Commit 84041347 authored by Sam Nooij's avatar Sam Nooij
Browse files

Remove unnecessary whitespaces

parent 9773f70d
"""
Authors: Sam Nooij
Organisation: Leiden University Medical Centre (LUMC)
Department: Medical Microbiology (MM) Research,
Department: Medical Microbiology (MM) Research,
Center for Microbiome Analyses and Therapeutics (CMAT)
Date: 2020-03-20
......@@ -10,7 +10,7 @@ Specifically for screening for genes of interest and their species
of origin.
Input: Jovian's output (classified scaffolds and trimmed reads)
Output: report on presence and abundance of species and
Output: report on presence and abundance of species and
genes of interest
Example use:
......@@ -18,7 +18,7 @@ Example use:
Or on the Shark cluster:
$ snakemake --use-conda --latency-wait 60 --jobs 16 \
--cluster "qsub -q all.q -pe BWA {threads} -l h_vmem={cluster.vmem} -cwd -j Y -o log/cluster/ -V" \
--cluster-config config/cluster_config.yaml
--cluster-config config/cluster_config.yaml
Or with SLURM:
$ snakemake -p --use-conda --latency-wait 60 --jobs 10 \
--cluster "sbatch --parsable -J Snakejob-{name}.{jobid} -N 1 -n {threads} --mem={cluster.vmem} -t {cluster.time} -D . -e log/SLURM/{name}-{jobid}.err -o log/SLURM/{name}-{jobid}.out" \
......@@ -74,7 +74,7 @@ else:
rule all:
input:
expand("data/tmp/all_taxClassified-{species}.tsv",
expand("data/tmp/all_taxClassified-{species}.tsv",
species = SPECIES),
#Filtered table for species of interest
......@@ -92,7 +92,7 @@ rule all:
species = SPECIES, ext = ["png", "pdf"]),
#pyANI Average Nucleotide Identity plots for each species
expand(REFERENCE_DIR + "{ref}.blastdb.{ext}",
expand(REFERENCE_DIR + "{ref}.blastdb.{ext}",
ref = REFERENCE_NAMES, ext = ["nhr", "nin", "nsq"]),
#Blast database files for each reference
......@@ -138,7 +138,7 @@ rule all:
"data/processed/Depth_of_coverage.tsv",
#Concatenated tables with depth of coverage
### Step 3: include processing steps to generate output ###
## First, filter out species of interest ##
......
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