Get insert sizes for normalization from insert size metrics

[marcelm]

The insert size (fragment length) currently needs to be configured in config.yaml. It is used during normalization to scale the number of reads such that the coverage becomes 1.

Instead, the median or mean fragment length as determined by Picard CollectInsertSizeMetrics could be used for this.

[cnluzon]

This should be resolved by #19 since deepTools was crashing sometimes and I took median fragment length from Picard as a parameter value for --extendReads.

[marcelm]

Sorry I wasn’t more specific: This issue is about rule compute_scaling_factors, which currently uses config["fragment_size"]. This issue can be closed when that is no longer necessary (and when the fragment_size setting has been removed from config.yaml).