Snakemake Ambiguity between 2 rules with similar output file type - bioinformatics

Question

I am trying to map 3 samples: SRR14724459, SRR14724473, and a combination of both SRR14724459_SRR14724473.
I have 2 rules that share a similar file type output (.bam), and even tho I am naming their wildcards different, I still get an ambiguity error:
Building DAG of jobs...
AmbiguousRuleException:
Rules map_hybrid and map are ambiguous for the file /gpfs/scratch/hpadre/snakemake_outputs/mapped_dir/SRR14724459_SRR14724473__0.9.bam.
Expected input files:
map_hybrid: /home/hpadre/ngs_artifacts_proj/output_directories/trimmed_dir/SRR14724459_SRR14724473_0.9/SRR14724459_R1_trimmed_SRR14724473_R1_trimmed_0.9.fastq /home/hpadre/ngs_artifacts_proj/output_directories/trimmed_dir/SRR14724459_SRR14724473_0.9/SRR14724459_R2_trimmed_SRR14724473_R2_trimmed_0.9.fastq
map: /home/hpadre/ngs_artifacts_proj/output_directories/trimmed_dir/SRR14724459_SRR14724473__0.9/SRR14724459_SRR14724473__0.9_R1_trimmed.fastq /home/hpadre/ngs_artifacts_proj/output_directories/trimmed_dir/SRR14724459_SRR14724473__0.9/SRR14724459_SRR14724473__0.9_R2_trimmed.fastq
From my Snakefile, here are my variables:
all_samples: ['SRR14724459', 'SRR14724473']
sample1: ['SRR14724459']
sample2: ['SRR14724473']
titration:[0.9]
This is my rule all:
rule all:
expand(MAPPED_DIR + "/{sample}.bam", sample=all_samples),
expand(MAPPED_DIR + "/{sample1}_{sample2}_{titration}.bam", zip, sample1=list_a_titrations, sample2=list_b_titrations, titration=tit_list)
This is my map rule:
rule map:
input:
r1 = TRIMMED_DIR + "/{sample}/{sample}_R1_trimmed.fastq",
r2 = TRIMMED_DIR + "/{sample}/{sample}_R2_trimmed.fastq"
output:
MAPPED_DIR + "/{sample}.bam"
threads: 28
params:
genome = HUMAN_GENOME_DIR
log:
LOG_DIR + "/map/{sample}_map.log"
benchmark:
BENCHMARK_DIR + "/map/{sample}_bwa_benchmark.txt"
wildcard_constraints:
word='[^0-9]*'
shell:
"""
bwa mem -t {threads} {params.genome} {input.r1} {input.r2} 2> {log} | samtools view -hSbo > {output}
"""
This is my map_hybrid:
rule map_hybrid:
input:
r1 = TRIMMED_DIR + "/{sample1}_{sample2}_{titration}/{sample1}_R1_trimmed_{sample2}_R1_trimmed_{titration}.fastq",
r2 = TRIMMED_DIR + "/{sample1}_{sample2}_{titration}/{sample1}_R2_trimmed_{sample2}_R2_trimmed_{titration}.fastq"
output:
MAPPED_DIR + "/{sample1}_{sample2}_{titration}.bam"
threads: 28
params:
genome = HUMAN_GENOME_DIR
log:
LOG_DIR + "/map/{sample1}_{sample2}_{titration}_map.log"
benchmark:
BENCHMARK_DIR + "/map/{sample1}_{sample2}_{titration}_bwa_benchmark.txt"
shell:
"""
set +e
bwa mem -t {threads} {params.genome} {input.r1} {input.r2} 2> {log} | samtools view -hSbo > {output}
exitcode=$?
if [ $exitcode -eq 1 ]
then
exit 1
else
exit 0
fi
"""
The expected input files SHOULD BE as so:
Expected input files:
map_hybrid: /home/hpadre/ngs_artifacts_proj/output_directories/trimmed_dir/SRR14724459_SRR14724473_0.9/SRR14724459_R1_trimmed_SRR14724473_R1_trimmed_0.9.fastq /home/hpadre/ngs_artifacts_proj/output_directories/trimmed_dir/SRR14724459_SRR14724473_0.9/SRR14724459_R2_trimmed_SRR14724473_R2_trimmed_0.9.fastq
map: /home/hpadre/ngs_artifacts_proj/output_directories/trimmed_dir/SRR14724459_R1_trimmed.fastq /home/hpadre/ngs_artifacts_proj/output_directories/trimmed_dir/SRR14724459_R2_trimmed.fastq
and also
/home/hpadre/ngs_artifacts_proj/output_directories/trimmed_dir/SRR14724473_R1_trimmed.fastq /home/hpadre/ngs_artifacts_proj/output_directories/trimmed_dir/SRR14724473_R2_trimmed.fastq

Answer 1

Your rules map and map_hybrid can both produce your desired files, for snakemake they are ambigious rules.
The names of the wildcards is irrelevant, what is relevant is whether the wildcards in both rules can match the same output filepath.
That is the case here.
While rule map_hybrid can produce the output file SRR14724459_R2_trimmed_SRR14724473_R2_trimmed_0.9.fastq where the wildcard matches are
sample1=SRR14724459
sample2=SRR14724473
the rule map can also produce this output with the wildcard match
sample=SRR14724459_R2_trimmed_SRR14724473
To prevent ambiguity you can use the wildcard_constraint, so that the {sample} wildcard only matches strings starting with SRR followed by numbers:
sample='SRR\d+'
Integrated into your rule map:
rule map:
input:
r1 = TRIMMED_DIR + "/{sample}/{sample}_R1_trimmed.fastq",
r2 = TRIMMED_DIR + "/{sample}/{sample}_R2_trimmed.fastq"
output:
MAPPED_DIR + "/{sample}.bam"
threads: 28
params:
genome = HUMAN_GENOME_DIR
log:
LOG_DIR + "/map/{sample}_map.log"
benchmark:
BENCHMARK_DIR + "/map/{sample}_bwa_benchmark.txt"
wildcard_constraints:
word='[^0-9]*',
sample='SRR\d+'
shell:
"""
bwa mem -t {threads} {params.genome} {input.r1} {input.r2} 2> {log} | samtools view -hSbo > {output}
"""
it should resolve the ambiguity.