Best-paractice of cross-workflow specification of files

[snakemake-workflows]

Best-paractice of cross-workflow specification of files

[ning-y]

Here's a first attempt:

Workflow 1 input reads are determined by YAML configuration file, and the final assembly file is tagged either in its contents e.g. header lines, or filename; with a hash representing the input reads used to generate it e.g. hash of read hashes.

Workflow 2 takes input reads and input assembly also by YAML configuration file. It checks either on each run or through a dummy output that the input assembly's information about which input reads were used to generate it matches with the set of input reads it was given.

[SilasK]

Your idea would be to define the path to the files

Something like:

config.yam

read_file_format: "QC/qc_reads/{sample}_{fraction}.fastq.gz"
assembly_file_format: "Assembly/assemblies/{sample}.fasta.gz"

[SilasK]

One could also use a tsv file in which we will specify the headers in a config file.

Ideally using the https://snakemake.readthedocs.io/en/stable/snakefiles/configuration.html#configuring-scientific-experiments-via-peps