snakemake: optional input for rules

Question

I was wondering if there is a way to have optional inputs in rules. An example case is excluding unpaired reads for alignment (or having only unpaired reads). A pseudo rule example:

rule hisat2_align:
    input:
        rU: lambda wildcards: ('-U '+ read_files[wildcards.reads]['unpaired']) if wildcards.read_type=='trimmed' else '',
        r1: lambda wildcards: '-1 '+ read_files[wildcards.reads]['R1'],
        r2: lambda wildcards: '-2 '+ read_files[wildcards.reads]['R2']
    output:
        'aligned.sam'
    params:
        idx: 'index_prefix',
        extra: ''
    shell:
        'hisat2 {params.extra} -x {params.idx} {input.rU} {input.r1} {input.r2}'

Here, not having trimmed reads (rU='') would result in missing input file error. I can go around this through a duplicate rule with adjusted input/shell statement or handling the input through params (i'm sure there are other ways). I'm trying to handle this neatly so that this step can be run through a snakemake wrapper (currently a custom one).

The closest example I've seen is on https://groups.google.com/d/msg/snakemake/qX7RfXDTDe4/XTMOoJpMAAAJ and Johannes' answer. But there we have a conditional assignment (eg. input: 'a' if condition else 'b') not an optional one.

Any help/guidance will be appreciated.

ps. optional input can help with varying number of hisat2 indexes as well (as noted here: https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/hisat2.html).

EDIT

To clarify the potential inputs:

1) Use single-end reads alone and declare them in rU. Reads files for the sample might be

sample1_single_1.fastq.gz
sample1_single_2.fastq.gz

In this case r1 and r2 maybe empty lists or not declared at all in the rule.

2) Use paired-end reads and declared them in r1 and r2. Reads files for the sample might be

sample1_paired_1_R1.fastq.gz
sample1_paired_1_R2.fastq.gz
sample1_paired_2_R1.fastq.gz
sample1_paired_2_R2.fastq.gz

In this case `rU`` maybe empty list or not declared at all in the rule.

3) Use paired and single-end reads together (e.g. output from trimmomatic where some pairs are broken). Reads files for the sample might be

sample1_paired_1_R1.fastq.gz
sample1_paired_1_R2.fastq.gz
sample1_paired_2_R1.fastq.gz
sample1_paired_2_R2.fastq.gz
sample1_unpaired_1_R1.fastq.gz
sample1_unpaired_1_R2.fastq.gz
sample1_unpaired_2_R1.fastq.gz
sample1_unpaired_2_R2.fastq.gz

As a solution. I ended up using @timofeyprodanov approach. I didn't realize an empty list can be used for this. Thanks for all the answers and comments!

Answer 1

I usually do it using expand with either empty or non-empty list:

rule a:
    input:
        expand('filename', proxy=[] if no_input else [None])

Answer 2

In order to create a conditional input in snakemake and avoid a missing input file error you can use [] instead of "".

rule example:
    input:
        in1="this_input_is_always_there.json",
        in2="this_input_is_conditional.json" if condition else [],

In your example, by replacing

rU: lambda wildcards: ('-U '+ read_files[wildcards.reads]['unpaired']) if wildcards.read_type=='trimmed' else '',

with

rU: lambda wildcards: ('-U '+ read_files[wildcards.reads]['unpaired']) if wildcards.read_type=='trimmed' else [],

you achieve the conditionality of the input without having to use expand or a additional function.