Refactoring step 07 to process all datasets at once (Part I).

17-Enrichment_all/CP_enrich.sh → 07-Enrichment/CP_enrich.sh

 #!/bin/bash -l
-#SBATCH -J geneder:17:cp_enrich
+#SBATCH -J geneder:07:cp_enrich
 #SBATCH --mail-type=all
 #SBATCH --mail-user=leon-charles.tranchevent@uni.lu
 #SBATCH -N 1
 #SBATCH -n 25
-#SBATCH --time=0-06:00:00
+#SBATCH --time=0-08:00:00
 #SBATCH -p batch
-#SBATCH --qos=qos-batch
+#SBATCH --qos=normal
 
 echo "== Starting run at $(date)"
 echo "== Job ID: ${SLURM_JOBID}"
@@ -15,9 +15,9 @@ echo "== Submit dir. : ${SLURM_SUBMIT_DIR}"
 echo ""
 
 # Defining global parameters.
-INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/16/
-OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/17/
-CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/17-Enrichment_all/
+INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/06/
+OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/07/
+CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/07-Enrichment/
 
 # Loading modules.
 module load lang/R/3.6.0-foss-2019a-bare

17-Enrichment_all/G2P_enrich.sh → 07-Enrichment/G2P_enrich.sh

 #!/bin/bash -l
-#SBATCH -J geneder:17:g2p_enrich
+#SBATCH -J geneder:07:g2p_enrich
 #SBATCH --mail-type=all
 #SBATCH --mail-user=leon-charles.tranchevent@uni.lu
 #SBATCH -N 1
 #SBATCH -n 8
-#SBATCH --time=0-15:00:00
+#SBATCH --time=0-19:00:00
 #SBATCH -p batch
-#SBATCH --qos=qos-batch
+#SBATCH --qos=normal
 
 echo "== Starting run at $(date)"
 echo "== Job ID: ${SLURM_JOBID}"
@@ -15,9 +15,9 @@ echo "== Submit dir. : ${SLURM_SUBMIT_DIR}"
 echo ""
 
 # Defining global parameters.
-INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/16/
-OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/17/
-CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/17-Enrichment_all/
+INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/06/
+OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/07/
+CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/07-Enrichment/
 
 # Loading modules.
 module load lang/R/3.6.0-foss-2019a-bare

17-Enrichment_all/Makefile → 07-Enrichment/Makefile

-INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/16/
-OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/17/
-CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/17-Enrichment_all/
+INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/06/
+OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/07/
+CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/07-Enrichment/
 
 clean:
 	@rm -rf *~
@@ -13,9 +13,9 @@ enrich:
 	@sbatch ${CODE_FOLDER}CP_enrich.sh
 	@sbatch ${CODE_FOLDER}G2P_enrich.sh
 	@sbatch ${CODE_FOLDER}ROT_enrich.sh
-pfenrich:
-	@/bin/bash ${CODE_FOLDER}PF_enrich.sh
-#merge:
-#	@sbatch ${CODE_FOLDER}merge.sh
+##pfenrich:
+##	@/bin/bash ${CODE_FOLDER}PF_enrich.sh
+##merge:
+##	@sbatch ${CODE_FOLDER}merge.sh
 gsp:
 	@sbatch ${CODE_FOLDER}gender_specific_pathways.sh

17-Enrichment_all/PF_enrich.sh → 07-Enrichment/PF_enrich.sh

 #!/bin/bash -l
 
 # Defining global parameters.
-INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/16/
-OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/17/
-CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/17-Enrichment_all/
+INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/06/
+OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/07/
+CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/07-Enrichment/
 
 # Actual jobs
 #xvfb-run Rscript --vanilla ${CODE_FOLDER}/PF_enrich.R > ${OUTPUT_FOLDER}/PF_enrich_log.out 2> ${OUTPUT_FOLDER}/PF_enrich_log.err

17-Enrichment_all/README.md → 07-Enrichment/README.md

@@ -26,7 +26,7 @@ make gsp
 ```
 
 # Prerequisites
-A prerequisite is to have the results of the second integration (MA+RS, step 16).
+A prerequisite is to have the results of the integration (step 06).
 
 #TODO
 This steps needs to be completely changed as to incorporate the latest change in the workflow (new rankings and so on).

17-Enrichment_all/ROT_enrich.sh → 07-Enrichment/ROT_enrich.sh

 #!/bin/bash -l
-#SBATCH -J geneder:17:rot_enrich
+#SBATCH -J geneder:07:rot_enrich
 #SBATCH --mail-type=all
 #SBATCH --mail-user=leon-charles.tranchevent@uni.lu
 #SBATCH -N 1
 #SBATCH -n 8
-#SBATCH --time=0-18:00:00
+#SBATCH --time=0-22:00:00
 #SBATCH -p batch
-#SBATCH --qos=qos-batch
+#SBATCH --qos=normal
 
 echo "== Starting run at $(date)"
 echo "== Job ID: ${SLURM_JOBID}"
@@ -15,9 +15,9 @@ echo "== Submit dir. : ${SLURM_SUBMIT_DIR}"
 echo ""
 
 # Defining global parameters.
-INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/16/
-OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/17/
-CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/17-Enrichment_all/
+INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/06/
+OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/07/
+CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/07-Enrichment/
 
 # Loading modules.
 module load lang/R/3.6.0-foss-2019a-bare

17-Enrichment_all/gender_specific_pathways.sh → 07-Enrichment/gender_specific_pathways.sh

 #!/bin/bash -l
-#SBATCH -J geneder:17:gsp
+#SBATCH -J geneder:07:gsp
 #SBATCH --mail-type=all
 #SBATCH --mail-user=leon-charles.tranchevent@uni.lu
 #SBATCH -N 1
 #SBATCH -n 8
 #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}"
@@ -15,9 +15,9 @@ echo "== Submit dir. : ${SLURM_SUBMIT_DIR}"
 echo ""
 
 # Defining global parameters.
-INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/16/
-OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/17/
-CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/17-Enrichment_all/
+INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/06/
+OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/07/
+CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/07-Enrichment/
 
 # Loading modules.
 module load lang/R/3.6.0-foss-2019a-bare

07-Enrichment/local_config.yml

+local_input_data_dir: !!str '06/'
+local_data_dir: !!str '07/'
+local_code_dir: !!str '07-Enrichment/'

17-Enrichment_all/merge.sh → 07-Enrichment/merge.sh

 #!/bin/bash -l
-#SBATCH -J geneder:17:merge
+#SBATCH -J geneder:07:merge
 #SBATCH --mail-type=all
 #SBATCH --mail-user=leon-charles.tranchevent@uni.lu
 #SBATCH -N 1
 #SBATCH -n 8
 #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}"
@@ -15,9 +15,9 @@ echo "== Submit dir. : ${SLURM_SUBMIT_DIR}"
 echo ""
 
 # Defining global parameters.
-INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/16/
-OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/17/
-CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/17-Enrichment_all/
+INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/06/
+OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/07/
+CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/07-Enrichment/
 
 # Loading modules.
 module load lang/R/3.6.0-foss-2019a-bare

17-Enrichment_all/local_config.yml

-local_input_data_dir: !!str '16/'
-local_data_dir: !!str '17/'
-local_code_dir: !!str '17-Enrichment_all/'