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bhattlab / bhattlab_workflows

Computational workflows for metagenomics tasks, by the Bhatt lab
http://www.bhattlab.com
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Snakemake work-file (Syntax error in preprocessing workflow) #2

Closed chrissev closed 5 years ago

chrissev commented 5 years ago

This was my command: snakemake --configfile ~/asbhatt/chris/project/gutdecon/testpoop/testpoop1.yaml.txt -s ~/asbhatt/chris/tools/bhattlab_workflows/preprocessing/preprocessing.snakefile

Here is my .yaml file specify directories raw_reads_directory: ~/asbhatt/chris/project/gutdecon/18-11-1_chris_gutdecon1/2.test_subset output_directory: ~/asbhatt/chris/project/gutdecon/testpoop/testpoopoutput

specify parameters for TrimGalore -- automatically chcecks the adaptor type trim_galore: quality: 30 start_trim: 15 end_trim: 0 min_read_length: 60

rm_host_reads: host_pre: bowtie_index_prefix (i.e. hg19 or mm10) host_genome: /path/to/genome/fastq/prefix

Here's my Output SyntaxError in line 35 of /home/cseveryn/asbhatt/chris/tools/bhattlab_workflows/preprocessing/preprocessing.snakefile: invalid syntax

Thank you so much. :^)

tamburinif commented 5 years ago

Looks like you aren’t specifying an output file to create?

tamburinif commented 5 years ago

I don’t know how this workflow is set up though, I can take a closer look when I get back to my computer

elimoss commented 5 years ago

There was an extra comma. I fixed this, waiting for Chris to test and verify.