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WIP: upgrade to sourmash_plugin_branchwater v0.9.0 #20

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WIP: upgrade to sourmash_plugin_branchwater v0.9.0 #20

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a162f45
switch fastgather to .sig.zip
ctb Feb 20, 2024
437cef3
upd
ctb Feb 20, 2024
14b408b
this last commit may not be good
ctb May 16, 2024
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33 changes: 8 additions & 25 deletions Snakefile
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
# @CTB switch to using manifests?

# import utility functions:
from slainte_functions import *

Expand Down Expand Up @@ -199,25 +201,6 @@ rule make_matrix_pdf:
sourmash plot {input} --output-dir=outputs/
"""

rule unpack_database:
input:
config['databases']
output:
directory(config.get('database_sketches_dir', 'interim/database_sketches.d'))
shell: """
sourmash sig split {input} --outdir {output} -E .sig.gz \
-k {GATHER_KSIZE}
"""

rule list_databases:
input:
config.get('database_sketches_dir', 'interim/database_sketches.d')
output:
"interim/list.database-sketches.txt"
shell: """
find {input} -name "*.sig.gz" > {output}
"""

rule extract_genome_sketch:
input:
"sketches/genomes/{name}.sig.zip",
Expand All @@ -238,8 +221,8 @@ rule extract_individual_sketch:

rule metag_fastgather:
input:
query="sketches/metag/{name}.{k}.sig.gz",
db="interim/list.database-sketches.txt"
query="sketches/metag/{name}.sig.zip",
db = config['databases'],
output:
"outputs/metag_gather/{name}.{k}.fastgather.csv",
threads: 64
Expand Down Expand Up @@ -305,11 +288,11 @@ rule list_genomes:

rule list_metag:
input:
expand("sketches/metag/{n}.{{k}}.sig.gz", n=METAGENOME_NAMES),
expand("sketches/metag/{n}.sig.zip", n=METAGENOME_NAMES),
output:
"interim/list.metag-sketches.{k}.txt"
"interim/manifest.metag-sketches.csv"
shell: """
ls -1 {input} > {output}
sourmash sig collect {input} -F csv -o {output}
"""

rule list_individual_metag_sketches:
Expand All @@ -323,7 +306,7 @@ rule list_individual_metag_sketches:

rule metag_x_individual_sketches_csv:
input:
metag="interim/list.metag-sketches.{k}.txt",
metag="interim/manifest.metag-sketches.csv",
individual="interim/list.metag-individual-sketches.{k}.txt",
output:
"outputs/check/metag.x.individual.{k}.manysearch.raw.csv"
Expand Down