Name the metadata yaml files to using the full filename
and extension of the corresponding workflow output file.
This is needed to avoid name collisions between yaml files
in the same module.

Cp bed tagalign

See merge request !5

Add unique param names/files for converting bed to tagalign
for control and exp files. This is needed to avoid issues with
parsing due to repeated names.

Rename id vars

Rename variables `control_ids` to `control_sample_ids` and `experiment_ids` to `experiment_sample_ids` for clarity.

See merge request !4

Workaround for passing run_spp_nodups.R a filename ending in .gz
for -savn argument.  The script calls gzip internally, which bails
out since the file already has a gz extension.  Instead, rename
file without gz extension and then run gzip.

Add .bam for result and .narrowPeak.gz for bed file types.

Group bed peak results

See merge request !3

Add conf.py entry for the number of result file lines to use for
each document in the bed and peak collections.

Instead of one result file line per document, add them in batches
to reduce the overall number of documents in the collections.
Each document now contains a `result_lines` entry, which is a list
of dictionaries, one result file line per list element.