Have Snakemake recognize complete files upon relaunch - snakemake

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}')