From 1191863e1c03327c304e1e07925fc3a575806fc3 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 13 Mar 2019 17:15:16 +0100 Subject: [PATCH 1/2] Removed params.config_profile_name, added params.hostnames --- README.md | 9 ++++++++- conf/binac.config | 2 +- conf/ccga.config | 3 +-- conf/cfc.config | 1 - conf/crick.config | 3 +-- conf/gis.config | 15 ++++++--------- conf/hebbe.config | 3 +-- conf/mendel.config | 1 - conf/munin.config | 1 - conf/phoenix.config | 1 - conf/shh.config | 1 - conf/uct_hex.config | 2 -- conf/uppmax-devel.config | 1 - conf/uppmax.config | 1 - conf/uzh.config | 1 - nfcore_custom.config | 14 +++++++++++--- 16 files changed, 29 insertions(+), 30 deletions(-) diff --git a/README.md b/README.md index 6a53642..acb2ea4 100644 --- a/README.md +++ b/README.md @@ -58,7 +58,14 @@ nextflow run /path/to/pipeline/ -c /path/to/my/configs/configs-master/conf/my_co If you decide to upload your custom config file to `nf-core/configs` then this will ensure that your custom config file will be automatically downloaded, and available at run-time to all nf-core pipelines, and to everyone within your organisation. You will simply have to specify `-profile ` in the command used to run the pipeline. See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples. -Please also make sure to add an extra `params` section with `params. config_profile_name`, `params.config_profile_description`, `params.config_profile_contact` and `params.config_profile_url` set to reasonable values. Users will get information on who wrote the configuration profile then when executing a nf-core pipeline and can report back if there are things missing for example. +Please also make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` and `params.config_profile_url` set to reasonable values. Users will get information on who wrote the configuration profile then when executing a nf-core pipeline and can report back if there are things missing for example. + +## Checking user hostnames + +If your cluster has a set of consistent hostnames, nf-core pipelines can check that users are using your profile. +Add one or more hostname substrings to `params.hostnames` under a key that matches the profile name. +If the user's hostname contains this string at the start of a run or when a run fails and their profile +does not contain the profile name, a warning message will be printed. ### Testing diff --git a/conf/binac.config b/conf/binac.config index 12da68d..3cd1edc 100644 --- a/conf/binac.config +++ b/conf/binac.config @@ -1,10 +1,10 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'BINAC' config_profile_description = 'BINAC cluster profile provided by nf-core/configs.' config_profile_contact = 'Alexander Peltzer (@apeltzer)' config_profile_url = 'https://www.bwhpc-c5.de/wiki/index.php/Category:BwForCluster_BinAC' } + singularity { enabled = true } diff --git a/conf/ccga.config b/conf/ccga.config index 7dff7c7..f29db9c 100644 --- a/conf/ccga.config +++ b/conf/ccga.config @@ -1,6 +1,5 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'CCGA' config_profile_description = 'CCGA cluster profile provided by nf-core/configs.' config_profile_contact = 'Marc Hoeppner (@marchoeppner)' config_profile_url = 'https://www.ikmb.uni-kiel.de/' @@ -25,7 +24,7 @@ process { clusterOptions = { "--qos=ikmb_a" } } - + params { // illumina iGenomes reference file paths on RZCluster igenomes_base = '/ifs/data/nfs_share/ikmb_repository/references/iGenomes/references/' diff --git a/conf/cfc.config b/conf/cfc.config index fc8cc34..783e233 100644 --- a/conf/cfc.config +++ b/conf/cfc.config @@ -1,6 +1,5 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'CFC' config_profile_description = 'QBiC Core Facility cluster profile provided by nf-core/configs.' config_profile_contact = 'Alexander Peltzer (@apeltzer)' config_profile_url = 'http://qbic.uni-tuebingen.de/' diff --git a/conf/crick.config b/conf/crick.config index de8c89b..10ddba5 100755 --- a/conf/crick.config +++ b/conf/crick.config @@ -1,8 +1,7 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'CRICK' config_profile_description = 'The Francis Crick Institute CAMP HPC cluster profile provided by nf-core/configs.' - config_profile_contact = 'Harshil Patel (@drpatelh )' + config_profile_contact = 'Harshil Patel (@drpatelh)' config_profile_url = 'https://www.crick.ac.uk/research/platforms-and-facilities/scientific-computing/technologies' } diff --git a/conf/gis.config b/conf/gis.config index 3fcb72e..e1645e5 100644 --- a/conf/gis.config +++ b/conf/gis.config @@ -1,11 +1,9 @@ -/* - * ------------------------------------------------- - * Nextflow config file for GIS (Aquila) - * ------------------------------------------------- - * Defines reference genomes, using iGenome paths - * Imported under the default 'standard' Nextflow - * profile in nextflow.config - */ +//Profile config names for nf-core/configs +params { + config_profile_description = 'Genome Institute of Singapore (Aquila) cluster profile provided by nf-core/configs.' + config_profile_contact = 'Andreas Wilm (@andreas-wilm)' + config_profile_url = 'https://www.a-star.edu.sg/gis/' +} process { executor = 'sge' @@ -20,4 +18,3 @@ params { // illumina iGenomes reference file paths on GIS Aquila igenomes_base = '/mnt/projects/rpd/genomes.testing/S3_igenomes/' } - diff --git a/conf/hebbe.config b/conf/hebbe.config index 76b8ac7..500ec31 100644 --- a/conf/hebbe.config +++ b/conf/hebbe.config @@ -1,8 +1,7 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'HEBBE' config_profile_description = 'Gothenburg Hebbe cluster profile provided by nf-core/configs.' - config_profile_contact = 'Phil Ewels (@ewels )' + config_profile_contact = 'Phil Ewels (@ewels)' config_profile_url = 'http://www.c3se.chalmers.se/index.php/Hebbe' } diff --git a/conf/mendel.config b/conf/mendel.config index 940a914..aee4ebc 100644 --- a/conf/mendel.config +++ b/conf/mendel.config @@ -1,6 +1,5 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'MENDEL' config_profile_description = 'GMI MENDEL cluster profile provided by nf-core/configs' config_profile_contact = 'Patrick Hüther (@phue)' config_profile_url = 'http://www.gmi.oeaw.ac.at/' diff --git a/conf/munin.config b/conf/munin.config index a24929e..5d95f01 100644 --- a/conf/munin.config +++ b/conf/munin.config @@ -1,6 +1,5 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'MUNIN' config_profile_description = 'Big iron cluster profile provided by nf-core/configs.' config_profile_contact = 'Szilveszter Juhos (@szilva)' config_profile_url = '' diff --git a/conf/phoenix.config b/conf/phoenix.config index 685e1e5..b457763 100644 --- a/conf/phoenix.config +++ b/conf/phoenix.config @@ -1,6 +1,5 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'PHOENIX' config_profile_description = 'University of Adelaide Phoenix HPC cluster profile provided by nf-core/configs' config_profile_contact = 'Yassine Souilmi / Alexander Peltzer (@yassineS, @apeltzer)' config_profile_url = 'https://www.adelaide.edu.au/phoenix/' diff --git a/conf/shh.config b/conf/shh.config index 13b7f5c..4088afd 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -1,6 +1,5 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'SHH' config_profile_description = 'MPI SHH cluster profile provided by nf-core/configs.' config_profile_contact = 'James Fellows Yates (@jfy133)' config_profile_url = 'https://shh.mpg.de' diff --git a/conf/uct_hex.config b/conf/uct_hex.config index a372000..6e0bbbe 100644 --- a/conf/uct_hex.config +++ b/conf/uct_hex.config @@ -1,6 +1,5 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'uct_hex' config_profile_description = 'University of Cape Town HEX cluster config file provided by nf-core/configs.' config_profile_contact = 'Katie Lennard (@kviljoen)' config_profile_url = 'http://hpc.uct.ac.za/index.php/hex-3/' @@ -22,4 +21,3 @@ executor{ executor = 'pbs' jobName = { "$task.tag" } } - diff --git a/conf/uppmax-devel.config b/conf/uppmax-devel.config index 760ff77..ad71ac4 100644 --- a/conf/uppmax-devel.config +++ b/conf/uppmax-devel.config @@ -1,6 +1,5 @@ // Profile config names for nf-core/configs params { - config_profile_name = 'UPPMAX-devel' config_profile_description = 'Testing & development profile for UPPMAX, provided by nf-core/configs.' config_profile_contact = 'Phil Ewels (@ewels)' config_profile_url = 'https://www.uppmax.uu.se/' diff --git a/conf/uppmax.config b/conf/uppmax.config index 939b8a7..d2fbc5d 100644 --- a/conf/uppmax.config +++ b/conf/uppmax.config @@ -1,6 +1,5 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'UPPMAX' config_profile_description = 'Swedish UPPMAX cluster profile provided by nf-core/configs.' config_profile_contact = 'Phil Ewels (@ewels)' config_profile_url = 'https://www.uppmax.uu.se/' diff --git a/conf/uzh.config b/conf/uzh.config index 70aad1b..c888096 100644 --- a/conf/uzh.config +++ b/conf/uzh.config @@ -1,6 +1,5 @@ //Profile config names for nf-core/configs params{ - config_profile_name = 'UZH' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' diff --git a/nfcore_custom.config b/nfcore_custom.config index dfcb4d2..f1c9bd4 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -23,9 +23,17 @@ profiles { phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } shh { includeConfig "${params.custom_config_base}/conf/shh.config" } uct_hex { includeConfig "${params.custom_config_base}/conf/uct_hex.config" } - uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config" - includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" - } + uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config" includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" } uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" } uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" } } + +// If user hostnames contain one of these substring and they are +// not running the associated profile, it will trigger a warning message +// Should be defined here for all profiles (not within profile config) +params { + // This is a groovy map, not a nextflow parameter set + hostnames = [ + uppmax: ['.uppmax.uu.se'] + ] +} From d0ca05a22147485c76baeeb897d7201d80c33f0b Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 13 Mar 2019 17:33:23 +0100 Subject: [PATCH 2/2] ; --- nfcore_custom.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nfcore_custom.config b/nfcore_custom.config index f1c9bd4..b21fe62 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -23,7 +23,7 @@ profiles { phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } shh { includeConfig "${params.custom_config_base}/conf/shh.config" } uct_hex { includeConfig "${params.custom_config_base}/conf/uct_hex.config" } - uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config" includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" } + uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"; includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" } uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" } uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" } }