How to introduce a new wildcard in a snakemake pipeline with several rules - wildcard

Question

It has been several times that I face this problem and would like to understand finally: is it possible to introduce a new wildcard in a rule in a snakemake pipeline?
workdir: "/path/to/"
(SAMPLES,) =glob_wildcards('/path/to/trimmed/{sample}.trimmed.fastq.gz')
rule all:
input:
expand("dup/{sample}.dup.bam", sample=SAMPLES),
expand("merged/{sample}.merged.bam", sample=SAMPLES)
rule bwa_mem:
input:
bwa_index_done = "ref",
fastq="path/to/trimmed/{sample}.trimmed.fastq.gz"
output:
bam = "{sample}.bam"
threads: 10
shell:
"""/Tools/bwa-0.7.12/bwa mem -t {threads} ref {input.fastq} | /Tools/samtools-1.10/samtools sort -o {output.bam}"""
rule samtools merge:
input:
lane1="{sample}_L1.bam",
lane2="{sample}_L2.bam",
lane3="{sample}_L3.bam",
lane4="{sample}_L4.bam"
output:
outf = "merged/{sample}.merged.bam"
threads: 4
shell:
"""Tools/samtools-1.10/samtools merge -# {threads} {output.outf} {input.lane1} {input.lane2} {input.lane3} {input.lane4}"""
My input files:
RD1_1_L1.fastq.gz - RD1_100_L1.fastq.gz
RD1_1_L2.fastq.gz - RD1_100_L2.fastq.gz
RD1_1_L3.fastq.gz - RD1_100_L3.fastq.gz
RD1_1_L4.fastq.gz - RD1_100_L4.fastq.gz
RD2_100_L1.fastq.gz - RD2_200_L1.fastq.gz
RD2_100_L2.fastq.gz - RD2_200_L2.fastq.gz
RD2_100_L3.fastq.gz - RD2_200_L3.fastq.gz
RD2_100_L4.fastq.gz - RD2_200_L4.fastq.gz
While trimming it is ok to use it as one single sample, but when merging I need to specify L1, L2, L3 and L4. So is it possible to introduce a new wildcard somehow specific for a rule?

Answer 1

is it possible to introduce a new wildcard somehow specific for a rule?
I'm not 100% sure what you mean by that but I think the answer is yes.
Looking at your example, maybe this is what you are trying to do:
SAMPLES = ['RD1_1', 'RD2_100', 'RD1_100', 'RD2_200']
LANE = ['L1', 'L2', 'L3', 'L4']
rule all:
input:
expand("merged/{sample}.merged.bam", sample= SAMPLES)
rule trim:
input:
fastq= "{sample}_{L}.fastq.gz"
output:
fastq="trimmed/{sample}_{L}.trimmed.fastq.gz"
shell:
r"""
trim {input} {output}
"""
rule bwa_mem:
input:
fastq="trimmed/{sample}_{L}.trimmed.fastq.gz"
output:
bam= "{sample}_{L}.bam"
shell:
r"""
bwa mem {input} {output}
"""
rule samtools merge:
input:
expand('{{sample}}_{L}.bam', L= LANE),
output:
outf= "merged/{sample}.merged.bam",
shell:
r"""
samtools merge {output} {input}
"""
It assumes that all samples have lanes 1 to 4 which is not great but hopefully you get the idea.