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Hoohm / dropSeqPipe

A SingleCell RNASeq pre-processing snakemake workflow
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No rule to produce meta #85

Closed abmmki closed 4 years ago

abmmki commented 5 years ago

Trying to download and generate Meta-data using following command

snakemake --cores 16 meta --use-conda --directory ~/PROJECTS/Dropseq16

~/.conda/envs/myconda/lib/python3.6/site-packages/snakemake/workflow.py:70: FutureWarning: read_table is deprecated, use read_csv instead.

self._workdir = None Building DAG of jobs... MissingRuleException: No rule to produce meta (if you use input functions make sure that they don't raise unexpected exceptions).

Ensembl file location

ftp://ftp.ensembl.org/pub/release-90/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.dna.toplevel.fa.gz

I need to manually edit the "download_meta_single.smk" file to have correct FTP site pattern

am I missing something ? Why I am getting such error

thanks

Hoohm commented 5 years ago

Hello @abmmki

This rule doesn't exist anymore, the doc has to be updated.

It is now called: download_meta

Let me know if this works

Hoohm commented 4 years ago

I assume it worked. Closing this