From c8de9be7014ee85359caddc04aefd725974d5d6b Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Tue, 31 Mar 2020 15:17:24 +0200 Subject: [PATCH 1/5] Adding UPPMAX specific config for ampliseq --- conf/pipeline/ampliseq/uppmax.config | 15 +++++++++++++++ docs/pipeline/ampliseq/uppmax.md | 17 +++++++++++++++++ pipeline/ampliseq.config | 6 +++++- 3 files changed, 37 insertions(+), 1 deletion(-) create mode 100644 conf/pipeline/ampliseq/uppmax.config create mode 100644 docs/pipeline/ampliseq/uppmax.md diff --git a/conf/pipeline/ampliseq/uppmax.config b/conf/pipeline/ampliseq/uppmax.config new file mode 100644 index 0000000..36a1c3b --- /dev/null +++ b/conf/pipeline/ampliseq/uppmax.config @@ -0,0 +1,15 @@ +// Profile config names for nf-core/configs + +params { + // Specific nf-core/configs params + config_profile_contact = 'Daniel Lundin (daniel.lundin@lnu.se)' + config_profile_description = 'nf-core/ampliseq UPPMAX profile provided by nf-core/configs' +} + +withName: make_SILVA_132_16S_classifier { + clusterOptions = { "-A $params.project -C fat -p node -N 1 ${params.clusterOptions ?: ''}" } +} + +withName: classifier { + clusterOptions = { "-A $params.project -C fat -p node -N 1 ${params.clusterOptions ?: ''}" } +} diff --git a/docs/pipeline/ampliseq/uppmax.md b/docs/pipeline/ampliseq/uppmax.md new file mode 100644 index 0000000..7061bdc --- /dev/null +++ b/docs/pipeline/ampliseq/uppmax.md @@ -0,0 +1,17 @@ +# nf-core/configs: uppmax ampliseq specific configuration + +Extra specific configuration for the ampliseq pipeline. + +## Usage + +To use, run the pipeline with `-profile uppmax`. + +This will download and launch the ampliseq specific [`uppmax.config`](../../../conf/pipeline/ampliseq/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX cluster. + +Example: `nextflow run nf-core/ampliseq -profile uppmax` + +## ampliseq specific configurations for uppmax + +Specific configurations for UPPMAX has been made for ampliseq. + +* Makes sure that a fat node is allocated for training and applying a Bayesian classifier. diff --git a/pipeline/ampliseq.config b/pipeline/ampliseq.config index 6009d68..7b36722 100644 --- a/pipeline/ampliseq.config +++ b/pipeline/ampliseq.config @@ -10,4 +10,8 @@ profiles { binac { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/binac.config" } -} \ No newline at end of file +} + +profiles { + uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/uppmax.config" } +} From 79ef94de4782f17b154dce6821e50c9e36fb8697 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Tue, 31 Mar 2020 15:33:04 +0200 Subject: [PATCH 2/5] Update pipeline/ampliseq.config Co-Authored-By: Maxime Garcia --- pipeline/ampliseq.config | 1 - 1 file changed, 1 deletion(-) diff --git a/pipeline/ampliseq.config b/pipeline/ampliseq.config index 7b36722..167877c 100644 --- a/pipeline/ampliseq.config +++ b/pipeline/ampliseq.config @@ -12,6 +12,5 @@ profiles { binac { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/binac.config" } } -profiles { uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/uppmax.config" } } From 5a557ed7d5b08091eb9f89c6df4c4439c73dbeaa Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Tue, 31 Mar 2020 15:33:12 +0200 Subject: [PATCH 3/5] Update pipeline/ampliseq.config Co-Authored-By: Maxime Garcia --- pipeline/ampliseq.config | 1 - 1 file changed, 1 deletion(-) diff --git a/pipeline/ampliseq.config b/pipeline/ampliseq.config index 167877c..c86e152 100644 --- a/pipeline/ampliseq.config +++ b/pipeline/ampliseq.config @@ -11,6 +11,5 @@ profiles { binac { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/binac.config" } } - uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/uppmax.config" } } From e0f9374272c2e97954b611fa3738de70d3e076ba Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Tue, 31 Mar 2020 15:33:19 +0200 Subject: [PATCH 4/5] Update pipeline/ampliseq.config Co-Authored-By: Maxime Garcia --- pipeline/ampliseq.config | 1 - 1 file changed, 1 deletion(-) diff --git a/pipeline/ampliseq.config b/pipeline/ampliseq.config index c86e152..9cb19f7 100644 --- a/pipeline/ampliseq.config +++ b/pipeline/ampliseq.config @@ -10,6 +10,5 @@ profiles { binac { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/binac.config" } -} uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/uppmax.config" } } From e77cd380929e33a430ef62925cdbb81dd4f8ed50 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Tue, 31 Mar 2020 15:42:25 +0200 Subject: [PATCH 5/5] Adding ampliseq/UPPMAX doc to README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 95c1d79..49283ed 100644 --- a/README.md +++ b/README.md @@ -165,6 +165,7 @@ Currently documentation is available for the following pipeline within the speci * ampliseq * [BINAC](docs/pipeline/ampliseq/binac.md) + * [UPPMAX](docs/pipeline/ampliseq/uppmax.md) * eager * [SHH](docs/pipeline/eager/shh.md) * rnafusion