VATLAB/SoS

Hello, I have what I think is a simple question but haven't been able to get it to work. I'm processing genomes that are a mix of single-ended and paired-end reads. Before mapping them to a reference the commands are different between single and paired, so I have two parallel pipelines. But after mapping them, they're all bam files and I'd like to continue processing using just one pipeline. To show you what I mean, first I grab all the fastq files and join the ones that are paired. The filenames have the sample name followed by "_R1.fastq.gz" or "_R2.fastq.gz" to indicate a forward or reverse read.

[global]
import glob
import itertools
import os

fastq_files = sorted(glob.glob("/data/*.fastq.gz"))

grouped_fastq_dict = dict()
for k, v in itertools.groupby(fastq_files, lambda a: os.path.split(a)[1].split("_R", 1)[0]):
    grouped_fastq_dict[k] = list(v)

single_read, paired_read = dict(), dict()
for k,v in grouped_fastq_dict.items():
    if len(v) == 1:
        single_read[k] = v
    elif len(v) == 2:
        paired_read[k] = v
    else:
        print(f'Error: {k} has < 1 or more than 2 associated fastq files')

Then I process them and map them to a reference

[trimmomatic-single]
input: single_read, group_by=1
output: trim_single = f'/data/{_input.labels[0]}/{_input:bnn}_trimmed.fastq.gz'
run: expand=True
    trimmomatic SE -phred33 {_input} {_output} LEADING:10 TRAILING:10 SLIDINGWINDOW:4:16 MINLEN:40

[trimmomatic-paired]
input: paired_read, group_by=2
output: trim_paired_1=f'/data/{_input.labels[0]}/{_input[0]:bnn}_trimmed.fastq.gz',
trim_unpaired_1=f'/data/{_input.labels[0]}/{_input[0]:bnn}_trimmed_unpaired.fastq.gz',
trim_paired_2=f'/data/{_input.labels[0]}/{_input[1]:bnn}_trimmed.fastq.gz',
trim_unpaired_2=f'/data/{_input.labels[0]}/{_input[1]:bnn}_trimmed_unpaired.fastq.gz'
run: expand=True
    trimmomatic PE -phred33 {_input} {_output["trim_paired_1"]} {_output["trim_unpaired_1"]} \
    {_output["trim_paired_2"]} {_output["trim_unpaired_2"]} LEADING:10 TRAILING:10 SLIDINGWINDOW:4:16 MINLEN:40

[map-single]
input: output_from("trimmomatic-single"), group_by=1
output: bam = f'/data/{_input.name.split("_R")[0]}_GCF_000195955.2_filtered_sorted.bam'

id=_input.name.split("_R")[0]
rg=f'\"@RG\\tID:{id}\\tPL:Illumina\\tSM:{id}\"'

run: expand=True
    bwa mem -v 3 -Y -R {rg} {reference} {_input} | samtools view -bu - | \
    samtools sort -T /data2/helen_mixed_infection/data/bam/tmp.{id} -o {_output}

[map-paired]
input: output_from("trimmomatic-paired")["trim_paired_1"], output_from("trimmomatic-paired")["trim_paired_2"], group_by="pairs"
output: bam = f'/data/{_input["trim_paired_1"].name.split("_R")[0]}_GCF_000195955.2_filtered_sorted.bam'

id=_input["trim_paired_1"].name.split("_R")[0]
rg = f'\"@RG\\tID:{id}\\tPL:Illumina\\tSM:{id}\"'

run: expand=True
    bwa mem -v 3 -Y -R {rg} {reference} {_input} | samtools view -bu - | \
    samtools sort -T /data2/helen_mixed_infection/data/bam/tmp.{id} -o {_output}

But now I want to combine the output of the two parallel pipelines into the next step

[duplicate_marking]
input: output_from("map-single"),  output_from("map-paired"), group_by=1
output: dedup=f'{_input:n}_dedup.bam'
bash: expand=True
    export JAVA_OPTS='-Xmx3g'
    picard MarkDuplicates I={_input} O={_output} M={_output:n}.duplicate_metrics \
    REMOVE_DUPLICATES=false ASSUME_SORT_ORDER=coordinate

But SoS complains because the output from map-single and map-paired are of different lengths. How can I use the output from both steps as the input to my step duplicate-marking?