Missing input files for rule fastp_fq

[puva]

Dear Developer, we just downloaded Spritz on our server (Linux Centos 7). After setup as described in your tutorial, we got the following error:

snakemake --resources mem_mb=40000 --verbose --printshellcmds --use-conda --dryrun
...
MissingInputException in line 132 of /mnt/projects/tmp_spritz/Spritz/Spritz/rules/align.smk:
Missing input files for rule fastp_fq_uncompressed:
{dir}/Ds3_2.fastq
{dir}/Ds3_1.fastq

Running snakemake in debug-mode (--debug-dag), we got:

Building DAG of jobs...
candidate job all
        wildcards: 
candidate job finish_isoform
        wildcards: dir=/mnt/projects/tmp_spritz/Spritz/Spritz/2021-03-09
candidate job custom_protein_xml
        wildcards: dir=/mnt/projects/tmp_spritz/Spritz/Spritz/2021-03-09
candidate job generate_snpeff_database
        wildcards: 
candidate job download_ensembl_references
        wildcards: 
selected job download_ensembl_references
        wildcards: 
candidate job reorder_genome_fasta
        wildcards: 
candidate job download_ensembl_references
        wildcards: 
selected job download_ensembl_references
        wildcards: 
selected job reorder_genome_fasta
        wildcards: 
candidate job download_snpeff
        wildcards: 
selected job download_snpeff
        wildcards: 
candidate job copy_gff3_to_snpeff
        wildcards: 
candidate job remove_exon_and_utr_information
        wildcards: dir=/mnt/projects/tmp_spritz/Spritz/Spritz/2021-03-09
candidate job cdna_alignment_orf_to_genome_orf
        wildcards: dir=/mnt/projects/tmp_spritz/Spritz/Spritz/2021-03-09
candidate job Predict
        wildcards: dir=/mnt/projects/tmp_spritz/Spritz/Spritz/2021-03-09
candidate job LongOrfs
        wildcards: dir=/mnt/projects/tmp_spritz/Spritz/Spritz/2021-03-09
candidate job gtf_file_to_cDNA_seqs
        wildcards: dir=/mnt/projects/tmp_spritz/Spritz/Spritz/2021-03-09
candidate job merge_transcripts
        wildcards: dir=/mnt/projects/tmp_spritz/Spritz/Spritz/2021-03-09
candidate job assemble_transcripts_fq
        wildcards: dir={dir}, fq=Ds3
candidate job hisat2_align_bam_fq
        wildcards: dir={dir}, fq=Ds3
candidate job fastp_fq_uncompressed
        wildcards: dir={dir}, fq=Ds3
candidate job fastp_fq
        wildcards: dir={dir}, fq=Ds3

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.

Thank you

[puva]

Fixed - we were using an old version of snakemake