0.2.1

Critical bugfix for GEX libraries.

Two factors contributed to this bug

1. The initial implementation of cellranger_cli_options didn't anticipate that we would specify is_nuclei: False for all samples, only that we'd include is_nuclei: True when needed. However, our samplesheet creation script didn't stick to that.

2. This function in modules/functions.nf is also to blame

def join_map_items(it) {
  it.collect { it.value ? /$it.key="$it.value"/ : /$it.key/ } join " "
}

which is equivalent to the following python:

def join_dict_items(d):
    tmp = []
    for key, value in d.items():
        if value:
            tmp.append(f"{key}={value}")
        else:
            tmp.append(f"{key}")
    return " ".join(tmp)

The if/else logic was supposed to make it so

• keys like '--include-introns': null would get transformed to just '--include-introns'
• keys like '--samples': SAMPLE1,SAMPLE2 would get transformed to --samples=SAMPLE1,SAMPLE2
  However, it doesn't account for 'key': false, because that will evaluate the same as 'key': null. It doesn't help that cellranger doesn't respect --include-introns=false.

0.2.0

This release was used to reprocess Cube samples.

Full Changelog: 0.1.0...0.2.0

0.1.0

Preliminary alpha release.