From cece8536636aade75dc2b38fe0cede689726dedc Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 10 Mar 2020 21:03:24 -0500 Subject: [PATCH 01/15] fix(ganymede): use singularity/2.4.5 Our 3.2.1 doesn't work right with snakemake or nextflow --- conf/utd_ganymede.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/utd_ganymede.config b/conf/utd_ganymede.config index 8b72448..465deb5 100644 --- a/conf/utd_ganymede.config +++ b/conf/utd_ganymede.config @@ -12,7 +12,7 @@ singularity { } process { - beforeScript = 'module load singularity' + beforeScript = 'module load singularity/2.4.5' executor = 'slurm' queue = 'genomics' } From dd1ddf864b100c416fd376905d6d602d7db9e76a Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Wed, 11 Mar 2020 14:01:28 +0100 Subject: [PATCH 02/15] update sarek munin config --- conf/pipeline/sarek/munin.config | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/conf/pipeline/sarek/munin.config b/conf/pipeline/sarek/munin.config index e4413f2..ff31a7f 100644 --- a/conf/pipeline/sarek/munin.config +++ b/conf/pipeline/sarek/munin.config @@ -1,4 +1,4 @@ -// Profile config names for nf-core/configs + // sarek/munin specific profile config params { // Specific nf-core/configs params @@ -6,17 +6,23 @@ params { config_profile_description = 'nf-core/sarek MUNIN profile provided by nf-core/configs' // Specific nf-core/sarek params - annotation_cache = true - pon = '/data1/PON/vcfs/BTB.PON.vcf.gz' - pon_index = '/data1/PON/vcfs/BTB.PON.vcf.gz.tbi' - snpEff_cache = '/data1/cache/snpEff/' - vep_cache = '/data1/cache/VEP/' + annotation_cache = true + cadd_cache = true + cadd_indels = '/data1/cache/CADD/v1.4/InDels.tsv.gz' + cadd_indels_tbi = '/data1/cache/CADD/v1.4/InDels.tsv.gz.tbi' + cadd_wg_snvs = '/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz' + cadd_wg_snvs_tbi = '/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi' + pon = '/data1/PON/vcfs/BTB.PON.vcf.gz' + pon_index = '/data1/PON/vcfs/BTB.PON.vcf.gz.tbi' + snpeff_cache = '/data1/cache/snpEff/' + vep_cache = '/data1/cache/VEP/' + vep_cache_version = 95 } // Specific nf-core/sarek process configuration process { withLabel:sentieon { - module = {params.sentieon ? 'sentieon/201808.05' : null} + module = {params.sentieon ? 'sentieon/201911.00' : null} container = {params.sentieon ? null : container} } } From d24a296a016e437ec62babc81bd2004f35629be5 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Wed, 11 Mar 2020 14:02:01 +0100 Subject: [PATCH 03/15] add munin/rnafusion specific config --- conf/pipeline/rnafusion/munin.config | 64 ++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 conf/pipeline/rnafusion/munin.config diff --git a/conf/pipeline/rnafusion/munin.config b/conf/pipeline/rnafusion/munin.config new file mode 100644 index 0000000..d44a1f3 --- /dev/null +++ b/conf/pipeline/rnafusion/munin.config @@ -0,0 +1,64 @@ +/* + * ------------------------------------------------- + * Nextflow config file for Munin Singularity + * ------------------------------------------------- + */ + +params { + max_cpus = 24 + max_memory = 256.GB + max_time = 72.h + container_version = '1.1.0' + + // Tool versions + arriba_version = '1.1.0' + ericscript_version = '0.5.5' + fusioncatcher_version = '1.20' + fusion_inspector_version = '1.3.1-star2.7.0f' + pizzly_version = '0.37.3' + squid_version = '1.5-star2.7.0f' + star_fusion_version = '1.6.0' + + // Paths + reference_base = '/data1/references/rnafusion' + containerPath = "file:///data1/containers/rnafusion_containers_v${container_version}" + containerPathCommon = "file:///data1/containers/rnafusion_common" + + // References + fasta = "${params.reference_base}/1.1.0/Homo_sapiens.GRCh38_r97.all.fa" + gtf = "${params.reference_base}/1.1.0/Homo_sapiens.GRCh38_r97.gtf" + transcript = "${params.reference_base}/1.1.0/Homo_sapiens.GRCh38_r97.cdna.all.fa.gz" + databases = "${params.reference_base}/1.1.0/databases" + + star_index = "${params.reference_base}/1.1.0/star_index/star" + arriba_ref = "${params.reference_base}/arriba_ref" + fusioncatcher_ref = "${params.reference_base}/fusioncatcher_ref/human_v98" + star_fusion_ref = "${params.reference_base}/star_fusion/1.6.0/ensembl/ctat_genome_lib_build_dir" + ericscript_ref = "${params.reference_base}/ericscript_ref/ericscript_db_homosapiens_ensembl84" +} + +process { + container = "${params.containerPath}/rnafusion_1.1.0.img" + + withName: "arriba|arriba_visualization" { + container = "${params.containerPath}/rnafusion_arriba_v${params.arriba_version}.img" + } + withName: "star_fusion|download_star_fusion" { + container = "${params.containerPath}/rnafusion_star-fusion_v${params.star_fusion_version}.img" + } + withName:fusioncatcher { + container = "${params.containerPath}/rnafusion_fusioncatcher_v${params.fusioncatcher_version}.img" + } + withName:fusion_inspector { + container = "${params.containerPath}/rnafusion_fusion-inspector_v${params.fusion_inspector_version}.img" + } + withName:ericscript { + container = "${params.containerPathCommon}/rnafusion_ericscript_v${params.ericscript_version}.img" + } + withName:pizzly { + container = "${params.containerPathCommon}/rnafusion_pizzly_v${params.pizzly_version}.img" + } + withName:squid { + container = "${params.containerPath}/rnafusion_squid_v${params.squid_version}.img" + } +} \ No newline at end of file From 250035e71d0655c87f02a10749738505acd1c847 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Wed, 11 Mar 2020 14:11:23 +0100 Subject: [PATCH 04/15] fix path to config files --- docs/pipeline/ampliseq/binac.md | 2 +- docs/pipeline/eager/shh.md | 2 +- docs/pipeline/sarek/munin.md | 2 +- docs/pipeline/sarek/uppmax.md | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/pipeline/ampliseq/binac.md b/docs/pipeline/ampliseq/binac.md index a63e021..fb3403e 100644 --- a/docs/pipeline/ampliseq/binac.md +++ b/docs/pipeline/ampliseq/binac.md @@ -6,7 +6,7 @@ Extra specific configuration for the ampliseq pipeline. 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. +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` diff --git a/docs/pipeline/eager/shh.md b/docs/pipeline/eager/shh.md index a0dc092..b77ede4 100644 --- a/docs/pipeline/eager/shh.md +++ b/docs/pipeline/eager/shh.md @@ -6,7 +6,7 @@ Extra specific configuration for eager pipeline To use, run the pipeline with `-profile shh`. -This will download and launch the eager specific [`shh.config`](../conf/pipeline/eager/shh.config) which has been pre-configured with a setup suitable for the shh cluster. +This will download and launch the eager specific [`shh.config`](../../../conf/pipeline/eager/shh.config) which has been pre-configured with a setup suitable for the shh cluster. Example: `nextflow run nf-core/eager -profile shh` diff --git a/docs/pipeline/sarek/munin.md b/docs/pipeline/sarek/munin.md index ce411c1..fc1636f 100644 --- a/docs/pipeline/sarek/munin.md +++ b/docs/pipeline/sarek/munin.md @@ -6,7 +6,7 @@ Extra specific configuration for sarek pipeline To use, run the pipeline with `-profile munin`. -This will download and launch the sarek specific [`munin.config`](../conf/pipeline/sarek/munin.config) which has been pre-configured with a setup suitable for the MUNIN cluster. +This will download and launch the sarek specific [`munin.config`](../../../conf/pipeline/sarek/munin.config) which has been pre-configured with a setup suitable for the MUNIN cluster. Example: `nextflow run nf-core/sarek -profile munin` diff --git a/docs/pipeline/sarek/uppmax.md b/docs/pipeline/sarek/uppmax.md index ab8d85e..e612a41 100644 --- a/docs/pipeline/sarek/uppmax.md +++ b/docs/pipeline/sarek/uppmax.md @@ -6,7 +6,7 @@ Extra specific configuration for sarek pipeline To use, run the pipeline with `-profile uppmax`. -This will download and launch the sarek specific [`uppmax.config`](../conf/pipeline/sarek/uppmax.config) which has been pre-configured with a setup suitable for uppmax clusters. +This will download and launch the sarek specific [`uppmax.config`](../../../conf/pipeline/sarek/uppmax.config) which has been pre-configured with a setup suitable for uppmax clusters. Example: `nextflow run nf-core/sarek -profile uppmax` From 7c60096952539b7266cb82200f0dee77b5cef742 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Wed, 11 Mar 2020 14:17:24 +0100 Subject: [PATCH 05/15] update docs for munin/sarek specific config --- docs/pipeline/sarek/munin.md | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/docs/pipeline/sarek/munin.md b/docs/pipeline/sarek/munin.md index fc1636f..5f9511b 100644 --- a/docs/pipeline/sarek/munin.md +++ b/docs/pipeline/sarek/munin.md @@ -6,17 +6,22 @@ Extra specific configuration for sarek pipeline To use, run the pipeline with `-profile munin`. -This will download and launch the sarek specific [`munin.config`](../../../conf/pipeline/sarek/munin.config) which has been pre-configured with a setup suitable for the MUNIN cluster. +This will download and launch the sarek specific [`munin.config`](../../../conf/pipeline/sarek/munin.config) which has been pre-configured with a setup suitable for the `MUNIN` cluster. Example: `nextflow run nf-core/sarek -profile munin` ## Sarek specific configurations for MUNIN -Specific configurations for MUNIN has been made for sarek. +Specific configurations for `MUNIN` has been made for sarek. -* Params `annotation_cache` set to `true` -* Path to `snpEff_cache`: `/data1/cache/snpEff/` +* Params `annotation_cache` and `cadd_cache` set to `true` +* Params `vep_cache_version` set to `95` +* Path to `snpeff_cache`: `/data1/cache/snpEff/` * Path to `vep_cache`: `/data1/cache/VEP/` * Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz` * Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi` +* Path to `cadd_indels`: `/data1/cache/CADD/v1.4/InDels.tsv.gz` +* Path to `cadd_indels_tbi`: `/data1/cache/CADD/v1.4/InDels.tsv.gz.tbi` +* Path to `cadd_wg_snvs`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz` +* Path to `cadd_wg_snvs_tbi`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi` * Load module `Sentieon` for Processes with `sentieon` labels From d4bea56f5241d6dee2aa9ba9d7ec09cdbcf8210f Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Wed, 11 Mar 2020 14:23:23 +0100 Subject: [PATCH 06/15] add munin/rnafusion specific docs + markdownlint --- README.md | 104 ++++++++++++++++--------------- docs/pipeline/rnafusion/munin.md | 19 ++++++ 2 files changed, 72 insertions(+), 51 deletions(-) create mode 100644 docs/pipeline/rnafusion/munin.md diff --git a/README.md b/README.md index 94f999a..f38242d 100644 --- a/README.md +++ b/README.md @@ -6,19 +6,19 @@ A repository for hosting Nextflow configuration files containing custom paramete ## 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](#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 @@ -93,33 +93,33 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs Currently documentation is available for the following systems: -* [AWSBATCH](docs/awsbatch.md) -* [BIGPURPLE](docs/bigpurple.md) -* [BINAC](docs/binac.md) -* [CBE](docs/cbe.md) -* [CCGA_DX](docs/ccga_dx.md) -* [CCGA_MED](docs/ccga_med.md) -* [CFC](docs/cfc.md) -* [CRICK](docs/crick.md) -* [CZBIOHUB_AWS](docs/czbiohub.md) -* [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md) -* [DENBI_QBIC](docs/denbi_qbic.md) -* [EBC](docs/ebc.md) -* [GENOTOUL](docs/genotoul.md) -* [GENOUEST](docs/genouest.md) -* [GIS](docs/gis.md) -* [GOOGLE](docs/google.md) -* [HEBBE](docs/hebbe.md) -* [KRAKEN](docs/kraken.md) -* [MUNIN](docs/munin.md) -* [PASTEUR](docs/pasteur.md) -* [PHOENIX](docs/phoenix.md) -* [PRINCE](docs/prince.md) -* [SHH](docs/shh.md) -* [UCT_HEX](docs/uct_hex.md) -* [UPPMAX](docs/uppmax.md) -* [UTD_GANYMEDE](docs/utd_ganymede.md) -* [UZH](docs/uzh.md) +- [AWSBATCH](docs/awsbatch.md) +- [BIGPURPLE](docs/bigpurple.md) +- [BINAC](docs/binac.md) +- [CBE](docs/cbe.md) +- [CCGA_DX](docs/ccga_dx.md) +- [CCGA_MED](docs/ccga_med.md) +- [CFC](docs/cfc.md) +- [CRICK](docs/crick.md) +- [CZBIOHUB_AWS](docs/czbiohub.md) +- [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md) +- [DENBI_QBIC](docs/denbi_qbic.md) +- [EBC](docs/ebc.md) +- [GENOTOUL](docs/genotoul.md) +- [GENOUEST](docs/genouest.md) +- [GIS](docs/gis.md) +- [GOOGLE](docs/google.md) +- [HEBBE](docs/hebbe.md) +- [KRAKEN](docs/kraken.md) +- [MUNIN](docs/munin.md) +- [PASTEUR](docs/pasteur.md) +- [PHOENIX](docs/phoenix.md) +- [PRINCE](docs/prince.md) +- [SHH](docs/shh.md) +- [UCT_HEX](docs/uct_hex.md) +- [UPPMAX](docs/uppmax.md) +- [UTD_GANYMEDE](docs/utd_ganymede.md) +- [UZH](docs/uzh.md) ### Uploading to `nf-core/configs` @@ -163,13 +163,15 @@ 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) -* eager - * [SHH](docs/pipeline/eager/shh.md) -* sarek - * [MUNIN](docs/pipeline/sarek/munin.md) - * [UPPMAX](docs/pipeline/sarek/uppmax.md) +- ampliseq + - [BINAC](docs/pipeline/ampliseq/binac.md) +- eager + - [SHH](docs/pipeline/eager/shh.md) +- rnafusion + - [MUNIN](docs/pipeline/rnafusion/munin.md) +- sarek + - [MUNIN](docs/pipeline/sarek/munin.md) + - [UPPMAX](docs/pipeline/sarek/uppmax.md) ### Enabling pipeline-specific configs within a pipeline @@ -198,7 +200,7 @@ We will be notified automatically when you have created your pull request, and p [Fork](https://help.github.com/articles/fork-a-repo/) the [`nf-core/configs`](https://github.com/nf-core/configs/) repository to your own GitHub account. And add or edit the following files in the local clone of your fork. -* `pipeline/.config` +- `pipeline/.config` If not already created, create the `pipeline/.config` file, and add your custom profile to the profile scope @@ -208,18 +210,18 @@ profiles { } ``` -* `conf/pipeline//.config` +- `conf/pipeline//.config` Add the custom configuration file to the `conf/pipeline//` directory. Make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` to the top of `pipeline/.config` and set to reasonable values. Users will get information on who wrote the pipeline-specific configuration profile then when executing the nf-core pipeline and can report back if there are things missing for example. -* `docs/pipeline//.md` +- `docs/pipeline//.md` Add the documentation file to the `docs/pipeline//` directory. You will also need to edit and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) file in the top-level directory of the clone. -* `README.md` +- `README.md` Edit this file, and add the new pipeline-specific institutional profile to the list in the section Pipeline specific documentation diff --git a/docs/pipeline/rnafusion/munin.md b/docs/pipeline/rnafusion/munin.md new file mode 100644 index 0000000..daa1dd1 --- /dev/null +++ b/docs/pipeline/rnafusion/munin.md @@ -0,0 +1,19 @@ +# nf-core/configs: MUNIN rnafusion specific configuration + +Extra specific configuration for rnafusion pipeline + +## Usage + +To use, run the pipeline with `-profile munin`. + +This will download and launch the rnafusion specific [`munin.config`](../../../conf/pipeline/rnafusion/munin.config) which has been pre-configured with a setup suitable for the `MUNIN` cluster. + +Example: `nextflow run nf-core/rnafusion -profile munin` + +## rnafusion specific configurations for MUNIN + +Specific configurations for `MUNIN` has been made for rnafusion. + +* `cpus`, `memory` and `time` max requirements. +* Paths to specific containers +* Paths to specific references and indexes From 6be17167972fff5616c29c485ecb1ed0a0e50acb Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Wed, 11 Mar 2020 15:39:36 +0100 Subject: [PATCH 07/15] revert * to - changes --- README.md | 80 +++++++++++++++++++++++++++---------------------------- 1 file changed, 40 insertions(+), 40 deletions(-) diff --git a/README.md b/README.md index f38242d..3b60196 100644 --- a/README.md +++ b/README.md @@ -93,33 +93,33 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs Currently documentation is available for the following systems: -- [AWSBATCH](docs/awsbatch.md) -- [BIGPURPLE](docs/bigpurple.md) -- [BINAC](docs/binac.md) -- [CBE](docs/cbe.md) -- [CCGA_DX](docs/ccga_dx.md) -- [CCGA_MED](docs/ccga_med.md) -- [CFC](docs/cfc.md) -- [CRICK](docs/crick.md) -- [CZBIOHUB_AWS](docs/czbiohub.md) -- [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md) -- [DENBI_QBIC](docs/denbi_qbic.md) -- [EBC](docs/ebc.md) -- [GENOTOUL](docs/genotoul.md) -- [GENOUEST](docs/genouest.md) -- [GIS](docs/gis.md) -- [GOOGLE](docs/google.md) -- [HEBBE](docs/hebbe.md) -- [KRAKEN](docs/kraken.md) -- [MUNIN](docs/munin.md) -- [PASTEUR](docs/pasteur.md) -- [PHOENIX](docs/phoenix.md) -- [PRINCE](docs/prince.md) -- [SHH](docs/shh.md) -- [UCT_HEX](docs/uct_hex.md) -- [UPPMAX](docs/uppmax.md) -- [UTD_GANYMEDE](docs/utd_ganymede.md) -- [UZH](docs/uzh.md) +* [AWSBATCH](docs/awsbatch.md) +* [BIGPURPLE](docs/bigpurple.md) +* [BINAC](docs/binac.md) +* [CBE](docs/cbe.md) +* [CCGA_DX](docs/ccga_dx.md) +* [CCGA_MED](docs/ccga_med.md) +* [CFC](docs/cfc.md) +* [CRICK](docs/crick.md) +* [CZBIOHUB_AWS](docs/czbiohub.md) +* [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md) +* [DENBI_QBIC](docs/denbi_qbic.md) +* [EBC](docs/ebc.md) +* [GENOTOUL](docs/genotoul.md) +* [GENOUEST](docs/genouest.md) +* [GIS](docs/gis.md) +* [GOOGLE](docs/google.md) +* [HEBBE](docs/hebbe.md) +* [KRAKEN](docs/kraken.md) +* [MUNIN](docs/munin.md) +* [PASTEUR](docs/pasteur.md) +* [PHOENIX](docs/phoenix.md) +* [PRINCE](docs/prince.md) +* [SHH](docs/shh.md) +* [UCT_HEX](docs/uct_hex.md) +* [UPPMAX](docs/uppmax.md) +* [UTD_GANYMEDE](docs/utd_ganymede.md) +* [UZH](docs/uzh.md) ### Uploading to `nf-core/configs` @@ -163,15 +163,15 @@ 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) -- eager - - [SHH](docs/pipeline/eager/shh.md) -- rnafusion - - [MUNIN](docs/pipeline/rnafusion/munin.md) -- sarek - - [MUNIN](docs/pipeline/sarek/munin.md) - - [UPPMAX](docs/pipeline/sarek/uppmax.md) +* ampliseq + * [BINAC](docs/pipeline/ampliseq/binac.md) +* eager + * [SHH](docs/pipeline/eager/shh.md) +* rnafusion + * [MUNIN](docs/pipeline/rnafusion/munin.md) +* sarek + * [MUNIN](docs/pipeline/sarek/munin.md) + * [UPPMAX](docs/pipeline/sarek/uppmax.md) ### Enabling pipeline-specific configs within a pipeline @@ -200,7 +200,7 @@ We will be notified automatically when you have created your pull request, and p [Fork](https://help.github.com/articles/fork-a-repo/) the [`nf-core/configs`](https://github.com/nf-core/configs/) repository to your own GitHub account. And add or edit the following files in the local clone of your fork. -- `pipeline/.config` +* `pipeline/.config` If not already created, create the `pipeline/.config` file, and add your custom profile to the profile scope @@ -210,18 +210,18 @@ profiles { } ``` -- `conf/pipeline//.config` +* `conf/pipeline//.config` Add the custom configuration file to the `conf/pipeline//` directory. Make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` to the top of `pipeline/.config` and set to reasonable values. Users will get information on who wrote the pipeline-specific configuration profile then when executing the nf-core pipeline and can report back if there are things missing for example. -- `docs/pipeline//.md` +* `docs/pipeline//.md` Add the documentation file to the `docs/pipeline//` directory. You will also need to edit and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) file in the top-level directory of the clone. -- `README.md` +* `README.md` Edit this file, and add the new pipeline-specific institutional profile to the list in the section Pipeline specific documentation From 4a7f98a83b9de32869efbe993262afd2c88d9573 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Wed, 11 Mar 2020 15:41:58 +0100 Subject: [PATCH 08/15] update TOC --- README.md | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index 3b60196..95c1d79 100644 --- a/README.md +++ b/README.md @@ -6,19 +6,19 @@ A repository for hosting Nextflow configuration files containing custom paramete ## 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](#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 From 0f34d757a9eb061c6e1d075a769d9f83dea8f5dd Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Wed, 11 Mar 2020 15:48:17 +0100 Subject: [PATCH 09/15] Update munin.config --- conf/pipeline/rnafusion/munin.config | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/conf/pipeline/rnafusion/munin.config b/conf/pipeline/rnafusion/munin.config index d44a1f3..549d957 100644 --- a/conf/pipeline/rnafusion/munin.config +++ b/conf/pipeline/rnafusion/munin.config @@ -1,8 +1,4 @@ -/* - * ------------------------------------------------- - * Nextflow config file for Munin Singularity - * ------------------------------------------------- - */ +// rnafusion/munin specific profile config params { max_cpus = 24 @@ -61,4 +57,4 @@ process { withName:squid { container = "${params.containerPath}/rnafusion_squid_v${params.squid_version}.img" } -} \ No newline at end of file +} From b6d52fdb89665f022971e75fc4c0856275291ad3 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Wed, 11 Mar 2020 15:48:29 +0100 Subject: [PATCH 10/15] Update conf/pipeline/sarek/munin.config --- conf/pipeline/sarek/munin.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/pipeline/sarek/munin.config b/conf/pipeline/sarek/munin.config index ff31a7f..d22e5e9 100644 --- a/conf/pipeline/sarek/munin.config +++ b/conf/pipeline/sarek/munin.config @@ -1,4 +1,4 @@ - // sarek/munin specific profile config +// sarek/munin specific profile config params { // Specific nf-core/configs params From 123132d89a46ac9aec95373ef8a049204be4ea5f Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Thu, 12 Mar 2020 17:23:55 +0100 Subject: [PATCH 11/15] Update munin.config fix typo --- conf/pipeline/sarek/munin.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/pipeline/sarek/munin.config b/conf/pipeline/sarek/munin.config index d22e5e9..039d117 100644 --- a/conf/pipeline/sarek/munin.config +++ b/conf/pipeline/sarek/munin.config @@ -16,7 +16,7 @@ params { pon_index = '/data1/PON/vcfs/BTB.PON.vcf.gz.tbi' snpeff_cache = '/data1/cache/snpEff/' vep_cache = '/data1/cache/VEP/' - vep_cache_version = 95 + vep_cache_version = '95' } // Specific nf-core/sarek process configuration From 52369ba6adde0edff9f77e701e7119022ba943eb Mon Sep 17 00:00:00 2001 From: Olga Botvinnik Date: Tue, 17 Mar 2020 16:45:20 -0700 Subject: [PATCH 12/15] Add AaegL5.0 config --- conf/czbiohub_aws.config | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/conf/czbiohub_aws.config b/conf/czbiohub_aws.config index 9d17a48..b32fb6d 100644 --- a/conf/czbiohub_aws.config +++ b/conf/czbiohub_aws.config @@ -50,6 +50,7 @@ params { // No final slash because it's added later gencode_base = "s3://czbiohub-reference/gencode" transgenes_base = "s3://czbiohub-reference/transgenes" + refseq_base = "s3://czbiohub-reference/ncbi/genomes/refseq/" // AWS configurations awsregion = "us-west-2" @@ -79,6 +80,12 @@ params { transcript_fasta = "${params.gencode_base}/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa" star = "${params.gencode_base}/mouse/vM21/STARIndex/" } + 'AaegL5.0' { + fasta = "${params.refseq_base}/invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna" + gtf = "${params.refseq_base}/invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf" + bed = "${params.refseq_base}/invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed" + star = "${params.refseq_base}/invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/" + } } transgenes { From c81f693f738da41002c7cf4db105e3391c89a725 Mon Sep 17 00:00:00 2001 From: ggabernet Date: Mon, 23 Mar 2020 17:16:34 +0100 Subject: [PATCH 13/15] add cfc_dev config --- conf/cfc.config | 2 +- conf/cfc_dev.config | 28 ++++++++++++++++++++++++++++ 2 files changed, 29 insertions(+), 1 deletion(-) create mode 100644 conf/cfc_dev.config diff --git a/conf/cfc.config b/conf/cfc.config index d1a109a..62d3626 100644 --- a/conf/cfc.config +++ b/conf/cfc.config @@ -1,7 +1,7 @@ //Profile config names for nf-core/configs params { config_profile_description = 'QBiC Core Facility cluster profile provided by nf-core/configs.' - config_profile_contact = 'Alexander Peltzer (@apeltzer)' + config_profile_contact = 'Gisela Gabernet (@ggabernet)' config_profile_url = 'http://qbic.uni-tuebingen.de/' } diff --git a/conf/cfc_dev.config b/conf/cfc_dev.config new file mode 100644 index 0000000..a7ebf2f --- /dev/null +++ b/conf/cfc_dev.config @@ -0,0 +1,28 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'QBiC Core Facility cluster dev profile without container cache provided by nf-core/configs.' + config_profile_contact = 'Gisela Gabernet (@ggabernet)' + config_profile_url = 'http://qbic.uni-tuebingen.de/' +} + +singularity { + enabled = true +} + +process { + beforeScript = 'module load devel/singularity/3.4.2' + executor = 'slurm' + queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' } +} + +weblog{ + enabled = true + url = 'https://services.qbic.uni-tuebingen.de/flowstore/workflows' +} + +params { + igenomes_base = '/nfsmounts/igenomes' + max_memory = 1999.GB + max_cpus = 128 + max_time = 140.h +} \ No newline at end of file From d02e2b8a36d362d7a55df4636d4cdba382536338 Mon Sep 17 00:00:00 2001 From: ggabernet Date: Mon, 23 Mar 2020 17:22:02 +0100 Subject: [PATCH 14/15] add cfc_dev and warning for binac and cfc --- nfcore_custom.config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/nfcore_custom.config b/nfcore_custom.config index 383eaf0..ea2238a 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -17,6 +17,7 @@ profiles { ccga_dx { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" } ccga_med { includeConfig "${params.custom_config_base}/conf/ccga_med.config" } cfc { includeConfig "${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" } czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" } czbiohub_aws_highpriority { @@ -47,7 +48,9 @@ profiles { params { // This is a groovy map, not a nextflow parameter set hostnames = [ + binac: ['.binac.uni-tuebingen.de'], cbe: ['.cbe.vbc.ac.at'], + cfc: ['.hpc.uni-tuebingen.de'], crick: ['.thecrick.org'], genotoul: ['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest: ['.genouest.org'], From fa01e6c5c18861f22b153619981ab4ecf8421dbf Mon Sep 17 00:00:00 2001 From: ggabernet Date: Mon, 23 Mar 2020 17:27:36 +0100 Subject: [PATCH 15/15] add cfc_dev to test 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 0917dd2..bdc485b 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: matrix: - profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'utd_ganymede', 'uzh'] + profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'utd_ganymede', 'uzh'] steps: - uses: actions/checkout@v1 - name: Install Nextflow