Fragment length parameter not so necessary for bigWig generation

[cnluzon]

Since the pipeline runs on paired-end data and according to deepTools documentation on --extendReads parameter:

This parameter allows the extension of reads to fragment size. If set, each read is extended, without exception. NOTE: This feature is generally NOT recommended for spliced-read data, such as RNA-seq, as it would extend reads over skipped regions. Single-end: Requires a user specified value for the final fragment length. Reads that already exceed this fragment length will not be extended. Paired-end: Reads with mates are always extended to match the fragment size defined by the two read mates. Unmated reads, mate reads that map too far apart (>4x fragment length) or even map to different chromosomes are treated like single-end reads. The input of a fragment length value is optional. If no value is specified, it is estimated from the data (mean of the fragment size of all mate reads).

This is already estimated from the BAM alignment as a mean, should be accurate enough and it only affects a small subset of the reads, we could consider removing the parameter from the bigwig rules. However we would still need it for the scaling factors, so we cannot remove the parameter from minute.yaml unless #10 is solved first.