Commit c51b0cbe authored by Valentina Galata's avatar Valentina Galata
Browse files

reports: added bash script (and a note in readme)

parent e8081aa9
......@@ -114,6 +114,11 @@ This workflow creates plots and an HTML report for a sample using the output of
*TODO*
To execute this workflow for all samples:
```bash
./config/reports.sh "YourEnvName" "WhereToCreateCondEnvs"
```
## Creating figures for the paper
*TODO*
\ No newline at end of file
#!/bin/bash -l
# conda env name or path
SMK_ENV=$1
# where to install snakemake's conda environments
SMK_CONDA=$2
# config files
SMK_CONFIG="config/gdb/config.yaml config/nwc/config.yaml config/rumen/config.yaml config/zymo/config.yaml"
# activate main env. containing snakemake
conda activate "${SMK_ENV}"
# create reports
for configfile in ${SMK_CONFIG}; do
snakemake -s "workflow_report/Snakefile" --cores 1 --configfile "${configfile}" --use-conda --conda-prefix "${SMK_CONDA}" -rp
done
\ No newline at end of file
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