small fix

wtsi-hgi · Sep 21, 2023 · 0b307d9 · 0b307d9
1 parent 2919e33
commit 0b307d9
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Showing 3 changed files with 11 additions and 3 deletions.
diff --git a/assets/deploy_scripts/bsub.sh b/assets/deploy_scripts/bsub.sh
@@ -3,7 +3,11 @@ CWD1="$PWD"
 parentdir="$(dirname "$CWD1")"
 INPUT_FILE=$1
 export RUN_ID="${PWD##*/}"
+export SINGULARITY_TMPDIR=$PWD/work/tmp
+export TEMP=$PWD/work/tmp
+export TMP_DIR=$PWD/work/tmp
 export SINGULARITY_CACHEDIR='/software/hgi/containers/yascp'
+export SINGULARITY_DISABLE_CACHE='False'
 sample="$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

diff --git a/assets/deploy_scripts/nohup_start_nextflow_lsf.sh b/assets/deploy_scripts/nohup_start_nextflow_lsf.sh
@@ -21,6 +21,7 @@ export SINGULARITY_TMPDIR=$PWD/work/tmp
 export TEMP=$PWD/work/tmp
 export TMP_DIR=$PWD/work/tmp
 export SINGULARITY_CACHEDIR='/software/hgi/containers/yascp'
+export SINGULARITY_DISABLE_CACHE='False'
 echo $RUN_ID | nextflow run /software/hgi/pipelines/yascp -profile sanger -c $INPUT_FILE --nf_ci_loc $PWD -resume > nextflow.nohup.log 2>&1 & 
 
 # get process PID 

diff --git a/conf/base.conf b/conf/base.conf
@@ -146,10 +146,10 @@ process {
     time   = { 4.h  * task.attempt }
     containerOptions = " --cleanenv --containall -B "+params.tmpdir+":/tmp --env NUMBA_CACHE_DIR='"+params.tmpdir+"' --env MPLCONFIGDIR='"+params.tmpdir+"'"
 
-    errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
+    //# errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
     maxRetries    = 5
     maxErrors     = '-1'
-
+    errorStrategy = 'retry'
     // #Process-specific resource requirements
     // #NOTE - Please try and re-use the labels below as much as possible.
     // #       These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
@@ -272,6 +272,7 @@ process {
         errorStrategy = 'retry'
         memory = { 50.GB * task.attempt}
         maxRetries    = 8
+        cpus   = 2
     }
 
     withName: LISI{
@@ -292,7 +293,9 @@ process {
 
     withName: LISI{
         maxForks=7
-        memory =300.GB
+        errorStrategy = 'retry'
+        maxRetries    = 8
+        memory = { 200.GB * task.attempt}
     }
 
     withName: VIREO_GT_FIX_HEADER{