DSL2: Sharding tweaks

[TCLamnidis]

One of the "issues" with sharding at the moment is that once the mapped BAMs get collected again for merging, the order of files is inconsistent, meaning that downstream BAMs and their headers are unstable in terms of checksums.

The inconsistency comes from the record of the mapping command, which contains the shard filename. Example output from the test profile:

@PG     ID:bwa  PN:bwa  VN:0.7.17-r1188 CL:bwa samse -r @RG\tID:ILLUMINA-JK2782_JK2782_TGGCCGATCAACGA\tSM:JK2782\tLB:JK2782_TGGCCGATCAACGA\tPL:illumina\tPU:ILLUMINA-JK2782_TGGCCGATCAACGA-double_stranded-SE ./bwa/Mammoth_MT_Krause JK2782_Mammoth_MT_Krause.sai JK2782_JK2782_TGGCCGATCAACGA_L1.merged.part_002.fastq.gz

I think we could use some channel manipulation to sort the filenames going into shard merging, to ensure that the headers of downstream BAMs are consistent across runs (i.e. get the command to always show part_001).

I think at that point we could also change sharding to be turned on by default, as it makes sense to use it in most cases, instead of requiring users to configure the resources for their mapper manually.