Have Snakemake recognize complete files upon relaunch

Question

I have created this Snakemake workflow. This pipeline works really well; however, if any rule fails and I relaunch, Snakemake isnt recognizing all completed files. For instances, Sample A finishes all the way through and creates all files for rule all, but Sample B fails at rule Annotate UMI. When I relaunch, snakemake wants to do all jobs for both A and B, instead of just B. What do I need to get this to work?

sampleIDs = [A, B]
  
rule all:
    input:
        expand('PATH/{sampleID}_UMI_Concensus_Aligned.sortedByCoord.out.bam', sampleID=sampleIDs),
        expand('PATH/bams/{sampleID}_UMI_Concensus_Aligned.sortedByCoord.out.bam.bai', sampleID=sampleIDs),
        expand('/PATH/logfiles/{sampleID}_removed.txt', sampleID=sampleIDs)

# Some tools require unzipped fastqs
rule AnnotateUMI:
    # Modify each run
    input: 'PATH/{sampleID}_unisamp_L001_001.star_rg_added.sorted.dmark.bam'
    # Modify each run
    output: 'PATH/{sampleID}_L001_001.star_rg_added.sorted.dmark.bam.UMI.bam'
    # Modify each run
    params: 'PATH/{sampleID}_unisamp_L001_UMI.fastq.gz'
    threads: 36
    run:
         # Each user needs to set tool path
         shell('java -Xmx220g -jar PATH/fgbio-2.0.0.jar AnnotateBamWithUmis \
         -i {input} \
         -f {params} \
         -o {output}')


rule SortSam:
    input: rules.AnnotateUMI.output
    # Modify each run
    output: 'PATH/{sampleID}_Qsorted.MarkUMI.bam'
    params:
    threads: 32
    run:
         # Each user needs to set tool path
         shell('java -Xmx110g -jar PATH/picard.jar SortSam \
         INPUT={input} \
         OUTPUT={output} \
         SORT_ORDER=queryname')


rule MItag:
    input: rules.SortSam.output
    # Modify each run
    output: 'PATH/{sampleID}_Qsorted.MarkUMI.MQ.bam'
    params:
    threads: 32
    run:
         # Each user needs to set tool path
         shell('java -Xmx220g -jar PATH/fgbio-2.0.0.jar SetMateInformation \
         -i {input} \
         -o {output}')


rule GroupUMI:
    input: rules.MItag.output
    # Modify each run
    output: 'PATH/{sampleID}_grouped.Qsorted.MarkUMI.MQ.bam'
    params:
    threads: 32
    run:
         # Each user needs to set tool path
         shell('java -Xmx220g -jar PATH/fgbio-2.0.0.jar GroupReadsByUmi \
         -i {input} \
         -s adjacency \
         -e 1 \
         -m 20 \
         -o {output}')


rule ConcensusUMI:
    input: rules.GroupUMI.output
    # Modify each run
    output: 'PATH/{sampleID}_concensus.Qunsorted.MarkUMI.MQ.bam'
    params:
    threads: 32
    run:
         # Each user needs to set tool path
         shell('java -Xmx220g -jar PATH/fgbio-2.0.2.jar CallMolecularConsensusReads \
         --input={input} \
         --min-reads=1 \
         --output={output}')


rule STARmap:
    input: rules.ConcensusUMI.output
    # Modify each run
    output:
        log = 'PATH/{sampleID}_UMI_Concensus_Log.final.out',
        bam = 'PATH/{sampleID}_UMI_Concensus_Aligned.sortedByCoord.out.bam'
    # Modify each run
    params: 'PATH/{sampleID}_UMI_Concensus_'
    threads: 32
    run:
         # Each user needs to genome path
         shell('STAR \
         --runThreadN {threads} \
         --readFilesIn {input} \
         --readFilesType SAM PE \
         --readFilesCommand samtools view -h \
         --genomeDir PATH/STAR_hg19_v2.7.5c \
         --outSAMtype BAM SortedByCoordinate \
         --outSAMunmapped Within \
         --limitBAMsortRAM 220000000000 \
         --outFileNamePrefix {params}')


rule Index:
    input: rules.STARmap.output.bam
    # Modify each run
    output: 'PATH/{sampleID}_UMI_Concensus_Aligned.sortedByCoord.out.bam.bai'
    params:
    threads: 32
    run:
         shell('samtools index {input}')


rule BamRemove:
    input:
        AnnotateUMI_BAM = rules.AnnotateUMI.output,
        # Modify each run and include in future version to delete
        #AnnotateUMI_BAI = 'PATH/{sampleID}_L001_001.star_rg_added.sorted.dmark.bam.UMI.bai',
        SortSam = rules.SortSam.output,
        MItag = rules.MItag.output,
        GroupUMI = rules.GroupUMI.output,
        ConcensusUMI = rules.ConcensusUMI.output,
        STARmap = rules.STARmap.output.bam,
        Index = rules.Index.output
    # Modify each run
    output: touch('PATH/logfiles/{sampleID}_removed.txt')
    threads: 32
    run:
        shell('rm {input.AnnotateUMI_BAM} {input.SortSam} {input.MItag} {input.GroupUMI} {input.ConcensusUMI}')