From 98fca8a1ef2f182e4a19c83cec8d97c2036acaf9 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 3 Jan 2019 16:01:06 +0100 Subject: [PATCH 01/31] Add SHH Configuration --- conf/shh.config | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 conf/shh.config diff --git a/conf/shh.config b/conf/shh.config new file mode 100644 index 0000000..a402e5d --- /dev/null +++ b/conf/shh.config @@ -0,0 +1,38 @@ +/* + * ------------------------------------------------------------- + * Nextflow config file for use with Singularity at SHH Clusters + * ------------------------------------------------------------- + * Defines basic usage limits and singularity image id. + */ + +singularity { + enabled = true + cacheDir = "/projects1/users/$USER/nextflow/nf_cache/singularity/" +} + +/* +* To be improved by process specific resource requests +* By default, take the medium queue, smaller processes might just go to short (e.g. multiqc or similar things) +*/ + +process { + executor = 'slurm' + queue = 'medium' + + + withName:makeFastaIndex { + queue = 'short' + time = 2.h + } + withName:makeSeqDict { + queue = 'short' + time = 2.h + } +} + + +params { + max_memory = 734.GB + max_cpus = 64 + max_time = 48.h +} From 1051339461df4ffab5296f5c62cc64204928b89a Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 3 Jan 2019 16:02:07 +0100 Subject: [PATCH 02/31] Remove base config stuff --- conf/shh.config | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/conf/shh.config b/conf/shh.config index a402e5d..37b7516 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -18,16 +18,6 @@ singularity { process { executor = 'slurm' queue = 'medium' - - - withName:makeFastaIndex { - queue = 'short' - time = 2.h - } - withName:makeSeqDict { - queue = 'short' - time = 2.h - } } From d633cc87d0a2df08cff4693119a9a63f0e9d8f33 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 3 Jan 2019 16:03:45 +0100 Subject: [PATCH 03/31] Add SHH to config available --- nfcore_custom.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nfcore_custom.config b/nfcore_custom.config index f69a793..7a08d3e 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -19,6 +19,7 @@ profiles { hebbe { includeConfig "${config_base}/hebbe.config" } mendel { includeConfig "${config_base}/mendel.config" } phoenix { includeConfig "${config_base}/pheonix.config" } + shh { includeConfig "${config_base}/shh.config" } uct_hex { includeConfig "${config_base}/uct_hex.config" } uppmax_devel { includeConfig "${config_base}/uppmax.config" includeConfig "${config_base}/uppmax-devel.config" From a78fe147f08075d4de2e6866178c53693384ab0b Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 4 Jan 2019 10:19:39 +0100 Subject: [PATCH 04/31] Add more details on config profiles --- conf/binac.config | 10 ++++++++++ conf/shh.config | 7 +++++-- 2 files changed, 15 insertions(+), 2 deletions(-) diff --git a/conf/binac.config b/conf/binac.config index 5d13119..ac97fee 100644 --- a/conf/binac.config +++ b/conf/binac.config @@ -5,6 +5,14 @@ * Defines basic usage limits and singularity image id. */ +/* + * ------------------------------------------------------------- + * Name: BINAC + * Description: Configuration profile for BinAC clusters in Baden-Wuerttemberg/Germany. + * Contact person: Alexander Peltzer (@apeltzer) + * URL: https://www.bwhpc-c5.de/wiki/index.php/Category:BwForCluster_BinAC + * ------------------------------------------------------------- + */ singularity { enabled = true } @@ -20,4 +28,6 @@ params { max_memory = 128.GB max_cpus = 28 max_time = 48.h + + profile_description = 'BINAC Cluster Profile provided by nf-core/configs.' } diff --git a/conf/shh.config b/conf/shh.config index 37b7516..7580324 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -1,8 +1,10 @@ /* * ------------------------------------------------------------- - * Nextflow config file for use with Singularity at SHH Clusters + * Name: SHH + * Description: Configuration profile for MPI SHH Jena clusters. + * Contact person: James Fellows Yates (yates@shh.mpg.de) + * URL: https://shh.mpg.de * ------------------------------------------------------------- - * Defines basic usage limits and singularity image id. */ singularity { @@ -25,4 +27,5 @@ params { max_memory = 734.GB max_cpus = 64 max_time = 48.h + profile_description = 'MPI SHH Cluster Profile provided by nf-core/configs.' } From 87cea82c433a74122e6027b2153e18ce76dd1146 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 4 Jan 2019 10:21:16 +0100 Subject: [PATCH 05/31] Use james github handle --- conf/shh.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/shh.config b/conf/shh.config index 7580324..e5d2203 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -2,7 +2,7 @@ * ------------------------------------------------------------- * Name: SHH * Description: Configuration profile for MPI SHH Jena clusters. - * Contact person: James Fellows Yates (yates@shh.mpg.de) + * Contact person: James Fellows Yates (@jfy133) * URL: https://shh.mpg.de * ------------------------------------------------------------- */ From 078272745a66079229d2c101390220d5292962ab Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 4 Jan 2019 14:42:09 +0100 Subject: [PATCH 06/31] Update BINAC, CFC, SHH COnfig profiles --- conf/binac.config | 13 +++++-------- conf/cfc.config | 11 +++++++++-- conf/shh.config | 5 ++++- 3 files changed, 18 insertions(+), 11 deletions(-) diff --git a/conf/binac.config b/conf/binac.config index ac97fee..c255848 100644 --- a/conf/binac.config +++ b/conf/binac.config @@ -1,10 +1,3 @@ -/* - * ---------------------------------------------------------------------------- - * Nextflow config file for use with Singularity on BINAC cluster in Tuebingen - * ---------------------------------------------------------------------------- - * Defines basic usage limits and singularity image id. - */ - /* * ------------------------------------------------------------- * Name: BINAC @@ -13,6 +6,7 @@ * URL: https://www.bwhpc-c5.de/wiki/index.php/Category:BwForCluster_BinAC * ------------------------------------------------------------- */ + singularity { enabled = true } @@ -29,5 +23,8 @@ params { max_cpus = 28 max_time = 48.h - profile_description = 'BINAC Cluster Profile provided by nf-core/configs.' + 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' } diff --git a/conf/cfc.config b/conf/cfc.config index 40d0049..939f1f2 100644 --- a/conf/cfc.config +++ b/conf/cfc.config @@ -1,8 +1,10 @@ /* * ------------------------------------------------------------- - * Nextflow config file for use with Singularity on CFC at QBIC + * Name: CFC + * Description: Core Facility Cluster Profile provided by nf-core/configs. + * Contact person: Alexander Peltzer (@apeltzer) + * URL: http://qbic.uni-tuebingen.de/ * ------------------------------------------------------------- - * Defines basic usage limits and singularity image id. */ singularity { @@ -19,4 +21,9 @@ params { max_memory = 60.GB max_cpus = 24 max_time = 140.h + + config_profile_name = 'CFC' + config_profile_description = '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/shh.config b/conf/shh.config index e5d2203..8355695 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -27,5 +27,8 @@ params { max_memory = 734.GB max_cpus = 64 max_time = 48.h - profile_description = 'MPI SHH Cluster Profile provided by nf-core/configs.' + 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' } From 6ae7d02b14cf46d63998c2d6e06475e663efc586 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 4 Jan 2019 14:46:30 +0100 Subject: [PATCH 07/31] Add Mendel --- conf/mendel.config | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/conf/mendel.config b/conf/mendel.config index cf0d539..2b0f1e0 100644 --- a/conf/mendel.config +++ b/conf/mendel.config @@ -1,9 +1,20 @@ /* + * ------------------------------------------------------------- + * Name: CFC + * Description: MENDEL cluster profile provided by nf-core/configs + * Contact person: Philipp H (@phue) + * URL: http://www.gmi.oeaw.ac.at/ + * ------------------------------------------------------------- + */ + + /* * -------------------------------------------------------------------------------------- * Nextflow config file for the MENDEL cluster at the Gregor Mendel Institute in Vienna * ------------------------------------------------------------------------------------- */ + phue + singularity { enabled = true } @@ -17,4 +28,9 @@ process { params { max_time = 192.h igenomesIgnore = true + + config_profile_name = 'MENDEL' + config_profile_description = 'MENDEL cluster profile provided by nf-core/configs' + config_profile_contact = 'Philipp H (@phue)' + config_profile_url = 'http://www.gmi.oeaw.ac.at/' } From bc8e05f4b372e7803880a3982cea2308bacc34c1 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 4 Jan 2019 14:48:14 +0100 Subject: [PATCH 08/31] Add Phoenix --- conf/phoenix.config | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/conf/phoenix.config b/conf/phoenix.config index 81b7d44..91f20bf 100644 --- a/conf/phoenix.config +++ b/conf/phoenix.config @@ -1,8 +1,10 @@ /* - * ---------------------------------------------------------------------------- - * Nextflow config file for use with Singularity on Phoenix Cluster Adelaide - * ---------------------------------------------------------------------------- - * Defines basic usage limits and singularity image id. + * ------------------------------------------------------------- + * Name: PHOENIX + * Description: Phoenix Research cluster profile provided by nf-core/configs + * Contact person: Yassine Souilmi / Alexander Peltzer (@yassineS, @apeltzer) + * URL: https://www.adelaide.edu.au/phoenix/ + * ------------------------------------------------------------- */ singularity { @@ -20,4 +22,9 @@ params { max_memory = 128.GB max_cpus = 32 max_time = 48.h + + config_profile_name = 'PHOENIX' + config_profile_description = 'Phoenix Research 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/' } From 9c97680d4c23b7afe93979f3aff1a27c7e504d53 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 4 Jan 2019 14:49:52 +0100 Subject: [PATCH 09/31] Add UZH --- conf/uzh.config | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/conf/uzh.config b/conf/uzh.config index 68cd7dd..6bf4e59 100644 --- a/conf/uzh.config +++ b/conf/uzh.config @@ -1,9 +1,11 @@ /* - * -------------------------------------------------------------------------------- - * Nextflow config file for use with Singularity on University of Zurich Cluster - * -------------------------------------------------------------------------------- + * ------------------------------------------------------------- + * Name: UZH + * Description: UZH science cloud profile provided by nf-core/configs + * Contact person: Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer) + * URL: https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html + * ------------------------------------------------------------- */ - singularity { enabled = true } @@ -16,4 +18,9 @@ params { max_memory = 1800.GB max_cpus = 112 max_time = 168.h + + 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' } From 7af6b48b4d1721de46f53329c0be332d90639866 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 4 Jan 2019 14:55:22 +0100 Subject: [PATCH 10/31] Adjust general usage to separate params section --- conf/binac.config | 20 +++++++------------- conf/cfc.config | 20 +++++++------------- conf/crick.config | 7 +++++++ conf/mendel.config | 28 +++++++--------------------- conf/phoenix.config | 20 +++++++------------- conf/shh.config | 25 +++++++------------------ conf/uzh.config | 21 ++++++++------------- 7 files changed, 50 insertions(+), 91 deletions(-) diff --git a/conf/binac.config b/conf/binac.config index c255848..d256e5a 100644 --- a/conf/binac.config +++ b/conf/binac.config @@ -1,11 +1,10 @@ -/* - * ------------------------------------------------------------- - * Name: BINAC - * Description: Configuration profile for BinAC clusters in Baden-Wuerttemberg/Germany. - * Contact person: Alexander Peltzer (@apeltzer) - * URL: https://www.bwhpc-c5.de/wiki/index.php/Category:BwForCluster_BinAC - * ------------------------------------------------------------- - */ +//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 @@ -22,9 +21,4 @@ params { max_memory = 128.GB max_cpus = 28 max_time = 48.h - - 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' } diff --git a/conf/cfc.config b/conf/cfc.config index 939f1f2..ee7943d 100644 --- a/conf/cfc.config +++ b/conf/cfc.config @@ -1,11 +1,10 @@ -/* - * ------------------------------------------------------------- - * Name: CFC - * Description: Core Facility Cluster Profile provided by nf-core/configs. - * Contact person: Alexander Peltzer (@apeltzer) - * URL: http://qbic.uni-tuebingen.de/ - * ------------------------------------------------------------- - */ +//Profile config names for nf-core/configs +params { + config_profile_name = 'CFC' + config_profile_description = 'Core Facility Cluster Profile provided by nf-core/configs.' + config_profile_contact = 'Alexander Peltzer (@apeltzer)' + config_profile_url = 'http://qbic.uni-tuebingen.de/' +} singularity { enabled = true @@ -21,9 +20,4 @@ params { max_memory = 60.GB max_cpus = 24 max_time = 140.h - - config_profile_name = 'CFC' - config_profile_description = '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 aa356e8..a201c9b 100755 --- a/conf/crick.config +++ b/conf/crick.config @@ -3,6 +3,13 @@ * Nextflow config file for CAMP HPC @ The Crick * ------------------------------------------------- */ +//Profile config names for nf-core/configs +params { + config_profile_name = 'CRICK' + config_profile_description = 'CAMP HPC @ The Crick Cluster Profile provided by nf-core/configs.' + config_profile_contact = 'Harshil Patel (@drpatelh )' + config_profile_url = 'https://www.crick.ac.uk/research/platforms-and-facilities/scientific-computing/technologies' +} singularity { enabled = true diff --git a/conf/mendel.config b/conf/mendel.config index 2b0f1e0..ec076c7 100644 --- a/conf/mendel.config +++ b/conf/mendel.config @@ -1,19 +1,10 @@ -/* - * ------------------------------------------------------------- - * Name: CFC - * Description: MENDEL cluster profile provided by nf-core/configs - * Contact person: Philipp H (@phue) - * URL: http://www.gmi.oeaw.ac.at/ - * ------------------------------------------------------------- - */ - - /* - * -------------------------------------------------------------------------------------- - * Nextflow config file for the MENDEL cluster at the Gregor Mendel Institute in Vienna - * ------------------------------------------------------------------------------------- - */ - - phue +//Profile config names for nf-core/configs +params { + config_profile_name = 'MENDEL' + config_profile_description = 'MENDEL cluster profile provided by nf-core/configs' + config_profile_contact = 'Philipp H (@phue)' + config_profile_url = 'http://www.gmi.oeaw.ac.at/' +} singularity { enabled = true @@ -28,9 +19,4 @@ process { params { max_time = 192.h igenomesIgnore = true - - config_profile_name = 'MENDEL' - config_profile_description = 'MENDEL cluster profile provided by nf-core/configs' - config_profile_contact = 'Philipp H (@phue)' - config_profile_url = 'http://www.gmi.oeaw.ac.at/' } diff --git a/conf/phoenix.config b/conf/phoenix.config index 91f20bf..2987021 100644 --- a/conf/phoenix.config +++ b/conf/phoenix.config @@ -1,11 +1,10 @@ -/* - * ------------------------------------------------------------- - * Name: PHOENIX - * Description: Phoenix Research cluster profile provided by nf-core/configs - * Contact person: Yassine Souilmi / Alexander Peltzer (@yassineS, @apeltzer) - * URL: https://www.adelaide.edu.au/phoenix/ - * ------------------------------------------------------------- - */ +//Profile config names for nf-core/configs +params { + config_profile_name = 'PHOENIX' + config_profile_description = 'Phoenix Research 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/' +} singularity { enabled = true @@ -22,9 +21,4 @@ params { max_memory = 128.GB max_cpus = 32 max_time = 48.h - - config_profile_name = 'PHOENIX' - config_profile_description = 'Phoenix Research 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 8355695..1410b3a 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -1,34 +1,23 @@ -/* - * ------------------------------------------------------------- - * Name: SHH - * Description: Configuration profile for MPI SHH Jena clusters. - * Contact person: James Fellows Yates (@jfy133) - * URL: https://shh.mpg.de - * ------------------------------------------------------------- - */ +//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' +} singularity { enabled = true cacheDir = "/projects1/users/$USER/nextflow/nf_cache/singularity/" } -/* -* To be improved by process specific resource requests -* By default, take the medium queue, smaller processes might just go to short (e.g. multiqc or similar things) -*/ - process { executor = 'slurm' queue = 'medium' } - params { max_memory = 734.GB max_cpus = 64 max_time = 48.h - 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/uzh.config b/conf/uzh.config index 6bf4e59..70aad1b 100644 --- a/conf/uzh.config +++ b/conf/uzh.config @@ -1,11 +1,11 @@ -/* - * ------------------------------------------------------------- - * Name: UZH - * Description: UZH science cloud profile provided by nf-core/configs - * Contact person: Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer) - * URL: https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html - * ------------------------------------------------------------- - */ +//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' +} + singularity { enabled = true } @@ -18,9 +18,4 @@ params { max_memory = 1800.GB max_cpus = 112 max_time = 168.h - - 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' } From aca790bb4b53afb918d2479d3aaec7c3cc1e8ffe Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 4 Jan 2019 16:28:41 +0100 Subject: [PATCH 11/31] Add CCGA Profile --- conf/ccga.config | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/conf/ccga.config b/conf/ccga.config index bc9959d..2e83ae2 100644 --- a/conf/ccga.config +++ b/conf/ccga.config @@ -1,3 +1,11 @@ +//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/' +} + /* * ------------------------------------------------- * Nextflow config file with environment modules for RZCluster in Kiel From e07d8bd68708ddf9b6154da753e07baf7ccefe5f Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 4 Jan 2019 16:29:49 +0100 Subject: [PATCH 12/31] Get rid of header in CRICK config --- conf/crick.config | 5 ----- 1 file changed, 5 deletions(-) diff --git a/conf/crick.config b/conf/crick.config index a201c9b..8a05f40 100755 --- a/conf/crick.config +++ b/conf/crick.config @@ -1,8 +1,3 @@ -/* - * ------------------------------------------------- - * Nextflow config file for CAMP HPC @ The Crick - * ------------------------------------------------- - */ //Profile config names for nf-core/configs params { config_profile_name = 'CRICK' From 6f7a3cc42288fc89c22902e612e34ebcee2ae720 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 4 Jan 2019 16:30:40 +0100 Subject: [PATCH 13/31] Add Hebbe --- conf/hebbe.config | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/conf/hebbe.config b/conf/hebbe.config index e9dcb06..9187a85 100644 --- a/conf/hebbe.config +++ b/conf/hebbe.config @@ -1,10 +1,10 @@ -/* - * ------------------------------------------------- - * Gothenburg Hebbe Cluster config file - * ------------------------------------------------- - * http://www.c3se.chalmers.se/index.php/Hebbe - */ - +//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_url = 'http://www.c3se.chalmers.se/index.php/Hebbe' +} singularity { enabled = true From 2b814041ee8e9deaa5dec275ee7c0f4ad84d02b2 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 4 Jan 2019 16:33:54 +0100 Subject: [PATCH 14/31] Add in both uppmax profiles --- conf/uppmax-devel.config | 15 +++++++++++---- conf/uppmax.config | 13 +++++++++---- 2 files changed, 20 insertions(+), 8 deletions(-) diff --git a/conf/uppmax-devel.config b/conf/uppmax-devel.config index ef4bb0a..6de50ed 100644 --- a/conf/uppmax-devel.config +++ b/conf/uppmax-devel.config @@ -1,13 +1,20 @@ -/* - * ------------------------------------------------- - * Nextflow config file for UPPMAX (rackham / irma) - * ------------------------------------------------- +//Profile config names for nf-core/configs +params { + config_profile_name = 'UPPMAX-DEVEL' + config_profile_description = 'UPPMAX Development Cluster Profile provided by nf-core/configs.' + config_profile_contact = 'Phil Ewels (@ewels)' + config_profile_url = 'https://www.uppmax.uu.se/' +} + +/* Additional description: * To be applied after main UPPMAX config, overwrites config and * submits jobs to the `devcore` queue, which has much faster * queue times. All jobs are limited to 1 hour to be eligible * for this queue and only one job allowed at a time. */ + + executor { name = 'slurm' queueSize = 1 diff --git a/conf/uppmax.config b/conf/uppmax.config index f19829f..2442669 100644 --- a/conf/uppmax.config +++ b/conf/uppmax.config @@ -1,7 +1,12 @@ -/* - * ------------------------------------------------- - * Nextflow config file for UPPMAX (rackham / irma) - * ------------------------------------------------- +//Profile config names for nf-core/configs +params { + config_profile_name = 'UPPMAX' + config_profile_description = 'UPPMAX Cluster Profile provided by nf-core/configs.' + config_profile_contact = 'Phil Ewels (@ewels)' + config_profile_url = 'https://www.uppmax.uu.se/' +} + +/* Additional description: * Defines reference genomes, using iGenome paths * Imported under the default 'standard' Nextflow * profile in nextflow.config From 45b46fffe85dbe38f29a61b538ce4a03cdf14dc2 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 4 Jan 2019 16:38:41 +0100 Subject: [PATCH 15/31] Add some documentation on config description parameters --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 82603ba..7c931e5 100644 --- a/README.md +++ b/README.md @@ -34,6 +34,8 @@ If you want to use an existing config available in `nf-core/configs`, and you're 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. + ### Testing If you want to add a new custom config file to `nf-core/configs` please can you test that your pipeline of choice runs as expected by using the [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter. From 65a24c93a25e6d235f806ca548dad26772047ab9 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 4 Jan 2019 16:39:02 +0100 Subject: [PATCH 16/31] Typo fix --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 7c931e5..ce8bc7a 100644 --- a/README.md +++ b/README.md @@ -38,7 +38,7 @@ Please also make sure to add an extra `params` section with `params. config_pro ### Testing -If you want to add a new custom config file to `nf-core/configs` please can you test that your pipeline of choice runs as expected by using the [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter. +If you want to add a new custom config file to `nf-core/configs` please test that your pipeline of choice runs as expected by using the [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter. ```bash ## Example command for nf-core/rnaseq From ef41306a9fa462be3f5b7676c5b2d742d18645ba Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 4 Jan 2019 16:44:43 +0100 Subject: [PATCH 17/31] List cluster configs in README properly --- README.md | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/README.md b/README.md index ce8bc7a..31bfb85 100644 --- a/README.md +++ b/README.md @@ -51,6 +51,22 @@ You will have to create a [Markdown document](https://www.markdownguide.org/gett See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs) for examples. +Currently documentation is available for the following clusters: + +* [BINAC](docs/binac.md) +* [CCGA](docs/ccga.md) +* [CFC](docs/binac.md) +* [CRICK](docs/crick.md) +* [GIS](docs/gis.md) +* [HEBBE](docs/hebbe.md) +* [MENDEL](docs/mendel.md) +* [PHOENIX](docs/phoenix.md) +* [SHH](docs/shh.md) +* [UCT_HEX](docs/uct_hex.md) +* [UPPMAX-DEVEL](docs/uppmax-devel.md) +* [UPPMAX](docs/uppmax.md) +* [UZH](docs/uzh.md) + ### Uploading to `nf-core/configs` [Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/configs` repository to your own GitHub account. Within the local clone of your fork add the custom config file to the [`conf/`](https://github.com/nf-core/configs/tree/master/conf) directory, and the documentation file to the [`docs/`](https://github.com/nf-core/configs/tree/master/docs) directory. You will also need to edit and add your custom profile to the [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) file in the top-level directory of the clone. From bcd85940fa76e0cd6c009e3eba8d3bab6fb349d0 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 4 Jan 2019 17:12:59 +0100 Subject: [PATCH 18/31] Add Template for Documentation of Cluster Resources --- README.md | 2 +- docs/template.md | 31 +++++++++++++++++++++++++++++++ 2 files changed, 32 insertions(+), 1 deletion(-) create mode 100644 docs/template.md diff --git a/README.md b/README.md index 31bfb85..cce1ed2 100644 --- a/README.md +++ b/README.md @@ -47,7 +47,7 @@ nextflow run nf-core/rnaseq --reads '*_R{1,2}.fastq.gz' --genome GRCh37 -c '[pat ### Documentation -You will have to create a [Markdown document](https://www.markdownguide.org/getting-started/) outlining the details required to use the custom config file within your organisation. +You will have to create a [Markdown document](https://www.markdownguide.org/getting-started/) outlining the details required to use the custom config file within your organisation. You might orientate yourself using the [Template](docs/template.md) that we provide and filling out the information for your cluster there. See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs) for examples. diff --git a/docs/template.md b/docs/template.md new file mode 100644 index 0000000..d927039 --- /dev/null +++ b/docs/template.md @@ -0,0 +1,31 @@ +# nf-core/configs: PROFILE Configuration + +All nf-core pipelines have been successfully configured for use on the PROFILE CLUSTER at the insert institution here. + +To use, run the pipeline with `-profile PROFILENAME`. This will download and launch the [`profile.config`](../conf/profile.config) which has been pre-configured with a setup suitable for the PROFILE cluster. Using this profile, Nextflow will download a singularity image with all of the required software before execution of the pipeline. + +## Below are non-mandatory information e.g. on modules to load etc. + +Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on PROFILE CLUSTER. You can do this by issuing the commands below: + +```bash +## Load Nextflow and Singularity environment modules +module purge +module load Nextflow/0.32.0 +module load Singularity/2.6.0 + +## Example command for nf-core/atacseq +nextflow run nf-core/atacseq -profile PROFILE --genome GRCh37 --design /path/to/design.csv --email test.user@crick.ac.uk +``` + +## Below are non-mandatory information on iGenomes specific configuration + +A local copy of the iGenomes resource has been made available on PROFILE CLUSTER so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. You can do this by simply using the `--genome ` parameter. Some of the more exotic genomes may not have been downloaded onto PROFILE CLUSTER so have a look in the `igenomes_base` path specified in [`profile.config`](../conf/profile.config), and if your genome of interest isnt present please contact [local_contact_name_for_profile](mailto:local_contact_handle). + +Alternatively, if you are running the pipeline regularly for genomes that arent available in the iGenomes resource, we recommend creating a config file with paths to your reference genome indices (see [`reference genomes documentation`](https://github.com/nf-core/atacseq/blob/master/docs/configuration/reference_genomes.md) for instructions). + +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 PROFILE CLUSTER in order to run the pipeline. If in doubt contact IT. + +>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT. From c2fa8d544179e71c70359a649ea42ff0db1dc91e Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 4 Jan 2019 17:13:03 +0100 Subject: [PATCH 19/31] Add BINAC documentation --- docs/binac.md | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 docs/binac.md diff --git a/docs/binac.md b/docs/binac.md new file mode 100644 index 0000000..61dffc2 --- /dev/null +++ b/docs/binac.md @@ -0,0 +1,25 @@ +# nf-core/configs: BINAC Configuration + +All nf-core pipelines have been successfully configured for use on the BINAC cluster at the insert institution here. + +To use, run the pipeline with `-profile binac`. This will download and launch the [`binac.config`](../conf/binac.config) which has been pre-configured with a setup suitable for the BINAC cluster. Using this profile, Nextflow will download a singularity image with all of the required software before execution of the pipeline. + +## Below are non-mandatory information e.g. on modules to load etc. + +Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on BINAC cluster. You can do this by issuing the commands below: + +```bash +## Load Nextflow and Singularity environment modules +module purge +module load devel/java_jdk/1.8.0u112 +module load devel/singularity/3.0.1 + +## Example command for nf-core/atacseq +nextflow run nf-core/atacseq -profile PROFILE --genome GRCh37 --design /path/to/design.csv --email test.user@crick.ac.uk +``` + +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 BINAC in order to run the pipeline. If in doubt contact IT. + +>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT. From d5f41d837c9fd46bf81e17cd0e4a83b8f2d3ba39 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 4 Jan 2019 17:14:08 +0100 Subject: [PATCH 20/31] Remove non-required heading --- docs/binac.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/binac.md b/docs/binac.md index 61dffc2..aab96ad 100644 --- a/docs/binac.md +++ b/docs/binac.md @@ -4,8 +4,6 @@ All nf-core pipelines have been successfully configured for use on the BINAC clu To use, run the pipeline with `-profile binac`. This will download and launch the [`binac.config`](../conf/binac.config) which has been pre-configured with a setup suitable for the BINAC cluster. Using this profile, Nextflow will download a singularity image with all of the required software before execution of the pipeline. -## Below are non-mandatory information e.g. on modules to load etc. - Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on BINAC cluster. You can do this by issuing the commands below: ```bash From 0d7ae3717fa389e89c313f71c2993305736e34c7 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Sun, 6 Jan 2019 15:34:52 +0100 Subject: [PATCH 21/31] Add in docs for CFC cluster --- docs/cfc.md | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 docs/cfc.md diff --git a/docs/cfc.md b/docs/cfc.md new file mode 100644 index 0000000..a83f590 --- /dev/null +++ b/docs/cfc.md @@ -0,0 +1,23 @@ +# nf-core/configs: CFC Configuration + +All nf-core pipelines have been successfully configured for use on the CFC cluster at the insert institution here. + +To use, run the pipeline with `-profile cfc`. This will download and launch the [`cfc.config`](../conf/cfc.config) which has been pre-configured with a setup suitable for the CFC cluster. Using this profile, Nextflow will download a singularity image with all of the required software before execution of the pipeline. + +Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on CFC cluster. You can do this by issuing the commands below: + +```bash +## Load Nextflow and Singularity environment modules +module purge +module load devel/java_jdk/1.8.0u121 +module load qbic/singularity_slurm/3.0.1 + +## Example command for nf-core/atacseq +nextflow run nf-core/atacseq -profile PROFILE --genome GRCh37 --design /path/to/design.csv --email test.user@crick.ac.uk +``` + +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 CFC in order to run the pipeline. If in doubt contact IT. + +>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT. From ce4b0373facc5841e0ea0907b4530f9ce5ff6a4a Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Sun, 6 Jan 2019 15:35:26 +0100 Subject: [PATCH 22/31] Add in UZH --- docs/uzh.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 docs/uzh.md diff --git a/docs/uzh.md b/docs/uzh.md new file mode 100644 index 0000000..08a81d7 --- /dev/null +++ b/docs/uzh.md @@ -0,0 +1,15 @@ +# nf-core/configs: UZH Configuration + +All nf-core pipelines have been successfully configured for use on the UZH cluster at the insert institution here. + +To use, run the pipeline with `-profile UZH`. This will download and launch the [`uzh.config`](../conf/uzh.config) which has been pre-configured with a setup suitable for the UZH cluster. Using this profile, Nextflow will download a singularity image with all of the required software before execution of the pipeline. + +## Example command for nf-core/atacseq +nextflow run nf-core/atacseq -profile PROFILE --genome GRCh37 --design /path/to/design.csv --email test.user@crick.ac.uk +``` + +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 UZH in order to run the pipeline. If in doubt contact IT. + +>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT. From 6a12e763ea8f2c6a76c3b80ca16bb7c2f49e2974 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 7 Jan 2019 11:16:58 +0100 Subject: [PATCH 23/31] Get rid of examples --- docs/binac.md | 3 --- docs/cfc.md | 3 --- docs/crick.md | 3 --- docs/template.md | 3 --- docs/uzh.md | 4 ---- 5 files changed, 16 deletions(-) diff --git a/docs/binac.md b/docs/binac.md index aab96ad..7846383 100644 --- a/docs/binac.md +++ b/docs/binac.md @@ -11,9 +11,6 @@ Before running the pipeline you will need to load Nextflow and Singularity using module purge module load devel/java_jdk/1.8.0u112 module load devel/singularity/3.0.1 - -## Example command for nf-core/atacseq -nextflow run nf-core/atacseq -profile PROFILE --genome GRCh37 --design /path/to/design.csv --email test.user@crick.ac.uk ``` 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. diff --git a/docs/cfc.md b/docs/cfc.md index a83f590..7eb893d 100644 --- a/docs/cfc.md +++ b/docs/cfc.md @@ -11,9 +11,6 @@ Before running the pipeline you will need to load Nextflow and Singularity using module purge module load devel/java_jdk/1.8.0u121 module load qbic/singularity_slurm/3.0.1 - -## Example command for nf-core/atacseq -nextflow run nf-core/atacseq -profile PROFILE --genome GRCh37 --design /path/to/design.csv --email test.user@crick.ac.uk ``` 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. diff --git a/docs/crick.md b/docs/crick.md index 9fc559e..11abde2 100644 --- a/docs/crick.md +++ b/docs/crick.md @@ -11,9 +11,6 @@ Before running the pipeline you will need to load Nextflow and Singularity using module purge module load Nextflow/0.32.0 module load Singularity/2.6.0-foss-2016b - -## Example command for nf-core/atacseq -nextflow run nf-core/atacseq -profile crick --genome GRCh37 --design /path/to/design.csv --email test.user@crick.ac.uk ``` A local copy of the iGenomes resource has been made available on CAMP so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. You can do this by simply using the `--genome ` parameter. Some of the more exotic genomes may not have been downloaded onto CAMP so have a look in the `igenomes_base` path specified in [`crick.config`](../conf/crick.config), and if your genome of interest isnt present please contact [BABS](mailto:bioinformatics@crick.ac.uk). diff --git a/docs/template.md b/docs/template.md index d927039..bb2ea44 100644 --- a/docs/template.md +++ b/docs/template.md @@ -13,9 +13,6 @@ Before running the pipeline you will need to load Nextflow and Singularity using module purge module load Nextflow/0.32.0 module load Singularity/2.6.0 - -## Example command for nf-core/atacseq -nextflow run nf-core/atacseq -profile PROFILE --genome GRCh37 --design /path/to/design.csv --email test.user@crick.ac.uk ``` ## Below are non-mandatory information on iGenomes specific configuration diff --git a/docs/uzh.md b/docs/uzh.md index 08a81d7..ceb48f0 100644 --- a/docs/uzh.md +++ b/docs/uzh.md @@ -4,10 +4,6 @@ All nf-core pipelines have been successfully configured for use on the UZH clust To use, run the pipeline with `-profile UZH`. This will download and launch the [`uzh.config`](../conf/uzh.config) which has been pre-configured with a setup suitable for the UZH cluster. Using this profile, Nextflow will download a singularity image with all of the required software before execution of the pipeline. -## Example command for nf-core/atacseq -nextflow run nf-core/atacseq -profile PROFILE --genome GRCh37 --design /path/to/design.csv --email test.user@crick.ac.uk -``` - 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 UZH in order to run the pipeline. If in doubt contact IT. From 02e97811c63dcff972c1e0ff9322b5978a330503 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 7 Jan 2019 11:21:17 +0100 Subject: [PATCH 24/31] Get rid of template / iGenomes stuff --- docs/template.md | 5 +---- docs/uzh.md | 2 +- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/docs/template.md b/docs/template.md index bb2ea44..bd65ee1 100644 --- a/docs/template.md +++ b/docs/template.md @@ -17,11 +17,8 @@ module load Singularity/2.6.0 ## Below are non-mandatory information on iGenomes specific configuration -A local copy of the iGenomes resource has been made available on PROFILE CLUSTER so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. You can do this by simply using the `--genome ` parameter. Some of the more exotic genomes may not have been downloaded onto PROFILE CLUSTER so have a look in the `igenomes_base` path specified in [`profile.config`](../conf/profile.config), and if your genome of interest isnt present please contact [local_contact_name_for_profile](mailto:local_contact_handle). +A local copy of the iGenomes resource has been made available on PROFILE CLUSTER so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. You can do this by simply using the `--genome ` parameter. Some of the more exotic genomes may not have been downloaded onto PROFILE CLUSTER so have a look in the `igenomes_base` path specified in [`profile.config`](../conf/profile.config). -Alternatively, if you are running the pipeline regularly for genomes that arent available in the iGenomes resource, we recommend creating a config file with paths to your reference genome indices (see [`reference genomes documentation`](https://github.com/nf-core/atacseq/blob/master/docs/configuration/reference_genomes.md) for instructions). - -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 PROFILE CLUSTER in order to run the pipeline. If in doubt contact IT. diff --git a/docs/uzh.md b/docs/uzh.md index ceb48f0..fc4fbb2 100644 --- a/docs/uzh.md +++ b/docs/uzh.md @@ -2,7 +2,7 @@ All nf-core pipelines have been successfully configured for use on the UZH cluster at the insert institution here. -To use, run the pipeline with `-profile UZH`. This will download and launch the [`uzh.config`](../conf/uzh.config) which has been pre-configured with a setup suitable for the UZH cluster. Using this profile, Nextflow will download a singularity image with all of the required software before execution of the pipeline. +To use, run the pipeline with `-profile uzh`. This will download and launch the [`uzh.config`](../conf/uzh.config) which has been pre-configured with a setup suitable for the UZH cluster. Using this profile, Nextflow will download a singularity image with all of the required software before execution of the pipeline. 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. From 94e546fd4b38a760029911af1b28d1572b69f801 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Mon, 7 Jan 2019 12:10:41 +0100 Subject: [PATCH 25/31] Update docs/uzh.md Co-Authored-By: apeltzer --- docs/uzh.md | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/uzh.md b/docs/uzh.md index fc4fbb2..3c698ce 100644 --- a/docs/uzh.md +++ b/docs/uzh.md @@ -4,7 +4,6 @@ All nf-core pipelines have been successfully configured for use on the UZH clust To use, run the pipeline with `-profile uzh`. This will download and launch the [`uzh.config`](../conf/uzh.config) which has been pre-configured with a setup suitable for the UZH cluster. Using this profile, Nextflow will download a singularity image with all of the required software before execution of the pipeline. -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 UZH in order to run the pipeline. If in doubt contact IT. From 6d14461adcc94c066357f3794cc5bb65cae88c85 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Mon, 7 Jan 2019 12:11:02 +0100 Subject: [PATCH 26/31] Update docs/template.md Co-Authored-By: apeltzer --- docs/template.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/template.md b/docs/template.md index bd65ee1..7efd0a7 100644 --- a/docs/template.md +++ b/docs/template.md @@ -17,7 +17,8 @@ module load Singularity/2.6.0 ## Below are non-mandatory information on iGenomes specific configuration -A local copy of the iGenomes resource has been made available on PROFILE CLUSTER so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. You can do this by simply using the `--genome ` parameter. Some of the more exotic genomes may not have been downloaded onto PROFILE CLUSTER so have a look in the `igenomes_base` path specified in [`profile.config`](../conf/profile.config). +A local copy of the iGenomes resource has been made available on PROFILE CLUSTER so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. +You can do this by simply using the `--genome ` parameter. >NB: You will need an account to use the HPC cluster on PROFILE CLUSTER in order to run the pipeline. If in doubt contact IT. From 1758fbc11cfbd56a2395716bb1db725a3a6c8aad Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Mon, 7 Jan 2019 12:11:19 +0100 Subject: [PATCH 27/31] Update docs/cfc.md Co-Authored-By: apeltzer --- docs/cfc.md | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/cfc.md b/docs/cfc.md index 7eb893d..efdbffb 100644 --- a/docs/cfc.md +++ b/docs/cfc.md @@ -13,7 +13,6 @@ module load devel/java_jdk/1.8.0u121 module load qbic/singularity_slurm/3.0.1 ``` -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 CFC in order to run the pipeline. If in doubt contact IT. From 325dfe3968278233cd82dbcfa58d0b705a732242 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Mon, 7 Jan 2019 12:11:31 +0100 Subject: [PATCH 28/31] Update docs/binac.md Co-Authored-By: apeltzer --- docs/binac.md | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/binac.md b/docs/binac.md index 7846383..e7c6fbd 100644 --- a/docs/binac.md +++ b/docs/binac.md @@ -13,7 +13,6 @@ module load devel/java_jdk/1.8.0u112 module load devel/singularity/3.0.1 ``` -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 BINAC in order to run the pipeline. If in doubt contact IT. From d4ea56aaae522cb97b7d29445d665f30c19e2cbd Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 7 Jan 2019 12:14:04 +0100 Subject: [PATCH 29/31] Update UCT_Hex profile --- conf/uct_hex.config | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/conf/uct_hex.config b/conf/uct_hex.config index 422a143..a372000 100644 --- a/conf/uct_hex.config +++ b/conf/uct_hex.config @@ -1,9 +1,10 @@ -/* - * ------------------------------------------------- - * University of Cape Town HEX cluster config file - * ------------------------------------------------- - * http://hpc.uct.ac.za/index.php/hex-3/ - */ +//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/' +} singularity { enabled = true @@ -22,6 +23,3 @@ executor{ jobName = { "$task.tag" } } -params { - igenomes_base = '/scratch/DB/bio/rna-seq/references' -} From f81c67627e96827c081f321fc2f309124092adb1 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 7 Jan 2019 11:18:01 +0000 Subject: [PATCH 30/31] Update crick.config --- conf/crick.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/crick.config b/conf/crick.config index 8a05f40..a0d9906 100755 --- a/conf/crick.config +++ b/conf/crick.config @@ -1,9 +1,9 @@ //Profile config names for nf-core/configs params { config_profile_name = 'CRICK' - config_profile_description = 'CAMP HPC @ The Crick Cluster Profile provided by nf-core/configs.' + config_profile_description = 'Profile for CAMP HPC Cluster @ The Francis Crick Institute provided by nf-core/configs.' config_profile_contact = 'Harshil Patel (@drpatelh )' - config_profile_url = 'https://www.crick.ac.uk/research/platforms-and-facilities/scientific-computing/technologies' + config_profile_url = 'https://www.crick.ac.uk/research/platforms-and-facilities/bioinformatics-and-biostatistics' } singularity { From 59bc3b43bec602354ceff15d1b75aebe3a18c36a Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 7 Jan 2019 11:35:49 +0000 Subject: [PATCH 31/31] Update crick.config --- conf/crick.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/crick.config b/conf/crick.config index a0d9906..02a835d 100755 --- a/conf/crick.config +++ b/conf/crick.config @@ -1,9 +1,9 @@ //Profile config names for nf-core/configs params { config_profile_name = 'CRICK' - config_profile_description = 'Profile for CAMP HPC Cluster @ The Francis Crick Institute provided by nf-core/configs.' + config_profile_description = 'The Francis Crick Institute CAMP HPC Cluster Profile provided by nf-core/configs.' config_profile_contact = 'Harshil Patel (@drpatelh )' - config_profile_url = 'https://www.crick.ac.uk/research/platforms-and-facilities/bioinformatics-and-biostatistics' + config_profile_url = 'https://www.crick.ac.uk/research/platforms-and-facilities/scientific-computing/technologies' } singularity {