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updated nextflow config and runner script templates #166

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Merged
avikdatta merged 1 commit into from
Mar 3, 2026
Merged

updated nextflow config and runner script templates #166

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2 changes: 1 addition & 1 deletion template/nextflow_template/nextflow_generic_conf_v0.0.1.conf
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Expand Up @@ -92,7 +92,7 @@ timeline {
singularity {
autoMounts = true
cacheDir = "$NEXTFLOW_SINGULARITY_CACHE_DIR"
runOptions = "--env _JAVA_OPTIONS='-XX:ParallelGCThreads=1' -B {{ DIR_LIST }},$EPHEMERAL,$VEP_CACHE_DIR,$SNPEFF_CACHE_DIR,$INTERVAL_DIR,$LOCAL_IGENOME_PATH,$EPHEMERAL:/tmp,$EPHEMERAL:/var/tmp"
runOptions = "--env _JAVA_OPTIONS='-XX:ParallelGCThreads=1' -B {{ DIR_LIST }},$EPHEMERAL,$NEXTFLOW_REF,$EPHEMERAL:/tmp,$EPHEMERAL:/var/tmp"
}

conda {
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3 changes: 2 additions & 1 deletion template/nextflow_template/nfcore_generic_runner_v0.0.1.sh
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Expand Up @@ -12,7 +12,8 @@
## * WORKDIR: Work dir path

## IMPORT ENV
source /rds/general/project/genomics-facility-archive-2019/live/tgu/resources/pipeline_resource/nextflow/env.sh
#source /rds/general/project/genomics-facility-archive-2019/live/tgu/resources/pipeline_resource/nextflow/env.sh
source /rds/general/project/genomics-facility-archive-2019/live/PIPELINE_RESOURCES/NEXTFLOW_REF/NEXTFLOW_ENV/env.sh

cd {{ WORKDIR }}

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3 changes: 2 additions & 1 deletion template/nextflow_template/olink_nextflow_runner_v0.0.1.sh
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Expand Up @@ -3,7 +3,8 @@
# * WORKDIR
# * CONFIG_FILE
## ENVS
source /rds/general/project/genomics-facility-archive-2019/live/tgu/resources/pipeline_resource/nextflow/env.sh
#source /rds/general/project/genomics-facility-archive-2019/live/tgu/resources/pipeline_resource/nextflow/env.sh
source /rds/general/project/genomics-facility-archive-2019/live/PIPELINE_RESOURCES/NEXTFLOW_REF/NEXTFLOW_ENV/env.sh

export TMPDIR=$EPHEMERAL
export NXF_OPTS='-Xms1g -Xmx4g'
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