Commit 58c4002c authored by Leon-Charles Tranchevent's avatar Leon-Charles Tranchevent
Browse files

Refactoring steps 01 and 02 to process all datasets at once (microarray and RNA-seq).

parent 8b38640b
......@@ -37,12 +37,6 @@ for (i in seq_len(length(config$datasets))) {
dataset <- config$datasets[[i]]
dataset_name <- dataset$dataset_name
# We only do the QC when it is necessary.
if (dataset$first_qc != 'TRUE') {
message(paste0("[", Sys.time(), "] [", dataset_name, "] QC not necessary."))
next
}
# Clinical data can be used to identify bias in the experiments.
# By default, we have the disease status, but we can also have the gender.
dataset_groups <- c("Disease.status")
......@@ -55,6 +49,12 @@ for (i in seq_len(length(config$datasets))) {
# We run the quality control of the current dataset (if necessary).
if (selected_dataset_name == "" || selected_dataset_name == dataset_name) {
# We only do the QC when it is necessary.
if (dataset$first_qc != 'TRUE') {
message(paste0("[", Sys.time(), "] [", dataset_name, "] QC not necessary."))
next
}
# We define the I/Os
raw_data_subdir <- paste0(raw_data_dir, dataset_name, "/")
output_data_subdir <- paste0(output_data_dir, dataset_name, "/")
......
......@@ -5,9 +5,9 @@
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --mem=12GB
#SBATCH --time=0-00:50:00
#SBATCH --time=0-00:55:00
#SBATCH -p batch
#SBATCH --qos=qos-batch
#SBATCH --qos=normal
echo "== Starting run at $(date)"
echo "== Job ID: ${SLURM_JOBID}"
......
......@@ -6,7 +6,7 @@
#SBATCH -n 1
#SBATCH --time=0-00:01:00
#SBATCH -p batch
#SBATCH --qos=qos-batch
#SBATCH --qos=normal
echo "== Starting run at $(date)"
echo "== Job ID: ${SLURM_JOBID}"
......
......@@ -6,7 +6,7 @@
#SBATCH -n 1
#SBATCH --time=0-00:02:00
#SBATCH -p batch
#SBATCH --qos=qos-batch
#SBATCH --qos=normal
echo "== Starting run at $(date)"
echo "== Job ID: ${SLURM_JOBID}"
......
......@@ -4,9 +4,9 @@
#SBATCH --mail-user=leon-charles.tranchevent@uni.lu
#SBATCH -N 1
#SBATCH -n 20
#SBATCH --time=0-06:30:00
#SBATCH --time=0-07:00:00
#SBATCH -p batch
#SBATCH --qos=qos-batch
#SBATCH --qos=normal
echo "== Starting run at $(date)"
echo "== Job ID: ${SLURM_JOBID}"
......
......@@ -4,9 +4,9 @@
#SBATCH --mail-user=leon-charles.tranchevent@uni.lu
#SBATCH -N 1
#SBATCH -n 20
#SBATCH --time=0-01:00:00
#SBATCH --time=0-01:10:00
#SBATCH -p batch
#SBATCH --qos=qos-batch
#SBATCH --qos=normal
echo "== Starting run at $(date)"
echo "== Job ID: ${SLURM_JOBID}"
......
......@@ -223,7 +223,7 @@ datasets:
-
dataset_name: NBB
platform: RNAseq
array_type: RNAseq_EG
array_type: RNAseq-EG
clinical_descriptors: DG
first_qc: 'FALSE'
use_oligo: 'FALSE'
......
......@@ -71,3 +71,19 @@ platforms:
library_name: hugene10sttranscriptcluster.db
cdf_name: HuGene-1_0-st-v1.r3.cdf
mps_name: NA
-
vendor: RNAseq
platform_name: RNAseq-EG
biomart_name: ensembl_transcript_id
geo_name: NA
library_name: NA
cdf_name: NA
mps_name: NA
-
vendor: RNAseq
platform_name: HiSeq1000
biomart_name: NA
geo_name: NA
library_name: NA
cdf_name: NA
mps_name: NA
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