Error in Snakemake 'Unexpected keyword expand in rule definition' - snakemake

Question

As in the title, my Snakefile is giving me a SyntaxError for the expand function in the all rule. I am aware that this is typically caused by whitespace/indentation errors HOWEVER I have confirmed that there are no tabs in the file. I've gone through an deleted every whitespace as well as searched the file with grep. I appreciate any advice.
Error Message:
SyntaxError in line 14 of /PATH/to/Snakefile:
Unexpected keyword expand in rule definition (Snakefile, line 14)
Code:
from glob import glob
from numpy import unique
reads = glob('{}/*'.format(config['readDir']))
samples = []
for i in reads:
sampleName = i.replace('{}/'.format(config['readDir']), '')
sampleName = sampleName.replace('{}'.format(config['readSuffix1']), '')
sampleName = sampleName.replace('{}'.format(config['readSuffix2']), '')
samples.append(sampleName)
samples = unique(samples)
rule all:
expand('fastqc/{sample}_1_fastqc.html', sample=samples),
expand('gene_count/{sample}.count', sample=samples)
rule fastqc:
input:
r1 = config['readDir'] + '/{sample}' + config['readSuffix1'],
r2 = config['readDir'] + '/{sample}' + config['readSuffix2']
output:
o1 = 'fastqc/{sample}_1_fastqc.html',
o2 = 'fastqc/{sample}_2_fastqc.html'
params:
'fastqc'
shell:
'fastqc {input.r1} {input.r2} -o {params}'
rule trim:
input:
r1 = config['readDir'] + '/{sample}' + config['readSuffix1'],
r2 = config['readDir'] + '/{sample}' + config['readSuffix2']
output:
'trimmed_reads/{sample}_val_1.fq',
'trimmed_reads/{sample}_val_2.fq'
params:
outDir = 'trimmed_reads',
suffix = '{sample}',
minPhred = config['minPhred'],
minOverlap = config['minOverlap']
shell:
'trim_galore --paired --quality {params.minPhred} '
'--stringency {params.minOverlap} --basename {params.suffix} '
'--output_dir {params.outDir} {input.r1} {input.r2}'
rule align:
input:
r1 = 'trimmed_reads/{sample}_val_1.fq',
r2 = 'trimmed_reads/{sample}_val_2.fq'
output:
sam = temp('aligned_reads/{sample}.sam'),
bam = 'aligned_reads/{sample}.bam'
params:
ref = config['hisatRef']
threads:
config['threads']
log:
'logs/{sample}_hisat2.log'
shell:
'hisat2 --dta -p {threads} -x {params.ref} '
'-1 {input.r1} -2 {input.r2} -S {output.sam} 2> {log}; '
'samtools sort -# {threads} -o {output.bam} {output.sam}; '
rule sort_name:
input:
'aligned_reads/{sample}.bam'
output:
bam = temp('aligned_reads/{sample}_name_sorted.bam'),
index = temp('aligned_reads/{sample}_name_sorted.bam.bai')
threads:
config['threads']
shell:
'samtools sort -n -# {threads} -o {output.bam} {input}; '
rule count:
input:
bam = 'aligned_reads/{sample}.bam'
output:
'gene_count/{sample}.count'
params:
annotations = config['annotations'],
minMapq = config['minMapq'],
stranded = config['stranded']
shell:
'htseq-count -s {params.stranded} -a {params.minMapq} '
'--additional_attr=gene_name --additional_attr=gene_type '
'{input.bam} {params.annotations} > {output}'

Answer 1

This is an error from python as the rule all has two functions separated by a comma. In this case the second expand call is causing the error. You could replace the , with a + to resolve the error like given below.
expand('fastqc/{sample}_1_fastqc.html', sample=samples) + expand('gene_count/{sample}.count', sample=samples)
You could also combine both into a single expand function as follows
expand(['fastqc/{sample}_1_fastqc.html', 'gene_count/{sample}.count'], sample=samples)

Answer 2

Following code will solve this problem:
rule all:
input:
expand('fastqc/{sample}_1_fastqc.html', sample=samples),
expand('gene_count/{sample}.count', sample=samples)