This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
How can I use scatter/gather on a set of mixed paired-end and single-end libraries?
I have a number of samples that were sequenced using both paired-end and single-end libraries (and different numbers of each, of course). I'd like to scatter on the libraries (to generate fastq) and then run salmon on the gathered fastqs. Salmon is looking for "-1 READ_END_ONE_FILES -2 READ_END_TWO_FILES -r SINGLE_END_READS" in the command line, so I'd need to separate the reads accordingly. The fastq filenames all end in the standard _1.fastq.gz and _2.fastq.gz (when paired).