfanalyzer { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: mtnucratio { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: vcf2genome { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: qualimap { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: damageprofiler { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: circularmapper { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: circulargenerator { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: preseq { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' } } withName: genotyping_ug { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } } @@ -152,7 +152,7 @@ profiles { maxRetries = 2 // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion - clusterOptions = { "-S /bin/bash -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" } + clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" } withLabel:'sc_tiny'{ cpus = { check_max( 1, 'cpus' ) } @@ -199,31 +199,31 @@ profiles { // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use withName: makeSeqDict { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: fastqc { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: adapter_removal { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: dedup { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: markduplicates { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: library_merge { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: malt { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName:hostremoval_input_fastq { @@ -233,43 +233,43 @@ profiles { } withName: maltextract { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: multivcfanalyzer { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: mtnucratio { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: vcf2genome { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: qualimap { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: damageprofiler { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: circularmapper { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: circulargenerator { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: genotyping_ug { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: preseq { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' } } @@ -295,7 +295,7 @@ profiles { maxRetries = 2 // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion - clusterOptions = { "-S /bin/bash -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" } + clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" } withLabel:'sc_tiny'{ cpus = { check_max( 1, 'cpus' ) } @@ -342,27 +342,27 @@ profiles { // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use withName: makeSeqDict { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: fastqc { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: adapter_removal { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: dedup { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: markduplicates { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: library_merge { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName:hostremoval_input_fastq { @@ -372,47 +372,47 @@ profiles { } withName: malt { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: maltextract { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: multivcfanalyzer { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: mtnucratio { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: vcf2genome { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: qualimap { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: damageprofiler { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: circularmapper { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: circulargenerator { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: genotyping_ug { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } } withName: preseq { - clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' } } From 94cbb031c67ec386b70c479247c17205ebedd865 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 30 Aug 2021 13:29:44 +0200 Subject: [PATCH 22/33] Update eva.config --- conf/pipeline/eager/eva.config | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index f1caff6..95ce832 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -85,7 +85,9 @@ process { } withName: malt { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" } + cpus = { check_max( 32, 'cpus' ) } + memory = { check_max( 955.GB * task.attempt, 'memory' ) } } withName: maltextract { @@ -223,8 +225,10 @@ profiles { } withName: malt { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } - } + clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" } + cpus = { check_max( 32, 'cpus' ) } + memory = { check_max( 955.GB * task.attempt, 'memory' ) } + } withName:hostremoval_input_fastq { cpus = { check_max( 1, 'cpus' ) } @@ -372,8 +376,10 @@ profiles { } withName: malt { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } - } + clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" } + cpus = { check_max( 32, 'cpus' ) } + memory = { check_max( 955.GB * task.attempt, 'memory' ) } + } withName: maltextract { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } From 2c5e454d1632d6dea49180c7c5f9f84de63930cd Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Sat, 4 Sep 2021 15:13:41 -0500 Subject: [PATCH 23/33] Updated iGenomes path for odd local structure on Quest --- conf/nu_genomics.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config index 3598a31..9c7d4b4 100644 --- a/conf/nu_genomics.config +++ b/conf/nu_genomics.config @@ -7,7 +7,7 @@ params max_memory = 190.GB max_cpus = 40 max_time = 240.h - igenomes_base = "/projects/genomicsshare/AWS_iGenomes" + igenomes_base = "/projects/genomicsshare/AWS_iGenomes/references" } singularity From d5601fea846ab30b70b36988205ef27b37fb7c61 Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Sat, 4 Sep 2021 15:19:32 -0500 Subject: [PATCH 24/33] Forgot a slash :( --- conf/nu_genomics.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config index 9c7d4b4..60d4e19 100644 --- a/conf/nu_genomics.config +++ b/conf/nu_genomics.config @@ -7,7 +7,7 @@ params max_memory = 190.GB max_cpus = 40 max_time = 240.h - igenomes_base = "/projects/genomicsshare/AWS_iGenomes/references" + igenomes_base = "/projects/genomicsshare/AWS_iGenomes/references/" } singularity From a8d06ee35671f8a02066c9d932b8aa9e55595218 Mon Sep 17 00:00:00 2001 From: rogangrant Date: Sat, 4 Sep 2021 15:36:05 -0500 Subject: [PATCH 25/33] Revert "Forgot a slash :(" This reverts commit d5601fea846ab30b70b36988205ef27b37fb7c61. --- conf/nu_genomics.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config index 60d4e19..9c7d4b4 100644 --- a/conf/nu_genomics.config +++ b/conf/nu_genomics.config @@ -7,7 +7,7 @@ params max_memory = 190.GB max_cpus = 40 max_time = 240.h - igenomes_base = "/projects/genomicsshare/AWS_iGenomes/references/" + igenomes_base = "/projects/genomicsshare/AWS_iGenomes/references" } singularity From 59a0901b684624b955071dd82da65e66382dc49b Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sun, 5 Sep 2021 12:07:53 +0200 Subject: [PATCH 26/33] Add library merge steps to have overhead --- conf/pipeline/eager/eva.config | 28 ++++++++++++++++++++++++++-- 1 file changed, 26 insertions(+), 2 deletions(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 95ce832..765e01a 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -84,6 +84,14 @@ process { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } + withName: seqtype_merge { + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + } + + withName: additional_library_merge { + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + } + withName: malt { clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" } cpus = { check_max( 32, 'cpus' ) } @@ -222,7 +230,15 @@ profiles { withName: library_merge { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } - } + } + + withName: seqtype_merge { + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + } + + withName: additional_library_merge { + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + } withName: malt { clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" } @@ -367,7 +383,15 @@ profiles { withName: library_merge { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } - } + } + + withName: seqtype_merge { + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + } + + withName: additional_library_merge { + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + } withName:hostremoval_input_fastq { cpus = { check_max( 1, 'cpus' ) } From 39f54db09798c00dd96836d94d5d17885fe005a3 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sun, 5 Sep 2021 12:09:02 +0200 Subject: [PATCH 27/33] Update container cache --- conf/eva.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/eva.config b/conf/eva.config index ad71e12..8b52dda 100644 --- a/conf/eva.config +++ b/conf/eva.config @@ -39,7 +39,7 @@ profiles { } singularity { - cacheDir = "/mnt/archgen/users/singularity_scratch" + cacheDir = "/mnt/archgen/tools/singularity/containers/" } From a7aca37bc85e43a17ae0df942559a10b01a64542 Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Mon, 6 Sep 2021 15:15:46 -0500 Subject: [PATCH 28/33] Set autoMounts to true --- conf/nu_genomics.config | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config index 9c7d4b4..a8e9e02 100644 --- a/conf/nu_genomics.config +++ b/conf/nu_genomics.config @@ -13,6 +13,7 @@ params singularity { enabled = true + autoMounts = true cacheDir = "/projects/b1042/singularity_cache" } @@ -27,4 +28,4 @@ process executor { submitRateLimit = '1sec' -} \ No newline at end of file +} From 4286a3a3421d53c5df0c841295d72be6206afa51 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 8 Sep 2021 15:16:40 +0200 Subject: [PATCH 29/33] Bump additional library merge memor --- conf/pipeline/eager/eva.config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 765e01a..4db9fa1 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -90,6 +90,7 @@ process { withName: additional_library_merge { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + memory = { check_max( 4.GB * task.attempt, 'memory' ) } } withName: malt { @@ -238,6 +239,7 @@ profiles { withName: additional_library_merge { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + memory = { check_max( 4.GB * task.attempt, 'memory' ) } } withName: malt { @@ -383,6 +385,7 @@ profiles { withName: library_merge { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + memory = { check_max( 4.GB * task.attempt, 'memory' ) } } withName: seqtype_merge { From 7ec12b6736cf05b8cc53b99d2711ecb655949082 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 9 Sep 2021 13:10:05 +0200 Subject: [PATCH 30/33] Update eva.config --- conf/pipeline/eager/eva.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 4db9fa1..1e2c098 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -9,7 +9,7 @@ params { // Specific nf-core/eager process configuration process { - beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -XX:+PrintCommandLineFlags"' + beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"' maxRetries = 2 From d479926c7f5214fc5d60f1d579f592ef52504c87 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 9 Sep 2021 13:33:56 +0200 Subject: [PATCH 31/33] Update mpcdf.config --- conf/mpcdf.config | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/conf/mpcdf.config b/conf/mpcdf.config index c6c3c9c..3027d63 100644 --- a/conf/mpcdf.config +++ b/conf/mpcdf.config @@ -6,7 +6,10 @@ params { profiles { + cobra { + + cleanup = true process { beforeScript = 'module load singularity' @@ -31,8 +34,11 @@ profiles { max_time = 24.h } } + raven { + cleanup = true + process { beforeScript = 'module load singularity' executor = 'slurm' @@ -56,6 +62,7 @@ profiles { max_time = 24.h } } + debug { cleanup = false } From 0603aba34250975e6698b04a6a2067b14c841104 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 9 Sep 2021 13:54:01 +0200 Subject: [PATCH 32/33] Remove debugging stuff --- conf/pipeline/eager/eva.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 1e2c098..49b1d1f 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -158,7 +158,7 @@ profiles { process { - beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -XX:+PrintCommandLineFlags"' + beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"' maxRetries = 2 @@ -312,7 +312,7 @@ profiles { process { - beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -XX:+PrintCommandLineFlags"' + beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"' maxRetries = 2 From 7c639ac934f1d3d7e932d5585dece9e184b187e8 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 9 Sep 2021 14:47:20 +0200 Subject: [PATCH 33/33] Bump lib merge further --- conf/pipeline/eager/eva.config | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 49b1d1f..f3ad9da 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -385,7 +385,7 @@ profiles { withName: library_merge { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } - memory = { check_max( 4.GB * task.attempt, 'memory' ) } + memory = { check_max( 6.GB * task.attempt, 'memory' ) } } withName: seqtype_merge { @@ -394,6 +394,7 @@ profiles { withName: additional_library_merge { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + memory = { check_max( 6.GB * task.attempt, 'memory' ) } } withName:hostremoval_input_fastq {