From d8c27759761232798ce6a295a98426b66adb39ee Mon Sep 17 00:00:00 2001 From: Andrew Frank Date: Tue, 7 Jun 2022 09:41:41 -0400 Subject: [PATCH 1/6] Update google.config to fix custom VM memory error --- conf/google.config | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/conf/google.config b/conf/google.config index 41f0e1f..6e8a45a 100644 --- a/conf/google.config +++ b/conf/google.config @@ -19,4 +19,6 @@ google.lifeSciences.preemptible = params.google_preemptible if (google.lifeSciences.preemptible) { process.errorStrategy = { task.exitStatus in [8,10,14] ? 'retry' : 'terminate' } process.maxRetries = 5 -} \ No newline at end of file +} + +process.machineType = { task.memory > task.cpus * 6.GB ? ['custom', task.cpus, task.cpus * 6656].join('-') : null } From 8d5ae4c3ab53c8892bce378c58fb0e881c2e6cd0 Mon Sep 17 00:00:00 2001 From: Austyn Trull Date: Tue, 23 Aug 2022 15:30:13 -0500 Subject: [PATCH 2/6] Committing changes made by Brandon Wilk so that singularity containers will use scratch space --- conf/cheaha.config | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/conf/cheaha.config b/conf/cheaha.config index 323a625..578259c 100644 --- a/conf/cheaha.config +++ b/conf/cheaha.config @@ -5,9 +5,15 @@ params { config_profile_url = 'https://www.uab.edu/cores/ircp/bds' } +env { + TMPDIR="$USER_SCRATCH" + SINGULARITY_TMPDIR="$USER_SCRATCH" +} + singularity { enabled = true autoMounts = true + runOptions = "--contain --workdir $USER_SCRATCH" } process { From 90f638d3761a6b8fa6560e1a3d09a6a62a6ee44a Mon Sep 17 00:00:00 2001 From: Austyn Trull Date: Mon, 29 Aug 2022 10:47:46 -0500 Subject: [PATCH 3/6] Updating the cheaha documentation to clarify that /data/temporary-scratch/atrull will be used as storage for files that would normally go into one of the temporary locations when using Singularity --- docs/cheaha.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/cheaha.md b/docs/cheaha.md index 9d871c3..fb04c88 100644 --- a/docs/cheaha.md +++ b/docs/cheaha.md @@ -13,6 +13,8 @@ module load Singularity module load Nextflow ``` +Various tasks will be run inside of Singularity containers and all temp files typically written to `/tmp` and `/var/tmp` are instead written to the path pointed to by the `USER_SCRATCH` environment variable. This means that these temp files are stored in a user specific location, making them inaccessible to other users for pipeline reruns. Some of these temp files can be large and cleanup is also the responsibility of the user. + 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. > NB: You will need an account to use the HPC cluster on Cheaha in order to run the pipeline. If in doubt contact UAB IT Research Computing.

From 51871ea6fca317ed6fca37597cabea895d62cbba Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 31 Aug 2022 11:32:01 +0200 Subject: [PATCH 4/6] rnafusion setup for hasta usage --- conf/pipeline/rnafusion/hasta.config | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 conf/pipeline/rnafusion/hasta.config diff --git a/conf/pipeline/rnafusion/hasta.config b/conf/pipeline/rnafusion/hasta.config new file mode 100644 index 0000000..fdd7475 --- /dev/null +++ b/conf/pipeline/rnafusion/hasta.config @@ -0,0 +1,7 @@ +// rnafusion/hasta specific profile config for Clinical Genomics Stockholm usage + +params { + all = true + trim = true + fusioninspector_filter = true +} From 0851903f66068d4e05b43f6a296134098063a5a1 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 31 Aug 2022 14:19:07 +0200 Subject: [PATCH 5/6] include new config in pipeline configs file --- README.md | 1 + docs/pipeline/rnafusion/hasta.md | 19 +++++++++++++++++++ pipeline/rnafusion.config | 4 +++- 3 files changed, 23 insertions(+), 1 deletion(-) create mode 100644 docs/pipeline/rnafusion/hasta.md diff --git a/README.md b/README.md index 94ce55c..ae45869 100644 --- a/README.md +++ b/README.md @@ -198,6 +198,7 @@ Currently documentation is available for the following pipelines within specific - mag - [EVA](docs/pipeline/mag/eva.md) - rnafusion + - [HASTA](docs/pipeline/rnafusion/hasta.md) - [MUNIN](docs/pipeline/rnafusion/munin.md) - rnavar - [MUNIN](docs/pipeline/rnavar/munin.md) diff --git a/docs/pipeline/rnafusion/hasta.md b/docs/pipeline/rnafusion/hasta.md new file mode 100644 index 0000000..9f7813d --- /dev/null +++ b/docs/pipeline/rnafusion/hasta.md @@ -0,0 +1,19 @@ +# nf-core/configs: HASTA rnafusion specific configuration + +Extra specific configuration for rnafusion pipeline + +## Usage + +To use, run the pipeline with `-profile hasta`. + +This will download and launch the rnafusion specific [`hasta.config`](../../../conf/pipeline/rnafusion/munin.config) which has been pre-configured with a setup suitable for the `HASTA` cluster. + +Example: `nextflow run nf-core/rnafusion -profile hasta` + +## rnafusion specific configurations for HASTA + +Specific configurations for `HASTA` has been made for rnafusion. + +- Always run all the analysis steps (all = true) +- Use trimming (trim = true) +- Take the fusions identified by at least 2 fusion detection tools to the fusioninspector analysis (fusioninspector_filter = true) diff --git a/pipeline/rnafusion.config b/pipeline/rnafusion.config index 2d86d89..f5a4e47 100644 --- a/pipeline/rnafusion.config +++ b/pipeline/rnafusion.config @@ -9,5 +9,7 @@ */ profiles { + hasta { includeConfig "${params.custom_config_base}/conf/pipeline/rnafusion/hasta.config" } munin { includeConfig "${params.custom_config_base}/conf/pipeline/rnafusion/munin.config" } -} \ No newline at end of file + +} From 242101db16a342a45ef806e00ab20243327c4322 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 31 Aug 2022 14:26:32 +0200 Subject: [PATCH 6/6] fix extra space --- pipeline/rnafusion.config | 1 - 1 file changed, 1 deletion(-) diff --git a/pipeline/rnafusion.config b/pipeline/rnafusion.config index f5a4e47..894f6ab 100644 --- a/pipeline/rnafusion.config +++ b/pipeline/rnafusion.config @@ -11,5 +11,4 @@ profiles { hasta { includeConfig "${params.custom_config_base}/conf/pipeline/rnafusion/hasta.config" } munin { includeConfig "${params.custom_config_base}/conf/pipeline/rnafusion/munin.config" } - }