From adf0c0b0aebfa4d92548798001ca4f09f9db4bf2 Mon Sep 17 00:00:00 2001 From: hjulienn <hjulienn> Date: Thu, 19 Jan 2023 11:10:42 +0100 Subject: [PATCH] added date tag to the inittable name --- README.md | 13 ++++++++----- jass_pipeline.nf | 2 +- nextflow_local.config | 7 ------- 3 files changed, 9 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index 3057c85..feacf04 100644 --- a/README.md +++ b/README.md @@ -52,8 +52,9 @@ They correspond to the chromosome 21 and 22 for the East asian ancestry. Once done you can launch the pipeline as: ``` - nextflow run jass_pipeline.nf --ref_panel_WG {ABSOLUTE_PATH_TO_PIPELINE_FOLDER}Ref_Panel/1000G_EAS_0_01_chr22_21.csv --gwas_folder {ABSOLUTE_PATH_TO_PIPELINE_FOLDER}test_data/hg38_EAS/ --meta-data {ABSOLUTE_PATH_TO_PIPELINE_FOLDER}input_files/Data_test_EAS.csv --region {ABSOLUTE_PATH_TO_PIPELINE_FOLDER}input_files/All_Regions_ALL_ensemble_1000G_hg38_EAS.bed --group {ABSOLUTE_PATH_TO_PIPELINE_FOLDER}input_files/group.txt -with-report jass_report.html -c nextflow_local.config + nextflow run jass_pipeline.nf --ref_panel_WG {ABSOLUTE_PATH_TO_PIPELINE_FOLDER}Ref_Panel/1000G_EAS_0_01_chr22_21.csv --gwas_folder {ABSOLUTE_PATH_TO_PIPELINE_FOLDER}/test_data/hg38_EAS/ --meta-data {ABSOLUTE_PATH_TO_PIPELINE_FOLDER}/input_files/Data_test_EAS.csv --region {ABSOLUTE_PATH_TO_PIPELINE_FOLDER}/input_files/All_Regions_ALL_ensemble_1000G_hg38_EAS.bed --group {ABSOLUTE_PATH_TO_PIPELINE_FOLDER}/input_files/group.txt -with-report jass_report.html -c nextflow_local.config ``` +See the description of required parameters in the next section. You can specify parameter in the jass_pipeline.nf header if prefered. If all went well, you have cleaned the three summary statistic files, aligned them on the reference panel, and integrated them in one database. This database was used to perform a multi-trait GWAS on the three traits. @@ -73,9 +74,10 @@ See sections below, for running the imputation step and/or the LD-score step. The following Item are necessary to run JASS pipeline on real data -1. --meta_data : A path toward a meta-data file describing GWAS (see example file in ./input_files/test1.csv and [jass_preprocessing documentation](http://statistical-genetics.pages.pasteur.fr/jass_preprocessing/)) -2. --gwas_folder : A path toward a folder containing the summary statistics to analyze -3. --ref_panel_WG : a path toward a reference panel (all genome as 1 file). See below to download curated reference panels by ancestries derived from 1000G +1. --meta_data: A path toward a meta-data file describing GWAS (see example file in ./input_files/test1.csv and [jass_preprocessing documentation](http://statistical-genetics.pages.pasteur.fr/jass_preprocessing/)) +2. --gwas_folder: A path toward a folder containing the summary statistics to analyze +3. --ref_panel_WG: a path toward a reference panel (all genome as 1 file). See below to download curated reference panels by ancestries derived from 1000G V3 on hg38 assembly +4. --region: Quasi LD independent regions. These regions are used by JASS to determine quickly LD-independent hits accross the genome. The input_files folder contains one region file by ancestry on hg38 assembly. If working with a different assembly or population, you can provide 1Mb delimitations as a rough equivalent of these regions. ## Optional parameters @@ -84,9 +86,10 @@ The following Item are necessary to run JASS pipeline on real data ### to launch multi-trait GWAS at the end of the pipeline You can use this pipeline to launch a batch of multi-trait GWAS at the end of the pipeline +* --compute_project: flag indicating that you wish to perform multi trait GWAS at the end of the pipeline * --group If you wish to compute joint analyses with the pipeline, a group file with the each phenotype group written on a separated line -Alternatively, use the **jass create-project-data command line** on the inittable file (all your summary statistique harmonized) stored. +Alternatively, use the **jass create-project-data command line** on the inittable file (all your summary statistique harmonized) stored in the init_table folder. See JASS documentation for its usage (https://statistical-genetics.pages.pasteur.fr/jass/generating_joint_analysis.html). ### To launch imputation based on summary statistics diff --git a/jass_pipeline.nf b/jass_pipeline.nf index 4747e2a..3391106 100644 --- a/jass_pipeline.nf +++ b/jass_pipeline.nf @@ -323,7 +323,7 @@ process Create_inittable { date_init=\$(date +"%m_%d_%Y-%H:%M") init_name="inittable_NO_LDSC_\$date_init.hdf5" - jass create-inittable --input-data-path "./*.txt" --regions-map-path ${Regions} --description-file-path ${params.meta_data} --init-table-path inittable_no_LDSC.hdf5 + jass create-inittable --input-data-path "./*.txt" --regions-map-path ${Regions} --description-file-path ${params.meta_data} --init-table-path \$init_name """ } diff --git a/nextflow_local.config b/nextflow_local.config index b6bb49c..348687a 100644 --- a/nextflow_local.config +++ b/nextflow_local.config @@ -35,13 +35,6 @@ executor { process{ - withName: 'Compute_MAF' { - container='plink_1.90b5--heea4ae3_0.sif' - time='1h' - queue='dedicated,common,ggs' - cpus=1 - } - withName: 'Impute_GWAS' { memory={8.GB * task.attempt} time={72.h * task.attempt} -- GitLab