v1.3

wtsi-hgi · Dec 1, 2023 · 886b140 · 886b140
1 parent 9061c80
commit 886b140
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Showing 10 changed files with 10 additions and 10 deletions.
diff --git a/assets/deploy_scripts/bsub.sh b/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_versions/yascp_v1.3__work/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_v1.3/assets/deploy_scripts/nohup_start_nextflow_lsf.sh $INPUT_FILE
 echo "Submitted job can be killed with: bkill -J $sample"
diff --git a/assets/deploy_scripts/bsub__removeWork.sh b/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_versions/yascp_v1.3__work/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_v1.3/assets/deploy_scripts/nohup_start_nextflow_lsf__removeWork.sh $INPUT_FILE
 echo "Submitted job can be killed with: bkill -J $sample"
diff --git a/assets/deploy_scripts/bsub_test.sh b/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_versions/yascp_v1.3__work/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_v1.3/assets/deploy_scripts/nohup_start_nextflow_lsf_test.sh
 echo "Submitted job can be killed with: bkill -J yascp_test"
diff --git a/assets/deploy_scripts/bsub_test_celltypes.sh b/assets/deploy_scripts/bsub_test_celltypes.sh
@@ -25,5 +25,5 @@ fi
 
 sample="$RUN_ID.yascp"
 echo -e "\nSubmitting yascp (https://github.com/wtsi-hgi/yascp) in JUST_CELLTYPES mode with input file $INPUT_FILE"
-bsub -R'select[mem>4000] rusage[mem=4000]' -J yascp_celltypes -n 1 -M 4000 -o yascp_celltypes.o -e yascp_celltypes.e -q normal bash /software/hgi/pipelines/yascp_versions/yascp_v1.3__work/assets/deploy_scripts/nohup_start_nextflow_lsf_celltypes.sh  $INPUT_FILE
+bsub -R'select[mem>4000] rusage[mem=4000]' -J yascp_celltypes -n 1 -M 4000 -o yascp_celltypes.o -e yascp_celltypes.e -q normal bash /software/hgi/pipelines/yascp_versions/yascp_v1.3/assets/deploy_scripts/nohup_start_nextflow_lsf_celltypes.sh  $INPUT_FILE
 echo "Submitted job can be killed with: bkill -J yascp_celltypes"
diff --git a/assets/deploy_scripts/bsub_test_recluster.sh b/assets/deploy_scripts/bsub_test_recluster.sh
@@ -25,5 +25,5 @@ fi
 
 sample="$RUN_ID.yascp"
 echo -e "\nSubmitting yascp (https://github.com/wtsi-hgi/yascp) in JUST_RECLUSTER mode with input file $INPUT_FILE"
-bsub -R'select[mem>4000] rusage[mem=4000]' -J yascp_cluster -n 1 -M 4000 -o yascp_cluster.o -e yascp_cluster.e -q normal bash /software/hgi/pipelines/yascp_versions/yascp_v1.3__work/assets/deploy_scripts/nohup_start_nextflow_lsf_recluster.sh  $INPUT_FILE
+bsub -R'select[mem>4000] rusage[mem=4000]' -J yascp_cluster -n 1 -M 4000 -o yascp_cluster.o -e yascp_cluster.e -q normal bash /software/hgi/pipelines/yascp_versions/yascp_v1.3/assets/deploy_scripts/nohup_start_nextflow_lsf_recluster.sh  $INPUT_FILE
 echo "Submitted job can be killed with: bkill -J yascp_cluster"
diff --git a/assets/deploy_scripts/nohup_start_nextflow_lsf.sh b/assets/deploy_scripts/nohup_start_nextflow_lsf.sh
@@ -17,7 +17,7 @@ parentdir="$(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_versions/yascp_v1.3__work -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_v1.3 -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")

diff --git a/assets/deploy_scripts/nohup_start_nextflow_lsf__removeWork.sh b/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_versions/yascp_v1.3__work -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_v1.3 -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")

diff --git a/assets/deploy_scripts/nohup_start_nextflow_lsf_celltypes.sh b/assets/deploy_scripts/nohup_start_nextflow_lsf_celltypes.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_versions/yascp_v1.3__work -profile sanger -entry JUST_CELLTYPES -c $INPUT_FILE  --nf_ci_loc $PWD -resume > nextflow.nohup.log 2>&1 & 
+echo $RUN_ID | nextflow run /software/hgi/pipelines/yascp_versions/yascp_v1.3 -profile sanger -entry JUST_CELLTYPES -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")

diff --git a/assets/deploy_scripts/nohup_start_nextflow_lsf_recluster.sh b/assets/deploy_scripts/nohup_start_nextflow_lsf_recluster.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_versions/yascp_v1.3__work -profile sanger -entry JUST_RECLUSTER -c /software/hgi/pipelines/yascp_versions/yascp_v1.3__work/assets/deploy_scripts/input_setups/recluster_profile.nf -c $INPUT_FILE  --nf_ci_loc $PWD -resume > nextflow.nohup.log 2>&1 & 
+echo $RUN_ID | nextflow run /software/hgi/pipelines/yascp_versions/yascp_v1.3 -profile sanger -entry JUST_RECLUSTER -c /software/hgi/pipelines/yascp_versions/yascp_v1.3/assets/deploy_scripts/input_setups/recluster_profile.nf -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")

diff --git a/assets/deploy_scripts/nohup_start_nextflow_lsf_test.sh b/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_versions/yascp_v1.3__work -profile sanger,test --nf_ci_loc $PWD -resume > nextflow.nohup.log 2>&1 & 
+echo $RUN_ID | nextflow run /software/hgi/pipelines/yascp_versions/yascp_v1.3 -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")