WildcardError - No values given for wildcard - Snakemake - workflow

Question

I am really lost what exactly I can do to fix this error.
I am running snakemake to perform some post alignment quality checks.
My code looks like this:
SAMPLES = ["Exome_Tumor_sorted_mrkdup_bqsr", "Exome_Norm_sorted_mrkdup_bqsr",
"WGS_Tumor_merged_sorted_mrkdup_bqsr", "WGS_Norm_merged_sorted_mrkdup_bqsr"]
rule all:
input:
expand("post-alignment-qc/flagstat/{sample}.txt", sample=SAMPLES),
expand("post-alignment-qc/CollectInsertSizeMetics/{sample}.txt", sample=SAMPLES),
expand("post-alignment-qc/CollectAlignmentSummaryMetrics/{sample}.txt", sample=SAMPLES),
expand("post-alignment-qc/CollectGcBiasMetrics/{sample}_summary.txt", samples=SAMPLES) # this is the problem causing line
rule flagstat:
input:
bam = "align/{sample}.bam"
output:
"post-alignment-qc/flagstat/{sample}.txt"
log:
err='post-alignment-qc/logs/flagstat/{sample}_stderr.err'
shell:
"samtools flagstat {input} > {output} 2> {log.err}"
rule CollectInsertSizeMetics:
input:
bam = "align/{sample}.bam"
output:
txt="post-alignment-qc/CollectInsertSizeMetics/{sample}.txt",
pdf="post-alignment-qc/CollectInsertSizeMetics/{sample}.pdf"
log:
err='post-alignment-qc/logs/CollectInsertSizeMetics/{sample}_stderr.err',
out='post-alignment-qc/logs/CollectInsertSizeMetics/{sample}_stdout.txt'
shell:
"gatk CollectInsertSizeMetrics -I {input} -O {output.txt} -H {output.pdf} 2> {log.err}"
rule CollectAlignmentSummaryMetrics:
input:
bam = "align/{sample}.bam",
genome= "references/genome/ref_genome.fa"
output:
txt="post-alignment-qc/CollectAlignmentSummaryMetrics/{sample}.txt",
log:
err='post-alignment-qc/logs/CollectAlignmentSummaryMetrics/{sample}_stderr.err',
out='post-alignment-qc/logs/CollectAlignmentSummaryMetrics/{sample}_stdout.txt'
shell:
"gatk CollectAlignmentSummaryMetrics -I {input.bam} -O {output.txt} -R {input.genome} 2> {log.err}"
rule CollectGcBiasMetrics:
input:
bam = "align/{sample}.bam",
genome= "references/genome/ref_genome.fa"
output:
txt="post-alignment-qc/CollectGcBiasMetrics/{sample}_metrics.txt",
CHART="post-alignment-qc/CollectGcBiasMetrics/{sample}_metrics.pdf",
S="post-alignment-qc/CollectGcBiasMetrics/{sample}_summary.txt"
log:
err='post-alignment-qc/logs/CollectGcBiasMetrics/{sample}_stderr.err',
out='post-alignment-qc/logs/CollectGcBiasMetrics/{sample}_stdout.txt'
shell:
"gatk CollectGcBiasMetrics -I {input.bam} -O {output.txt} -R {input.genome} -CHART = {output.CHART} "
"-S {output.S} 2> {log.err}"
The error message says the following:
WildcardError in line 9 of Snakefile:
No values given for wildcard 'sample'.
File "Snakefile", line 9, in <module>
In my code above I have indicated the problem causing line. When I simply remove this line everything runs perfekt. I am really confused, because I pretty much copy and pasted each rule, and this is the only rule that causes any problems.
If someone could point out what I did wrong, I would be very thankful!
Cheers!

Answer 1

Seems like it could be a spelling mistake - in the highlighted line, you write samples=SAMPLES, but the wildcard is called {sample} without the "s".