Commit 8113b19d authored by Sarah Peter's avatar Sarah Peter

Save picard output to log file

parent 950f3c28
......@@ -28,4 +28,6 @@
```
* You can use the `params` directive again to specify the reference file.
* You might want to save the output that picard prints on the command-line (stderr) to a log file.
......@@ -63,7 +63,8 @@ rule alignment_metrics:
params:
idx = "reference/Mus_musculus.GRCm38.dna_sm.chromosome.12.fa"
conda: "envs/picard.yaml"
log: "logs/alignment_metrics_{sample}.log"
shell:
"""
picard CollectAlignmentSummaryMetrics R={params.idx} I={input} O={output}
picard CollectAlignmentSummaryMetrics R={params.idx} I={input} O={output} 2> {log}
"""
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