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Fix run templates july 25 #117

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Merged
avikdatta merged 2 commits into from
Jul 1, 2025
Merged

Fix run templates july 25 #117

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832d7b1
fix for cedllranger template
avikdatta Jul 1, 2025
2a818de
snakemake
avikdatta Jul 1, 2025
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2 changes: 1 addition & 1 deletion template/cellranger_template/cellranger_aggr_run_script_v1.sh
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Expand Up @@ -16,7 +16,7 @@
##

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

cd {{ WORKDIR }}

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2 changes: 1 addition & 1 deletion template/cellranger_template/cellranger_arc_aggr_run_script_v1.sh
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Expand Up @@ -18,7 +18,7 @@
##

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

cd {{ WORKDIR }}

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2 changes: 1 addition & 1 deletion template/cellranger_template/cellranger_arc_run_script_v1.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
##

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

cd {{ WORKDIR }}

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2 changes: 1 addition & 1 deletion template/cellranger_template/cellranger_multi_run_script_v1.sh
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Expand Up @@ -16,7 +16,7 @@
##

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

cd {{ WORKDIR }}

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2 changes: 1 addition & 1 deletion template/snakemake/rna-seq-star-deseq2/snakemake_report_v0.0.1.sh
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Expand Up @@ -15,7 +15,7 @@ module load anaconda3/personal
source activate snakemake

## SET PIPELINE CONF
SNAKEFILE=/project/tgu/resources/pipeline_resource/snakemake/workflow/rna-seq-star-deseq2/workflow/Snakefile
SNAKEFILE=/rds/general/project/genomics-facility-archive-2019/live/tgu/resources/pipeline_resource/snakemake/workflow/rna-seq-star-deseq2/workflow/Snakefile


## GO TO WORKDIR
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12 changes: 6 additions & 6 deletions template/snakemake/rna-seq-star-deseq2/snakemake_runner_v0.0.1.sh
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Expand Up @@ -15,13 +15,13 @@ module load anaconda3/personal
source activate snakemake

## SET CACHE DIR
export SNAKEMAKE_OUTPUT_CACHE=/project/tgu/resources/pipeline_resource/snakemake/cache_dir
export SNAKEMAKE_OUTPUT_CACHE=/rds/general/project/genomics-facility-archive-2019/live/tgu/resources/pipeline_resource/snakemake/cache_dir

## SET PIPELINE CONF
SNAKEFILE=/project/tgu/resources/pipeline_resource/snakemake/workflow/rna-seq-star-deseq2/workflow/Snakefile
CONDA_PREFIX_DIR=/project/tgu/resources/pipeline_resource/snakemake/conda_prefix_dir
SINGULARITY_PREFIX_DIR=/project/tgu/resources/pipeline_resource/snakemake/singularity_prefix_dir
CLUSTER_CONFIG_JSON=/project/tgu/resources/pipeline_resource/snakemake/cluster_config/rna-seq-star-deseq2_cluster.json
SNAKEFILE=/rds/general/project/genomics-facility-archive-2019/live/tgu/resources/pipeline_resource/snakemake/workflow/rna-seq-star-deseq2/workflow/Snakefile
CONDA_PREFIX_DIR=/rds/general/project/genomics-facility-archive-2019/live/tgu/resources/pipeline_resource/snakemake/conda_prefix_dir
SINGULARITY_PREFIX_DIR=/rds/general/project/genomics-facility-archive-2019/live/tgu/resources/pipeline_resource/snakemake/singularity_prefix_dir
CLUSTER_CONFIG_JSON=/rds/general/project/genomics-facility-archive-2019/live/tgu/resources/pipeline_resource/snakemake/cluster_config/rna-seq-star-deseq2_cluster.json
JOB_LIMIT=20

## GO TO WORKDIR
Expand Down Expand Up @@ -50,7 +50,7 @@ snakemake \
## module load anaconda3/personal
## source activate snakemake
## cd {{ SNAKEMAKE_WORK_DIR }}
## export SNAKEFILE=/project/tgu/resources/pipeline_resource/snakemake/workflow/rna-seq-star-deseq2/workflow/Snakefile
## export SNAKEFILE=/rds/general/project/genomics-facility-archive-2019/live/tgu/resources/pipeline_resource/snakemake/workflow/rna-seq-star-deseq2/workflow/Snakefile
## snakemake --snakefile $SNAKEFILE --configfile {{ CONFIG_YAML_PATH }} --unlock
##
##--------------------------------------------------------------------------------------