From 4828e78708ecf6ddb8a2a8db560bb72f72357330 Mon Sep 17 00:00:00 2001 From: Piotr Faba Date: Thu, 2 Jul 2020 21:57:44 +0200 Subject: [PATCH 1/7] fix error introduced earlier --- conf/bi.config | 21 ++++++++------------- 1 file changed, 8 insertions(+), 13 deletions(-) diff --git a/conf/bi.config b/conf/bi.config index 65059e3..3a77bb7 100644 --- a/conf/bi.config +++ b/conf/bi.config @@ -4,17 +4,12 @@ params{ config_profile_url = 'https://www.boehringer-ingelheim.com/' } -params.globalConfig = set_global_config() - - -def set_global_config() { - def config = System.getenv('NXF_GLOBAL_CONFIG') - if(config == null) - { - def errorMessage = "WARNING: For bi.config requires NXF_GLOBAL_CONFIG env var to be set. Point it to global.config file if you want to use this profile." - System.err.println(errorMessage) - }else{ - includeConfig config - } - return config +def configVar = System.getenv('NXF_GLOBAL_CONFIG') +if(configVar == null) +{ + def errorMessage = "WARNING: For bi.config requires NXF_GLOBAL_CONFIG env var to be set. Point it to global.config file if you want to use this profile." + System.err.println(errorMessage) +}else{ + params.globalConfig = configVar + includeConfig configVar } From 4181184f58892a6c42efba3e9bd1eceaf7a6fd73 Mon Sep 17 00:00:00 2001 From: Piotr Faba Date: Thu, 2 Jul 2020 22:00:37 +0200 Subject: [PATCH 2/7] fix spaces --- conf/bi.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/bi.config b/conf/bi.config index 3a77bb7..fe2ae17 100644 --- a/conf/bi.config +++ b/conf/bi.config @@ -10,6 +10,6 @@ if(configVar == null) def errorMessage = "WARNING: For bi.config requires NXF_GLOBAL_CONFIG env var to be set. Point it to global.config file if you want to use this profile." System.err.println(errorMessage) }else{ - params.globalConfig = configVar - includeConfig configVar + params.globalConfig = configVar + includeConfig configVar } From cb7a6f756af97154cc2867c484488408caa0babd Mon Sep 17 00:00:00 2001 From: Piotr Faba Date: Tue, 7 Jul 2020 13:48:28 +0200 Subject: [PATCH 3/7] reduce complexity --- conf/bi.config | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/conf/bi.config b/conf/bi.config index fe2ae17..1a218f1 100644 --- a/conf/bi.config +++ b/conf/bi.config @@ -4,12 +4,11 @@ params{ config_profile_url = 'https://www.boehringer-ingelheim.com/' } -def configVar = System.getenv('NXF_GLOBAL_CONFIG') -if(configVar == null) +params.globalConfig = System.getenv('NXF_GLOBAL_CONFIG') +if(params.globalConfig == null) { def errorMessage = "WARNING: For bi.config requires NXF_GLOBAL_CONFIG env var to be set. Point it to global.config file if you want to use this profile." System.err.println(errorMessage) }else{ - params.globalConfig = configVar - includeConfig configVar + includeConfig params.globalConfig } From 57ac9257a92ef2912163e02425359e2ace8f5aa7 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 20 Jul 2020 11:29:12 +0200 Subject: [PATCH 4/7] Remove now deprecated EAGER flag for HOPS profile --- conf/pipeline/eager/shh.config | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/pipeline/eager/shh.config b/conf/pipeline/eager/shh.config index c48db8b..777f516 100644 --- a/conf/pipeline/eager/shh.config +++ b/conf/pipeline/eager/shh.config @@ -76,7 +76,6 @@ profiles { bwaalnn = 0.01 bwaalnl = 16 run_bam_filtering = true - bam_discard_unmapped = true bam_unmapped_type = 'fastq' run_metagenomic_screening = true metagenomic_tool = 'malt' From 69a0bd572b646db68f9ff1f19cd059d7e59807a2 Mon Sep 17 00:00:00 2001 From: maxibor Date: Thu, 23 Jul 2020 15:38:28 +0200 Subject: [PATCH 5/7] add temporary CDAG setting for SHH config --- conf/shh.config | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/conf/shh.config b/conf/shh.config index 8defc1f..e0c7116 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -33,6 +33,10 @@ profiles { params { config_profile_description = 'CDAG MPI-SHH profile, provided by nf-core/configs.' } + // delete when CDAG will be fixed + process { + queue = 'long' + } } sdag { params { From b80407695941bedac700e6a70dd44a305b292eae Mon Sep 17 00:00:00 2001 From: drpatelh Date: Mon, 3 Aug 2020 11:38:10 +0100 Subject: [PATCH 6/7] Remove hard Singularity version --- conf/crick.config | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/crick.config b/conf/crick.config index 4bcd242..338bb76 100755 --- a/conf/crick.config +++ b/conf/crick.config @@ -11,7 +11,6 @@ singularity { } process { - beforeScript = 'module load Singularity/2.6.0-foss-2016b' executor = 'slurm' } From 165af5122f31f0ff63827366abcf5fc0c67e816a Mon Sep 17 00:00:00 2001 From: drpatelh Date: Mon, 3 Aug 2020 11:39:23 +0100 Subject: [PATCH 7/7] Update docs --- docs/crick.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/crick.md b/docs/crick.md index e18db65..5eae24f 100644 --- a/docs/crick.md +++ b/docs/crick.md @@ -10,7 +10,7 @@ Before running the pipeline you will need to load Nextflow and Singularity using ## Load Nextflow and Singularity environment modules module purge module load Nextflow/19.10.0 -module load Singularity/2.6.0-foss-2016b +module load Singularity ``` A local copy of the [AWS-iGenomes](https://github.com/ewels/AWS-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).