Keep merged fastq from multiple lanes after AdapterRemoval

[paulayu]

Currently the cleaned fastq files kept in AdapterRemoval output are all lane-separated, but keeping the merged clean fastq will help if we want to re-use the cleaned reads.

[jfy133]

Thanks He! I will look into it.

[jfy133]

(Accidental close, sorry!)

[jfy133]

Report from @aidaanva that I also forgot to publish the BAMs from the first BAM merging step