added a few fixes to the per-gene analysis

swvanderlaan · Apr 18, 2024 · 759629e · 759629e
1 parent e3a2d03
commit 759629e
Show file tree

Hide file tree

Showing 2 changed files with 24 additions and 24 deletions.
diff --git a/gwastoolkit.analyzer.sh b/gwastoolkit.analyzer.sh
@@ -187,9 +187,9 @@ echobold "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 echobold "                                            GWASTOOLKIT ANALYZER"
 echobold "           individual variant, per-gene, regional, or genome-wide association study of a trait"
 echobold ""
-echobold " Version    : v1.3.7"
+echobold " Version    : v1.3.8"
 echobold ""
-echobold " Last update: 2023-11-29"
+echobold " Last update: 2024-04-18"
 echobold " Written by : Sander W. van der Laan (s.w.vanderlaan-2@umcutrecht.nl)."
 echobold ""
 echobold " Testers    : - Saskia Haitjema (s.haitjema@umcutrecht.nl)"
@@ -704,8 +704,8 @@ fi
 
 		echo ""
 		### Run SNPTEST for each gene and phenotype
-    FINAL_JOB_ID=""
-    FINAL_JOB_ID_c=0
+	FINAL_JOB_ID=""
+	FINAL_JOB_ID_c=0
 		while IFS='' read -r REGIONOFINTEREST || [[ -n "$REGIONOFINTEREST" ]]; do
 			LINE=${REGIONOFINTEREST}
 			GENELOCUS=$(echo "${LINE}" | awk '{print $1}')

diff --git a/gwastoolkit.run.sh b/gwastoolkit.run.sh
@@ -99,9 +99,9 @@ echobold "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 echobold "                                               GWASTOOLKIT"
 echobold "           individual variant, per-gene, regional, or genome-wide association study of a trait"
 echobold ""
-echobold " Version    : v1.4.2"
+echobold " Version    : v1.4.3"
 echobold ""
-echobold " Last update: 2023-11-29"
+echobold " Last update: 2024-04-18"
 echobold " Written by :  Sander W. van der Laan (s.w.vanderlaan-2@umcutrecht.nl)."
 echobold ""
 echobold " Testers:     - Saskia Haitjema (s.haitjema@umcutrecht.nl)"
@@ -276,13 +276,13 @@ else
 			##### Create cleaner bash-script to send to qsub
 			printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.cleaner.sh ${CONFIGURATIONFILE} ${PHENOTYPE} " > ${PHENO_OUTPUT_DIR}/cleaner.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh
 			JOB_ID_CLEANER_i=$(sbatch --parsable -J CLEANER.${STUDY_TYPE}.${ANALYSIS_TYPE}.${EXCLUSION} --depend=afterany:$(squeue --noheader --format %i --name ANALYZER.DONE.${DATE_TRACK}) -o ${PHENO_OUTPUT_DIR}/cleaner.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.log -e ${PHENO_OUTPUT_DIR}/cleaner.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.errors --mem=${QMEMVARCLEANER} -t ${QTIMEVARCLEANER} --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PHENO_OUTPUT_DIR} ${PHENO_OUTPUT_DIR}/cleaner.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh)
-      if [[ ${JOB_IDS_c} == 0 ]]; then
-        JOB_IDS_PHENO="${JOB_ID_CLEANER_i}"
-        JOB_IDS_c=$((JOB_IDS_c + 1))
-      else
-        JOB_IDS_PHENO="${JOB_IDS_PHENO},${JOB_ID_CLEANER_i}"
-        JOB_IDS_c=$((JOB_IDS_c + 1))
-      fi
+		if [[ ${JOB_IDS_c} == 0 ]]; then
+			JOB_IDS_PHENO="${JOB_ID_CLEANER_i}"
+			JOB_IDS_c=$((JOB_IDS_c + 1))
+		else
+			JOB_IDS_PHENO="${JOB_IDS_PHENO},${JOB_ID_CLEANER_i}"
+			JOB_IDS_c=$((JOB_IDS_c + 1))
+		fi
 		done
 			###### Create summariser bash-script to send to qsub -- SEE REMARKS ABOVE
 			printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/summariser.sh ${CONFIGURATIONFILE} " > ${PROJECT}/summariser.${STUDY_TYPE}.${ANALYSIS_TYPE}.${EXCLUSION}.sh
@@ -300,10 +300,10 @@ else
 		echo "Creating jobs to perform a per-analysis on your phenotype(s)..."
 		${GWASTOOLKITDIR}/gwastoolkit.analyzer.sh ${CONFIGURATIONFILE} ${DATE_TRACK}
 
-		### Create QC bash-script to send to qsub
-    JOB_IDS_c=0
-    ### This variable holds the Job_IDs which we will use for setting dependency on the wrapper script
-    JOB_IDS_PHENO=""
+	### Create QC bash-script to send to qsub
+	JOB_IDS_c=0
+	### This variable holds the Job_IDs which we will use for setting dependency on the wrapper script
+	JOB_IDS_PHENO=""
 		while IFS='' read -r GENEOFINTEREST || [[ -n "$GENEOFINTEREST" ]]; do
 			for GENE in ${GENEOFINTEREST}; do
 				for PHENOTYPE in ${PHENOTYPES}; do
@@ -328,13 +328,13 @@ else
 					##### Submit cleaner script
 					JOB_ID_CLEANER_i=$(sbatch --parsable -J CLEANER.${STUDY_TYPE}.${ANALYSIS_TYPE}.${EXCLUSION}.${GENE}_${RANGE} --depend=afterany:${JOB_ID_LZ} -o ${PHENO_OUTPUT_DIR}/cleaner.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.${GENE}_${RANGE}.log -e ${PHENO_OUTPUT_DIR}/cleaner.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.${GENE}_${RANGE}.errors --mem=${QMEMGENECLEANER} -t ${QTIMEGENECLEANER} --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PHENO_OUTPUT_DIR} ${PHENO_OUTPUT_DIR}/cleaner.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.${GENE}_${RANGE}.sh)
 					echo ""
-          if [[ ${JOB_IDS_c} == 0 ]]; then
-            JOB_IDS_PHENO="${JOB_ID_CLEANER_i}"
-            JOB_IDS_c=$((JOB_IDS_c + 1))
-          else
-            JOB_IDS_PHENO="${JOB_IDS_PHENO},${JOB_ID_CLEANER_i}"
-            JOB_IDS_c=$((JOB_IDS_c + 1))
-          fi
+			if [[ ${JOB_IDS_c} == 0 ]]; then
+				JOB_IDS_PHENO="${JOB_ID_CLEANER_i}"
+				JOB_IDS_c=$((JOB_IDS_c + 1))
+			else
+				JOB_IDS_PHENO="${JOB_IDS_PHENO},${JOB_ID_CLEANER_i}"
+				JOB_IDS_c=$((JOB_IDS_c + 1))
+			fi
 				done
 			done
 		done < ${GENES_FILE}