From 5e6981d0ee5ea25891902d11a6b709a73a22a1ec Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 11 Dec 2019 15:59:25 +0100 Subject: [PATCH 1/4] Export TZ in binac config --- conf/binac.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/conf/binac.config b/conf/binac.config index 8c3d493..d0dcef8 100644 --- a/conf/binac.config +++ b/conf/binac.config @@ -10,6 +10,11 @@ singularity { envWhitelist = 'TZ' } +env { + TZ='Europe/Berlin' +} + + process { beforeScript = 'module load devel/singularity/3.4.2' executor = 'pbs' From 49cd35918a22b336448f8584278ac7a498d8c44d Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 11 Dec 2019 15:59:58 +0100 Subject: [PATCH 2/4] Remove whitespace --- conf/binac.config | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/binac.config b/conf/binac.config index d0dcef8..28b071d 100644 --- a/conf/binac.config +++ b/conf/binac.config @@ -14,7 +14,6 @@ env { TZ='Europe/Berlin' } - process { beforeScript = 'module load devel/singularity/3.4.2' executor = 'pbs' From a6d08ed6460fd7090a182025957d141f52026989 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 11 Dec 2019 16:09:44 +0100 Subject: [PATCH 3/4] Adjust custom pipeline config for ampliseq on BINAC --- README.md | 31 ++++++++++++++++------------- conf/binac.config | 4 ---- conf/pipeline/ampliseq/binac.config | 11 ++++++++++ docs/pipeline/ampliseq/binac.md | 17 ++++++++++++++++ pipeline/ampliseq.config | 13 ++++++++++++ 5 files changed, 58 insertions(+), 18 deletions(-) create mode 100644 conf/pipeline/ampliseq/binac.config create mode 100644 docs/pipeline/ampliseq/binac.md create mode 100644 pipeline/ampliseq.config diff --git a/README.md b/README.md index e001d3e..fe813f5 100644 --- a/README.md +++ b/README.md @@ -6,20 +6,21 @@ A repository for hosting Nextflow configuration files containing custom paramete ## Table of contents -* [Table of contents](#table-of-contents) -* [Using an existing config](#using-an-existing-config) - * [Configuration and parameters](#configuration-and-parameters) - * [Offline usage](#offline-usage) -* [Adding a new config](#adding-a-new-config) - * [Checking user hostnames](#checking-user-hostnames) - * [Testing](#testing) - * [Documentation](#documentation) - * [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs) -* [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config) - * [Pipeline-specific documentation](#pipeline-specific-documentation) - * [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline) - * [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files) -* [Help](#help) +* [nf-core/configs](#img-srcdocsimagesnfcore-configs_logopng-altnf-coreconfigs-titlenf-coreconfigs) + * [Table of contents](#table-of-contents) + * [Using an existing config](#using-an-existing-config) + * [Configuration and parameters](#configuration-and-parameters) + * [Offline usage](#offline-usage) + * [Adding a new config](#adding-a-new-config) + * [Checking user hostnames](#checking-user-hostnames) + * [Testing](#testing) + * [Documentation](#documentation) + * [Uploading to nf-core/configs](#uploading-to-nf-coreconfigs) + * [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config) + * [Pipeline-specific documentation](#pipeline-specific-documentation) + * [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline) + * [Create the pipeline-specific nf-core/configs files](#create-the-pipeline-specific-nf-coreconfigs-files) + * [Help](#help) ## Using an existing config @@ -154,6 +155,8 @@ Note that pipeline-specific configs are not required and should only be added if Currently documentation is available for the following pipeline within the specific profile: +* ampliseq + * [BINAC](docs/pipeline/ampliseq/binac.md) * sarek * [MUNIN](docs/pipeline/sarek/munin.md) * eager diff --git a/conf/binac.config b/conf/binac.config index 28b071d..8c3d493 100644 --- a/conf/binac.config +++ b/conf/binac.config @@ -10,10 +10,6 @@ singularity { envWhitelist = 'TZ' } -env { - TZ='Europe/Berlin' -} - process { beforeScript = 'module load devel/singularity/3.4.2' executor = 'pbs' diff --git a/conf/pipeline/ampliseq/binac.config b/conf/pipeline/ampliseq/binac.config new file mode 100644 index 0000000..13629cf --- /dev/null +++ b/conf/pipeline/ampliseq/binac.config @@ -0,0 +1,11 @@ +// Profile config names for nf-core/configs + +params { + // Specific nf-core/configs params + config_profile_contact = 'Alexander Peltzer (@apeltzer)' + config_profile_description = 'nf-core/ampliseq BINAC profile provided by nf-core/configs' +} + +env { + TZ='Europe/Berlin' +} \ No newline at end of file diff --git a/docs/pipeline/ampliseq/binac.md b/docs/pipeline/ampliseq/binac.md new file mode 100644 index 0000000..a63e021 --- /dev/null +++ b/docs/pipeline/ampliseq/binac.md @@ -0,0 +1,17 @@ +# nf-core/configs: binac ampliseq specific configuration + +Extra specific configuration for the ampliseq pipeline. + +## Usage + +To use, run the pipeline with `-profile binac`. + +This will download and launch the ampliseq specific [`binac.config`](../conf/pipeline/ampliseq/binac.config) which has been pre-configured with a setup suitable for the BINAC cluster. + +Example: `nextflow run nf-core/ampliseq -profile binac` + +## ampliseq specific configurations for binac + +Specific configurations for BINAC has been made for ampliseq. + +* Specifies the `TZ` `ENV` variable to be `Europe/Berlin` to fix a QIIME2 issue diff --git a/pipeline/ampliseq.config b/pipeline/ampliseq.config new file mode 100644 index 0000000..6009d68 --- /dev/null +++ b/pipeline/ampliseq.config @@ -0,0 +1,13 @@ +/* + * ------------------------------------------------- + * nfcore/ampliseq custom profile Nextflow config file + * ------------------------------------------------- + * Config options for custom environments. + * Cluster-specific config options should be saved + * in the conf/pipeline/ampliseq folder and imported + * under a profile name here. + */ + +profiles { + binac { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/binac.config" } +} \ No newline at end of file From ecc850fd83f5f31294bb421290cde294e45e03ce Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 11 Dec 2019 16:13:15 +0100 Subject: [PATCH 4/4] Omit this in TOC --- README.md | 31 +++++++++++++++---------------- 1 file changed, 15 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index fe813f5..7f2665e 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# [![nf-core/configs](docs/images/nfcore-configs_logo.png "nf-core/configs")](https://github.com/nf-core/configs) +# [![nf-core/configs](docs/images/nfcore-configs_logo.png "nf-core/configs")](https://github.com/nf-core/configs) [![Lint Status](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg)](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg) @@ -6,21 +6,20 @@ A repository for hosting Nextflow configuration files containing custom paramete ## Table of contents -* [nf-core/configs](#img-srcdocsimagesnfcore-configs_logopng-altnf-coreconfigs-titlenf-coreconfigs) - * [Table of contents](#table-of-contents) - * [Using an existing config](#using-an-existing-config) - * [Configuration and parameters](#configuration-and-parameters) - * [Offline usage](#offline-usage) - * [Adding a new config](#adding-a-new-config) - * [Checking user hostnames](#checking-user-hostnames) - * [Testing](#testing) - * [Documentation](#documentation) - * [Uploading to nf-core/configs](#uploading-to-nf-coreconfigs) - * [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config) - * [Pipeline-specific documentation](#pipeline-specific-documentation) - * [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline) - * [Create the pipeline-specific nf-core/configs files](#create-the-pipeline-specific-nf-coreconfigs-files) - * [Help](#help) +* [Table of contents](#table-of-contents) +* [Using an existing config](#using-an-existing-config) + * [Configuration and parameters](#configuration-and-parameters) + * [Offline usage](#offline-usage) +* [Adding a new config](#adding-a-new-config) + * [Checking user hostnames](#checking-user-hostnames) + * [Testing](#testing) + * [Documentation](#documentation) + * [Uploading to nf-core/configs](#uploading-to-nf-coreconfigs) +* [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config) + * [Pipeline-specific documentation](#pipeline-specific-documentation) + * [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline) + * [Create the pipeline-specific nf-core/configs files](#create-the-pipeline-specific-nf-coreconfigs-files) +* [Help](#help) ## Using an existing config