As you can see, several wildcards are not correctly assigned, e.g.:
dir={dir}
instead of
dir=/mnt/projects/tmp_spritz/Spritz/Spritz/2021-03-09
Our config.yaml is:
sra: [] # paired-end SRAs, comma separated, can leave empty, e.g. SRR629563
fq: ["Ds3"] # paired-end fastq prefixes, comma separated, can leave empty, e.g. TestPairedEnd
sra_se: [] # single-end SRAs, comma separated, can leave empty, e.g. SRR8070095
fq_se: [] # single-end fastq prefixes, comma separated, can leave empty, e.g. TestSingleEnd
analysisDirectory: ["/mnt/projects/tmp_spritz/Spritz/Spritz/2021-03-09"] # for paths to drive e.g. /mnt/c/AnalysisFolder
species: "Homo_sapiens"
genome: "GRCh38"
release: "100"
organism: "human" # based on uniprot
analyses: [isoform,variant]
spritzversion: "0.2.3" # should be the same here, common.smk, and MainWindow.xml.cs
and the folder /mnt/projects/tmp_spritz/Spritz/Spritz/2021-03-09 contains Ds3_1.fastq.gz and Ds3_2.fastq.gz.
Dear Developer, we just downloaded Spritz on our server (Linux Centos 7). After setup as described in your tutorial, we got the following error:
Running snakemake in debug-mode (--debug-dag), we got:
As you can see, several wildcards are not correctly assigned, e.g.:
dir={dir}
instead ofdir=/mnt/projects/tmp_spritz/Spritz/Spritz/2021-03-09
Our config.yaml is:
and the folder
/mnt/projects/tmp_spritz/Spritz/Spritz/2021-03-09
containsDs3_1.fastq.gz
andDs3_2.fastq.gz
.Thank you