From 4814bac1c342e9715539a28a0967b33d3df5e86d Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 12 May 2020 12:42:42 +0200 Subject: [PATCH 1/6] Fix sub-profiles --- conf/shh.config | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/conf/shh.config b/conf/shh.config index a6106be..852f1d3 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -33,11 +33,15 @@ params { profiles { cdag { + params { config_profile_description = 'MPI-SHH CDAG profile, provided by nf-core/configs.' + } } sdag { + params { config_profile_description = 'MPI-SHH SDAG profile, provided by nf-core/configs.' max_memory = 2.TB max_cpus = 128 + } } } From 8225e07819fbfc76aa1a4048e12d740c52181aff Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 12 May 2020 12:47:25 +0200 Subject: [PATCH 2/6] Condensed base params and added names for debugging --- conf/shh.config | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/conf/shh.config b/conf/shh.config index 852f1d3..f10f1f8 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -1,8 +1,13 @@ //Profile config names for nf-core/configs params { - config_profile_description = 'Generic MPI-SHH cluster(s) profile provided by nf-core/configs.' + config_profile_description = 'JFY Generic MPI-SHH cluster(s) profile provided by nf-core/configs.' config_profile_contact = 'James Fellows Yates (@jfy133), Maxime Borry (@Maxibor)' config_profile_url = 'https://shh.mpg.de' + max_memory = 256.GB + max_cpus = 32 + max_time = 720.h + //Illumina iGenomes reference file path + igenomes_base = "/projects1/public_data/igenomes/" } cleanup = true @@ -23,23 +28,15 @@ executor { queueSize = 16 } -params { - max_memory = 256.GB - max_cpus = 32 - max_time = 720.h - //Illumina iGenomes reference file path - igenomes_base = "/projects1/public_data/igenomes/" -} - profiles { cdag { params { - config_profile_description = 'MPI-SHH CDAG profile, provided by nf-core/configs.' + config_profile_description = 'JFY MPI-SHH CDAG profile, provided by nf-core/configs.' } } sdag { params { - config_profile_description = 'MPI-SHH SDAG profile, provided by nf-core/configs.' + config_profile_description = 'JFY MPI-SHH SDAG profile, provided by nf-core/configs.' max_memory = 2.TB max_cpus = 128 } From ff915ee5045345075b854712694408a7e555c0ce Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 12 May 2020 12:47:59 +0200 Subject: [PATCH 3/6] Update shh.config --- conf/pipeline/eager/shh.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/pipeline/eager/shh.config b/conf/pipeline/eager/shh.config index b07004d..1ed9112 100644 --- a/conf/pipeline/eager/shh.config +++ b/conf/pipeline/eager/shh.config @@ -3,7 +3,7 @@ params { // Specific nf-core/configs params config_profile_contact = 'James Fellows Yates (@jfy133)' - config_profile_description = 'nf-core/eager SHH profile provided by nf-core/configs' + config_profile_description = 'JFY nf-core/eager SHH profile provided by nf-core/configs' igenomes_base = "/projects1/public_data/igenomes/" } From e31e781f2938fc95adc91b4c22f79eacbc4e56e8 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 26 May 2020 11:07:06 +0200 Subject: [PATCH 4/6] Remove debugging --- conf/shh.config | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/shh.config b/conf/shh.config index f10f1f8..8defc1f 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -1,6 +1,6 @@ //Profile config names for nf-core/configs params { - config_profile_description = 'JFY Generic MPI-SHH cluster(s) profile provided by nf-core/configs.' + config_profile_description = 'Generic MPI-SHH cluster(s) profile provided by nf-core/configs.' config_profile_contact = 'James Fellows Yates (@jfy133), Maxime Borry (@Maxibor)' config_profile_url = 'https://shh.mpg.de' max_memory = 256.GB @@ -31,12 +31,12 @@ executor { profiles { cdag { params { - config_profile_description = 'JFY MPI-SHH CDAG profile, provided by nf-core/configs.' + config_profile_description = 'CDAG MPI-SHH profile, provided by nf-core/configs.' } } sdag { params { - config_profile_description = 'JFY MPI-SHH SDAG profile, provided by nf-core/configs.' + config_profile_description = 'SDAG MPI-SHH profile, provided by nf-core/configs.' max_memory = 2.TB max_cpus = 128 } From d070ed70d18bc3766fb71d053d898e022aae04cb Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 26 May 2020 11:11:42 +0200 Subject: [PATCH 5/6] Update BWA settings based on feedback --- conf/pipeline/eager/shh.config | 31 +++++++++++++++++++++++++++---- 1 file changed, 27 insertions(+), 4 deletions(-) diff --git a/conf/pipeline/eager/shh.config b/conf/pipeline/eager/shh.config index 1ed9112..94a0403 100644 --- a/conf/pipeline/eager/shh.config +++ b/conf/pipeline/eager/shh.config @@ -3,8 +3,12 @@ params { // Specific nf-core/configs params config_profile_contact = 'James Fellows Yates (@jfy133)' - config_profile_description = 'JFY nf-core/eager SHH profile provided by nf-core/configs' + config_profile_description = 'nf-core/eager SHH profile provided by nf-core/configs' igenomes_base = "/projects1/public_data/igenomes/" + + // default BWA + bwaalnn = 0.04 + bwaalnl = 32 } // Specific nf-core/eager process configuration @@ -18,7 +22,26 @@ process { } } -params { - bwaalnn = 0.01 - bwaalnl = 32 +profiles { + pathogen_loose { + params { + config_profile_description = 'Pathogen (loose) MPI-SHH profile, provided by nf-core/configs.' + bwaalnn = 0.01 + bwaalnl = 16 + } + } + pathogen_strict { + params { + config_profile_description = 'Pathogen (strict) MPI-SHH SDAG profile, provided by nf-core/configs.' + bwaalnn = 0.1 + bwaalnl = 32 + } + } + human { + params { + config_profile_description = 'Human MPI-SHH SDAG profile, provided by nf-core/configs.' + bwaalnn = 0.01 + bwaalnl = 16500 + } + } } From 0943ba088a2fdd23aabccb73ba96b41001f7d2de Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 26 May 2020 11:14:42 +0200 Subject: [PATCH 6/6] Mention SHH EAGER group-specific profiles --- docs/pipeline/eager/shh.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/pipeline/eager/shh.md b/docs/pipeline/eager/shh.md index 41d0893..d5fbcb3 100644 --- a/docs/pipeline/eager/shh.md +++ b/docs/pipeline/eager/shh.md @@ -14,5 +14,5 @@ Example: `nextflow run nf-core/eager -profile shh` Specific configurations for shh has been made for eager. -* If running with the MALT module turned on, the MALT process by default will be sent to the long queue with a resource requirement minimum of 725GB and 64 cores. If this fails, the process will be tried once more only and sent to the supercruncher queue. The module will not retry after this, and pipeline will fail. -* Modifies the bwa aln `-n` parameter to 0.01, rather than typical default of 0.04, and `-l` to 32 (rather than 1024) to syncronise the (unpublished) parameter with EAGER1 and typical/expected usage within the department. +* If running with the MALT module turned on, the MALT process by default will be sent to the long queue with a resource requirement minimum of 725GB and 64 cores. If this fails, the process will be tried once more only and sent to the supercruncher queue. The module will not retry after this, and pipeline will fail. Note, this will only work on SDAG. +* Provides additional group specific profiles, which adapt the `bwa aln` mapping parameters to each context: `pathogens_loose` (`-l 0.01 -n 16`), `pathogens_strict` (`-l 32, -n 0.1`) and `human` (`-l 16500, -n 0.01`).