STAR snakemake wrapper with configfile - snakemake

Question

I'm trying to use the STAR wrapper for snakemake (described here) but would like to include an option for an annotation file using the --sjdbGTFfile flag. My goal is to specify a gtf annotation file by referring to a configfile, but I can't seem to get it to work.
Relevant snippet of my config file:
annotations: ref_files/cal09_human/GRCh38.103_Cal09.gtf
The relevant rule looks like this:
rule map_reads:
message:
"""
Mapping trimmed reads from {wildcards.sample} to host genome
"""
input:
fq1 = "tmp/{sample}_R1_trimmed.fastq.gz",
fq2 = "tmp/{sample}_R2_trimmed.fastq.gz"
params:
index= config["genome_index"],
extra="--sjdbGTFfile {config[annotations]} \
--sjdbOverhang 149 \
--outFilterType BySJout \
--outFilterMultimapNmax 10 \
--alignSJoverhangMin 5 \
--alignSJDBoverhangMin 1 \
--outFilterMismatchNmax 999 \
--outFilterMismatchNoverReadLmax 0.04 \
--alignIntronMin 20 \
--alignIntronMax 1000000 \
--alignMatesGapMax 1000000 \
--outFilterIntronMotifs RemoveNoncanonicalUnannotated \
--outSAMtype BAM SortedByCoordinate \
--runMode alignReads"
output:
"star_mapping/{sample}_Aligned.sortedByCoord.out.bam"
log:
"logs/star/{sample}.log"
threads: 20
wrapper:
"0.74.0/bio/star/align"
I was specifying the config file as if it were within a shell command (like described here), but it's not working:
Jun 03 16:49:52 ..... started STAR run
Jun 03 16:49:52 ..... loading genome
Jun 03 16:50:32 ..... processing annotations GTF
FATAL error, could not open file pGe.sjdbGTFfile={config[annotations]}
Jun 03 16:50:32 ...... FATAL ERROR, exiting
I ran the following directly in the terminal and it runs just fine:
STAR --runThreadN 24 \
--genomeDir ref_files/cal09_human_star_index \
--sjdbGTFfile ref_files/cal09_human/GRCh38.103_Cal09.gtf \
--sjdbOverhang 149 \
--outFilterType BySJout \
--outFilterMultimapNmax 10 \
--alignSJoverhangMin 5 \
--alignSJDBoverhangMin 1 \
--outFilterMismatchNmax 999 \
--outFilterMismatchNoverReadLmax 0.04 \
--alignIntronMin 20 \
--alignIntronMax 1000000 \
--alignMatesGapMax 1000000 \
--outFilterIntronMotifs RemoveNoncanonicalUnannotated \
--outSAMtype BAM SortedByCoordinate \
--runMode alignReads
I double checked the I didn't make an obvious mistake like misspecifying the file path in the config file. Does anyone know of a way to achieve what I'm trying to do?

Answer 1

extra="--sjdbGTFfile {config[annotations]} \
--sjdbOverhang 149 ..."
It seems {config[annotations]} is not replaced with the dictionary value but it is instead passed as it is.
If you are on python 3.6+, try using (note the f)
extra=f"--sjdbGTFfile {config[annotations]} \
--sjdbOverhang 149 ..."
or, old style:
extra= "--sjdbGTFfile %s \
--sjdbOverhang 149 ..." % config[annotations]