refactor

.gitignore

 .config
 .snakemake
 output
-logs
-nohup.out
-container.sif
+
+*.err
+*.out
+*.sif
+*.simg
+*.html
+*.pdf
+
 .DS_Store
 .Rproj.user

scripts/download_container.sh

-wget https://zenodo.org/record/3376504/files/container.sif -O container.sif

scripts/map-hg38-dosage-to-gtex-variants.Rmd

@@ -38,7 +38,7 @@ out_file <- str_replace(
 )
 
 tbl_gtex_lookup <- vroom::vroom(
-        "GTEx_Analysis_2017-06-05_v8_WholeGenomeSeq_838Indiv_Analysis_Freeze.lookup_table.txt.gz"
+        "output/GTEx_v8_hg38p7_variant_lookup_table.txt.gz"
     ) %>%
     filter(
         # to make sure we do not lose corner cases, 

scripts/pull.sh

-mkdir -p output/imputed-gene-expressions
-rsync -avzhe ssh --progress \
-    kk656@login-cpu.hpc.cam.ac.uk:/home/kk656/scratch/impute-gene-expression/output/imputed-gene-expressions \
-    output/imputed-gene-expressions

scripts/slurm-snakemake.sh

-mkdir -p logs
-nohup snakemake $1 \
-    --jobs 13 \
-    --use-singularity \
-    --cluster-config cluster.json \
-    --cluster "sbatch -A {cluster.account} -p {cluster.partition} --ntasks {cluster.ntasks} --cpus-per-task {cluster.ncpu} --nodes {cluster.nodes} -t {cluster.time} --job-name {cluster.name} --output {cluster.output} --error {cluster.error}" &