bug fix

assets/deploy_scripts/bsub.sh

@@ -21,5 +21,5 @@ if ["$varname" = ''];
 fi
 sample="$RUN_ID"
 echo -e "\n Submitting yascp (https://github.com/wtsi-hgi/yascp) with input file $INPUT_FILE"
-bsub -R'select[mem>8000] rusage[mem=8000]' -J $sample -n 1 -M 8000 -o $sample.o -e $sample.e -q long bash /software/hgi/pipelines/yascp/assets/deploy_scripts/nohup_start_nextflow_lsf.sh $INPUT_FILE
+bsub -R'select[mem>8000] rusage[mem=8000]' -J $sample -n 1 -M 8000 -o $sample.o -e $sample.e -q long bash /software/hgi/pipelines/yascp_versions/yascp_v1.2/assets/deploy_scripts/nohup_start_nextflow_lsf.sh $INPUT_FILE
 echo "Submitted job can be killed with: bkill -J $sample"

assets/deploy_scripts/bsub__removeWork.sh

@@ -5,5 +5,5 @@ INPUT_FILE=$1
 export RUN_ID="${PWD##*/}"
 sample="$RUN_ID.yascp"
 echo "Cleaning the work directory (https://github.com/wtsi-hgi/yascp) with input file $INPUT_FILE by using '-entry WORK_DIR_REMOVAL --remove_work_dir' "
-bsub -R'select[mem>4000] rusage[mem=4000]' -J $sample -n 1 -M 4000 -o $sample.o -e $sample.e -q long bash /software/hgi/pipelines/yascp/assets/deploy_scripts/nohup_start_nextflow_lsf__removeWork.sh $INPUT_FILE
+bsub -R'select[mem>4000] rusage[mem=4000]' -J $sample -n 1 -M 4000 -o $sample.o -e $sample.e -q long bash /software/hgi/pipelines/yascp_versions/yascp_v1.2/assets/deploy_scripts/nohup_start_nextflow_lsf__removeWork.sh $INPUT_FILE
 echo "Submitted job can be killed with: bkill -J $sample"

assets/deploy_scripts/bsub_test.sh

@@ -25,5 +25,5 @@ fi
 
 sample="$RUN_ID.yascp"
 echo -e "\nSubmitting yascp (https://github.com/wtsi-hgi/yascp) in test mode withsample OneK1k dataset"
-bsub -R'select[mem>4000] rusage[mem=4000]' -J yascp_test -n 1 -M 4000 -o yascp_test.o -e yascp_test.e -q normal bash /software/hgi/pipelines/yascp/assets/deploy_scripts/nohup_start_nextflow_lsf_test.sh
+bsub -R'select[mem>4000] rusage[mem=4000]' -J yascp_test -n 1 -M 4000 -o yascp_test.o -e yascp_test.e -q normal bash /software/hgi/pipelines/yascp_versions/yascp_v1.2/assets/deploy_scripts/nohup_start_nextflow_lsf_test.sh
 echo "Submitted job can be killed with: bkill -J yascp_test"

assets/deploy_scripts/nohup_start_nextflow_lsf.sh

@@ -17,7 +17,7 @@ parentdir="$(dirname "$CWD1")"
 export RUN_ID="${PWD##*/}"
 mkdir $PWD/work || echo 'exists'
 mkdir $PWD/work/tmp || echo 'exists'
-echo $RUN_ID | nextflow run /software/hgi/pipelines/yascp -profile sanger -c $INPUT_FILE --nf_ci_loc $PWD -resume > nextflow.nohup.log 2>&1 & 
+echo $RUN_ID | nextflow run /software/hgi/pipelines/yascp_versions/yascp_v1.2 -profile sanger -c $INPUT_FILE --nf_ci_loc $PWD -resume > nextflow.nohup.log 2>&1 & 
 
 # get process PID 
 sleep 1 && export PID=$(pgrep -f "\\-\\-nf_ci_loc $RUN_DIR")

assets/deploy_scripts/nohup_start_nextflow_lsf__removeWork.sh

@@ -21,7 +21,7 @@ export RUN_ID="${PWD##*/}"
 # export TEMP=$PWD/tmp
 # export TMP_DIR=$PWD/tmp
 
-echo $RUN_ID | nextflow run /software/hgi/pipelines/yascp -profile sanger  -c $INPUT_FILE --nf_ci_loc $PWD -entry WORK_DIR_REMOVAL --remove_work_dir -resume > nextflow.nohup.log 2>&1 & 
+echo $RUN_ID | nextflow run /software/hgi/pipelines/yascp_versions/yascp_v1.2 -profile sanger  -c $INPUT_FILE --nf_ci_loc $PWD -entry WORK_DIR_REMOVAL --remove_work_dir -resume > nextflow.nohup.log 2>&1 & 
 
 # get process PID 
 sleep 1 && export PID=$(pgrep -f "\\-\\-nf_ci_loc $RUN_DIR")

assets/deploy_scripts/nohup_start_nextflow_lsf_test.sh

@@ -16,7 +16,7 @@ parentdir="$(dirname "$CWD1")"
 export RUN_ID="${PWD##*/}"
 mkdir $PWD/work || echo 'exists'
 mkdir $PWD/work/tmp || echo 'exists'
-echo $RUN_ID | nextflow run /software/hgi/pipelines/yascp -profile sanger,test -c /software/hgi/pipelines/yascp/conf/extra_confs/sanger/base.conf --nf_ci_loc $PWD -resume > nextflow.nohup.log 2>&1 & 
+echo $RUN_ID | nextflow run /software/hgi/pipelines/yascp_versions/yascp_v1.2 -profile sanger,test --nf_ci_loc $PWD -resume > nextflow.nohup.log 2>&1 & 
 
 # get process PID 
 sleep 1 && export PID=$(pgrep -f "\\-\\-nf_ci_loc $RUN_DIR")

bin/generate_combined_celltype_anotation_file.py

@@ -15,18 +15,23 @@
 def combine_reports(all_alternitive,mode):
     all_indexes_full=set({})
     for d1 in all_alternitive:
-
-        Dataset = pd.read_csv(d1,sep='\t',index_col=0)
-        if(len(Dataset.columns)==0):
-            Dataset = pd.read_csv(d1,sep=',',index_col=0)
+        if d1=='fake_file.fq':
+            Dataset = pd.DataFrame()
+        else:
+            Dataset = pd.read_csv(d1,sep='\t',index_col=0)
+            if(len(Dataset.columns)==0):
+                Dataset = pd.read_csv(d1,sep=',',index_col=0)
         Dataset=Dataset.add_prefix(mode)
         all_indexes = set(Dataset.index)
         all_indexes_full = all_indexes_full.union(all_indexes)
     Data_All_alt=pd.DataFrame(index=list(set(all_indexes_full)))    
     for d1 in all_alternitive:
-        Dataset = pd.read_csv(d1,sep='\t',index_col=0)
-        if(len(Dataset.columns)==0):
-            Dataset = pd.read_csv(d1,sep=',',index_col=0)
+        if d1=='fake_file.fq':
+            Dataset = pd.DataFrame()
+        else:
+            Dataset = pd.read_csv(d1,sep='\t',index_col=0)
+            if(len(Dataset.columns)==0):
+                Dataset = pd.read_csv(d1,sep=',',index_col=0)
         Dataset=Dataset.add_prefix(mode)
         for col1 in Dataset.columns:
             try: