From 6c7a08634b98371564bdfbda4da011ef4666208d Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Sat, 19 Oct 2024 10:06:08 +0100 Subject: [PATCH] update template 3.0.2 - versions issues --- conf/test_dda_id.config | 5 ----- conf/test_dia.config | 12 +++++++----- conf/test_full_dia.config | 13 ++++++++----- conf/test_full_lfq.config | 13 ++++++++----- conf/test_full_tmt.config | 12 ++++++++---- conf/test_latest_dia.config | 13 ++++++++----- conf/test_lfq_sage.config | 13 ++++++++----- conf/test_localize.config | 13 ++++++++----- conf/test_tmt.config | 12 ++++++++---- conf/test_tmt_corr.config | 12 ++++++++---- 10 files changed, 71 insertions(+), 47 deletions(-) diff --git a/conf/test_dda_id.config b/conf/test_dda_id.config index 0bbd9311c..e5b8da006 100644 --- a/conf/test_dda_id.config +++ b/conf/test_dda_id.config @@ -14,11 +14,6 @@ params { config_profile_name = 'Real full-size test profile for DDA ID' config_profile_description = 'Real full-size test dataset to check pipeline function of the DDA identification branch of the pipeline' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 48.h - outdir = "./results_lfq_dda_id" // Input data diff --git a/conf/test_dia.config b/conf/test_dia.config index deb1d03c9..ce041b928 100644 --- a/conf/test_dia.config +++ b/conf/test_dia.config @@ -10,15 +10,17 @@ ------------------------------------------------------------------------------------------------ */ +process { + resourceLimits = [ + cpus: 4, + memory: '6.GB', + time: '48.h' + ] +} params { config_profile_name = 'Test profile for DIA' config_profile_description = 'Minimal test dataset to check pipeline function for the data-independent acquisition pipeline branch.' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 48.h - outdir = './results_dia' // Input data diff --git a/conf/test_full_dia.config b/conf/test_full_dia.config index 1cfdd16d5..2bfb1142c 100644 --- a/conf/test_full_dia.config +++ b/conf/test_full_dia.config @@ -10,15 +10,18 @@ ------------------------------------------------------------------------------------------------ */ +process { + resourceLimits = [ + cpus: 4, + memory: '6.GB', + time: '48.h' + ] +} + params { config_profile_name = 'Real full-size test profile for DIA' config_profile_description = 'Real full-size test dataset to check pipeline function for the data-independent acquisition pipeline branch.' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 48.h - outdir = './results_dia_full' // Input data diff --git a/conf/test_full_lfq.config b/conf/test_full_lfq.config index 4e4684f16..1b2ccc5d2 100644 --- a/conf/test_full_lfq.config +++ b/conf/test_full_lfq.config @@ -10,15 +10,18 @@ ------------------------------------------------------------------------------------------------ */ +process { + resourceLimits = [ + cpus: 4, + memory: '12.GB', + time: '48.h' + ] +} + params { config_profile_name = 'Real full-size test profile for DDA LFQ' config_profile_description = 'Real full-size test dataset to check pipeline function of the label-free quantification branch of the pipeline' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 48.h - outdir = "./results_lfq_full" // Input data diff --git a/conf/test_full_tmt.config b/conf/test_full_tmt.config index 11eea647f..32650ed58 100644 --- a/conf/test_full_tmt.config +++ b/conf/test_full_tmt.config @@ -10,16 +10,20 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '12.GB', + time: '48.h' + ] +} + params { config_profile_name = 'Real full test profile DDA ISO' config_profile_description = 'Real full test dataset in isotopic labelling mode to check pipeline function and sanity of results' outdir = "./results_iso_full" - max_cpus = 2 - max_memory = 6.GB - max_time = 48.h - // Input data for full size test input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata-aws/tmt_full/PXD005486.sdrf.tsv' diff --git a/conf/test_latest_dia.config b/conf/test_latest_dia.config index 14eea22b7..ab99bf593 100644 --- a/conf/test_latest_dia.config +++ b/conf/test_latest_dia.config @@ -10,15 +10,18 @@ ------------------------------------------------------------------------------------------------ */ +process { + resourceLimits = [ + cpus: 4, + memory: '12.GB', + time: '48.h' + ] +} + params { config_profile_name = 'Test profile for latest DIA' config_profile_description = 'Minimal test dataset to check pipeline function for the data-independent acquisition pipeline branch for latest DIA-NN.' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 48.h - outdir = './results_latest_dia' // Input data diff --git a/conf/test_lfq_sage.config b/conf/test_lfq_sage.config index 8f7073b43..69234b6fb 100644 --- a/conf/test_lfq_sage.config +++ b/conf/test_lfq_sage.config @@ -10,15 +10,18 @@ ------------------------------------------------------------------------------------------------ */ +process { + resourceLimits = [ + cpus: 4, + memory: '12.GB', + time: '48.h' + ] +} + params { config_profile_name = 'Test profile for DDA LFQ with Sage' config_profile_description = 'Minimal test dataset to check pipeline function of the label-free quantification branch of the pipeline with the search engine Sage' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 48.h - outdir = "./results_lfq" tracedir = "${params.outdir}/pipeline_info" diff --git a/conf/test_localize.config b/conf/test_localize.config index ef32bddda..32d6bb6fa 100644 --- a/conf/test_localize.config +++ b/conf/test_localize.config @@ -10,15 +10,18 @@ ---------------------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '12.GB', + time: '48.h' + ] +} + params { config_profile_name = 'Test PTM-localization profile' config_profile_description = 'Minimal test dataset to check pipeline function for PTM-localization, SDRF parsing and ConsensusID.' - // Limit resources so that this can run on Travis - max_cpus = 2 - max_memory = 6.GB - max_time = 1.h - outdir = "./results_localize" // Input data diff --git a/conf/test_tmt.config b/conf/test_tmt.config index 7184f1a49..c220c3f6e 100644 --- a/conf/test_tmt.config +++ b/conf/test_tmt.config @@ -10,16 +10,20 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '12.GB', + time: '48.h' + ] +} + params { config_profile_name = 'Full test profile DDA ISO' config_profile_description = 'Full test dataset in isotopic labelling mode to check pipeline function and sanity of results' outdir = "./results_iso" - max_cpus = 2 - max_memory = 6.GB - max_time = 48.h - // Input data for full size test input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/tmt_ci/PXD000001.sdrf.tsv' diff --git a/conf/test_tmt_corr.config b/conf/test_tmt_corr.config index 561d1f31b..276b675d1 100644 --- a/conf/test_tmt_corr.config +++ b/conf/test_tmt_corr.config @@ -10,16 +10,20 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '12.GB', + time: '48.h' + ] +} + params { config_profile_name = 'Full test profile DDA ISO' config_profile_description = 'Full test dataset in isotopic labelling mode to check pipeline function and sanity of results' outdir = "./results_iso" - max_cpus = 2 - max_memory = 6.GB - max_time = 48.h - // Input data for full size test input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/tmt_ci/PXD000001.sdrf.tsv'