use REMOVE_GTF_BRACKETS gtf (ch_gtf) as input to RNA_ALIGN, instead of ch_filtered_gtf

[iraiosub]

fixes #133 use REMOVE_GTF_BRACKETS gtf output (ch_gtf) as input to RNA_ALIGN, instead of ch_filtered_gtf.
This is necessary because all the transcripts need to be present for accurate mapping with STAR (junctions).

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[iraiosub]

@kkuret and i thought this might be best, but let us know if indeed the filtered GTF should be used for alignment