Hocnonsense
commented
10 months ago In your example, comparisonGroup seems to be defined by id, so you may specify certern output (not parent dir) in the same comparisonGroup as output.
However, i'm surprized that your id for assembly is not the id in the config["Samples"]? So I assume that you have a list of read ids named real_sample_id_list
rule assembly:
conda:
"env/conda-assembly.yaml",
input:
clean_fwd = os.path.join(output_dir, "fastq", "{id}", "{id}.clean_fwd.fastq.gz"),
clean_rev = os.path.join(output_dir, "fastq", "{id}", "{id}.clean_rev.fastq.gz"),
output:
assembly_output = directory(output_dir+"/assembly/comparisonGroup{comparisonGroup}/{id}_assembly"),
shell:
"""
shovill --R1 {input.clean_fwd} --R2 {input.clean_rev} --outdir {output.assembly_output} --assembler skesa
"""
rule create_assembly_groups:
input:
comparisonGroup = lambda _: [
i for i in real_sample_id_list if config["Samples"][i[:7]]["comparisonGroup"] == _["comparisonGroup"]
],
output:
assembly_group_only_contigs = directory(output_dir+"/assemblyContigsOnly/comparisonGroup{comparisonGroup}"),
params:
comparisonGroup = output_dir+"/assembly/comparisonGroup{comparisonGroup}",
shell:
"""
python scripts/contigsOnly.py {params.assembly_comp_group} {output.assembly_group_only_contigs}
"""
github-actions[bot]
Hi for the snakemake team, I'd love your help with something. When I try to use a parent directory of an output of one rule as the input to another rule I get a missingInputException although I create the needed dir for the rule but its not mentiond as the official output of the rule that creates it because it's his parent dir. the two rules looks like this: rule assembly: conda: "env/conda-assembly.yaml" input: clean_fwd = os.path.join(output_dir, "fastq", "{id}", "{id}.clean_fwd.fastq.gz"), clean_rev = os.path.join(output_dir, "fastq", "{id}", "{id}.clean_rev.fastq.gz"), params: comparisonGroup = lambda wildcards: config["Samples"][wildcards.id[:7]]["comparisonGroup"] output: assembly_output = directory(output_dir+"/assembly/{comparisonGroup}/{id}_assembly") shell: """ shovill --R1 {input.clean_fwd} --R2 {input.clean_rev} --outdir {output.assembly_output} --assembler skesa
rule create_assembly_groups: input: assembly_comp_group = output_dir+"/assembly/comparisonGroup{comparisonGroup}" output: assembly_group_only_contigs = directory(output_dir+"/assemblyContigsOnly/comparisonGroup{comparisonGroup}") shell: """ python scripts/contigsOnly.py {input.assembly_comp_group} {output.assembly_group_only_contigs}