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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 Workflow #3

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 78 of /home/cseveryn/asbhatt/chris/tools/bhattlab_workflows/preprocessing/preprocessing.snakefile: invalid syntax

Thank you! =^)

jribado commented 5 years ago

Fixed -- make sure the file suffixes are changes to _R1/R2.fastq.gz as per the README before attempting to run again.

jribado commented 5 years ago

Also! The lines that start with 'specify' should have a # at the start to indicate they are a comment in case there are issues there like in the example.

elimoss commented 5 years ago

The reason there aren’t is because hash is interpreted in the git markup syntax as a header, which made the formatting very strange.

On November 5, 2018 at 6:27:41 PM, jribado (notifications@github.com) wrote:

Also! The lines that start with 'specify' should have a # at the start to indicate they are a comment in case there are issues there like in the example.

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