Delete unwanted Snakemake Outputs - snakemake

Question

I have looked at a few other post about Snakemake and deleting unneeded data to clean up diskspace. I have designed a rule called: rule BamRemove that touches my rule all. However, my the workflow manager isnt recognizing. I am getting this error: WildcardError in line 35 of /PATH:
No values given for wildcard 'SampleID'. I am not seeing why. Any help to get this to work would be nice.
sampleIDs = d.keys()
rule all:
input:
expand('bams/{sampleID}_UMI_Concensus_Aligned.sortedByCoord.out.bam', sampleID=sampleIDs),
expand('bams/{sampleID}_UMI_Concensus_Aligned.sortedByCoord.out.bam.bai', sampleID=sampleIDs),
expand('logs/{SampleID}_removed.txt', sampleID=sampleIDs) #Line 35
# Some tools require unzipped fastqs
rule AnnotateUMI:
input: 'bams/{sampleID}_unisamp_L001_001.star_rg_added.sorted.dmark.bam'
output: 'bams/{sampleID}_L001_001.star_rg_added.sorted.dmark.bam.UMI.bam',
# Modify each run
params: '/data/Test/fastqs/{sampleID}_unisamp_L001_UMI.fastq.gz'
threads: 32
run:
# Each user needs to set tool path
shell('java -Xmx220g -jar /data/Tools/fgbio-2.0.0.jar AnnotateBamWithUmis \
-i {input} \
-f {params} \
-o {output}')
rule SortSam:
input: rules.AnnotateUMI.output
output: 'bams/{sampleID}_Qsorted.MarkUMI.bam'
params:
threads: 32
run:
# Each user needs to set tool path
shell('java -Xmx110g -jar /data/Tools/picard.jar SortSam \
INPUT={input} \
OUTPUT={output} \
SORT_ORDER=queryname')
rule MItag:
input: rules.SortSam.output
output: 'bams/{sampleID}_Qsorted.MarkUMI.MQ.bam'
params:
threads: 32
run:
# Each user needs to set tool path
shell('java -Xmx220g -jar /data/Tools/fgbio-2.0.0.jar SetMateInformation \
-i {input} \
-o {output}')
rule GroupUMI:
input: rules.MItag.output
output: 'bams/{sampleID}_grouped.Qsorted.MarkUMI.MQ.bam'
params:
threads: 32
run:
# Each user needs to set tool path
shell('java -Xmx220g -jar /data/Tools/fgbio-2.0.0.jar GroupReadsByUmi \
-i {input} \
-s adjacency \
-e 1 \
-m 20 \
-o {output}')
rule ConcensusUMI:
input: rules.GroupUMI.output
output: 'bams/{sampleID}_concensus.Qunsorted.MarkUMI.MQ.bam'
params:
threads: 32
run:
# Each user needs to set tool path
shell('java -Xmx220g -jar /data/Tools/fgbio-2.0.2.jar CallMolecularConsensusReads \
--input={input} \
--min-reads=1 \
--output={output}')
rule STARmap:
input: rules.ConcensusUMI.output
output:
log = 'bams/{sampleID}_UMI_Concensus_Log.final.out',
bam = 'bams/{sampleID}_UMI_Concensus_Aligned.sortedByCoord.out.bam'
params: 'bams/{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 /data/reference/star/STAR_hg19_v2.7.5c \
--outSAMtype BAM SortedByCoordinate \
--outSAMunmapped Within \
--limitBAMsortRAM 220000000000 \
--outFileNamePrefix {params}')
rule Index:
input: rules.STARmap.output.bam
output: 'bams/{sampleID}_UMI_Concensus_Aligned.sortedByCoord.out.bam.bai'
params:
threads: 32
run:
shell('samtools index {input}')
rule BamRemove:
input:
AnnotateUMI_BAM = rules.AnnotateUMI.output,
AnnotateUMI_BAI = '{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
output: touch('logs/{SampleID}_removed.txt')
threads: 32
run:
shell('rm {input}')

Answer 1

expand('logs/{SampleID}_removed.txt', sampleID=sampleIDs) #Line 35
^^^ ^^^
The error is due to SampleID being different from sampleID, make them consistent throughout the script.