Snakemake, config .yaml
Hi Everyone, can anyone help me with the error i am getting for the config file for snakemake
Config file is not valid JSON or YAML. In case of YAML, make sure to not mix whitespace and tab indentation.
My config file looks like this
RNA_Seqdir: /sfs/qumulo/qproject/CPHG/MILLER/CAD_QTL/coronary_QTL/expression
ref_dir: /scratch/mk9uc/Reference_genomes
#tools and software
tools:
fastq: fastqc
star: STAR
trimgalore: trim_galore
featurecount: featureCounts
rsem:
exp: rsem-calculate-expression
ref: rsem-prepare-reference
RNA_SeqC:
RNA-SeQC:java -jar RNA-SeQC.jar
# refernce files and genome indces
reference:
stargenome:
hg38:$ref_dir/starindex/hg38index
hg19:$ref_dir/starindex/hg19index
fasta:
hg38:$ref_dir/hg38/hg38.fa
hg19:$ref_dir/hg19/hg19.fa
gtf:
hg38:$ref_dir/hg38/gencode.v30.annotation.gtf
hg19:$ref_dir/hg19/gencode.v19.annotation.gtf
#directory for input and output files
datadir:
samples:$RNA_Seqdir/samples.txt
fastq: $RNA_Seqdir/demo_data
bam: $RNA_Seqdir/bam
quant:$RNA_Seqdir/quant
1 answer
From the YAML specification:
Mappings use a colon and space (“: ”) to mark each key: value pair.
Many of your key: value pairs are missing the space.
Log in to answer this question.
I assume you have already checked on this:
It is not possible to see that in the biostars formatted version.
everything on the config file is already Tab indented. have been stuck on this past two hours
start with a one-line config. add lines until the offender shows up.
Suggest running it through YAMLLint: http://www.yamllint.com/ . Also, I'd suggest you separate your
$RNA_Seqdirfrom the preceding colons