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Feat: Updating rules to generate project report with filtered kraken …
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@skchronicles
skchronicles committed Jan 17, 2025
1 parent 4fdaa75 commit 6b45ca7
Showing 1 changed file with 50 additions and 5 deletions.
55 changes: 50 additions & 5 deletions workflow/rules/metavirs.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -92,8 +92,10 @@ def get_annotated_contigs(wildcards):
i = [
join(workpath,"{0}".format(wildcards.name),"temp","{0}.metaspades_CAT.txt".format(wildcards.name)),
join(workpath,"{0}".format(wildcards.name),"temp","{0}.metaspades_kraken2.txt".format(wildcards.name)),
join(workpath,"{0}".format(wildcards.name),"temp","{0}.metaspades_kraken2_filtered.txt".format(wildcards.name)),
join(workpath,"{0}".format(wildcards.name),"temp","{0}.megahit_CAT.txt".format(wildcards.name)),
join(workpath,"{0}".format(wildcards.name),"temp","{0}.megahit_kraken2.txt".format(wildcards.name))
join(workpath,"{0}".format(wildcards.name),"temp","{0}.megahit_kraken2.txt".format(wildcards.name)),
join(workpath,"{0}".format(wildcards.name),"temp","{0}.megahit_kraken2_filtered.txt".format(wildcards.name))
]
return i
else:
Expand All @@ -102,7 +104,8 @@ def get_annotated_contigs(wildcards):
wildcards.name
i = [
join(workpath,"{0}".format(wildcards.name),"temp","{0}.megahit_CAT.txt".format(wildcards.name)),
join(workpath,"{0}".format(wildcards.name),"temp","{0}.megahit_kraken2.txt".format(wildcards.name))
join(workpath,"{0}".format(wildcards.name),"temp","{0}.megahit_kraken2.txt".format(wildcards.name)),
join(workpath,"{0}".format(wildcards.name),"temp","{0}.megahit_kraken2_filtered.txt".format(wildcards.name))
]
return i

Expand All @@ -120,15 +123,18 @@ def get_aggregated_results(wildcards):
# Return metaspades and megahit results
return [
join(workpath,"Project","temp","metaspades_kraken2.krona"),
join(workpath,"Project","temp","metaspades_kraken2_filtered.krona"),
join(workpath,"Project","temp","metaspades_CAT.krona"),
join(workpath,"Project","temp","megahit_kraken2.krona"),
join(workpath,"Project","temp","megahit_kraken2_filtered.krona"),
join(workpath,"Project","temp","megahit_CAT.krona")
]
else:
# All samples are single-end,
# return only megahit results
return [
join(workpath,"Project","temp","megahit_kraken2.krona"),
join(workpath,"Project","temp","megahit_kraken2_filtered.krona"),
join(workpath,"Project","temp","megahit_CAT.krona")
]

Expand Down Expand Up @@ -646,6 +652,7 @@ rule metaspades:
# Create a unfiltered and contig length
# filtered table with taxonomic information
awk -F '_' -v OFS='\\t' '$4+0>={params.filter_length} {{print}}' \\
{output.tmp1} \\
> {output.kflt}
cat {output.ktaxids} \\
| taxonkit reformat \\
Expand Down Expand Up @@ -860,6 +867,7 @@ rule megahit:
# Create a unfiltered and contig length
# filtered table with taxonomic information
awk -F '\\t' '{{split($1,a,"="); if (a[4] >= {params.filter_length}) print $0}}' \\
{output.tmp1} \\
> {output.kflt}
cat {output.ktaxids} \\
| taxonkit reformat \\
Expand Down Expand Up @@ -1255,23 +1263,33 @@ rule prep_aggregate_metaspades_scatter:
input:
f1=join(workpath,"{name}","temp","{name}.metaspades_kraken2.txt"),
f2=join(workpath,"{name}","temp","{name}.metaspades_CAT.txt"),
f3=join(workpath,"{name}","temp","{name}.metaspades_kraken2_filtered.txt"),
output:
f1=join(workpath,"Project","temp","{name}.metaspades.contigs.kraken2.krona.meta"),
f2=join(workpath,"Project","temp","{name}.metaspades.contigs.CAT.krona.meta"),
f3=join(workpath,"Project","temp","{name}.metaspades_filtered.contigs.kraken2.krona.meta"),
params:
rname='prepagg',
sample='{name}',
threads: int(allocated("threads", "prep_aggregate_metaspades_scatter", cluster))
container: config['images']['metavirs']
shell: """
# Adding sample name to results per-sample results,
# metaspades and kraken2
awk -v var="{params.sample}" \\
'{{print var"_"$0}}' \\
{input.f1} \\
> {output.f1}
# metaspades and CAT
awk -v var="{params.sample}" \\
'{{print var"_"$0}}' \\
{input.f2} \\
> {output.f2}
# Filtered metaspades and kraken
awk -v var="{params.sample}" \\
'{{print var"_"$0}}' \\
{input.f3} \\
> {output.f3}
"""


Expand All @@ -1290,24 +1308,33 @@ rule prep_aggregate_megahit_scatter:
input:
f1=join(workpath,"{name}","temp","{name}.megahit_kraken2.txt"),
f2=join(workpath,"{name}","temp","{name}.megahit_CAT.txt"),
f3=join(workpath,"{name}","temp","{name}.megahit_kraken2_filtered.txt"),
output:
f1=join(workpath,"Project","temp","{name}.megahit.contigs.kraken2.krona.meta"),
f2=join(workpath,"Project","temp","{name}.megahit.contigs.CAT.krona.meta"),
f3=join(workpath,"Project","temp","{name}.megahit_filtered.contigs.kraken2.krona.meta"),
params:
rname='prepagg',
sample='{name}',
threads: int(allocated("threads", "prep_aggregate_megahit_scatter", cluster))
container: config['images']['metavirs']
shell: """
# Create aggregated contig annotations
# Adding sample name to results per-sample results,
# metaspades and kraken2
awk -v var="{params.sample}" \\
'{{print var"_"$0}}' \\
{input.f1} \\
> {output.f1}
# metaspades and CAT
awk -v var="{params.sample}" \\
'{{print var"_"$0}}' \\
{input.f2} \\
> {output.f2}
# Filtered metaspades and kraken2
awk -v var="{params.sample}" \\
'{{print var"_"$0}}' \\
{input.f3} \\
> {output.f3}
"""


Expand All @@ -1326,24 +1353,33 @@ rule prep_aggregate_metaspades_gather:
input:
f1=expand(join(workpath,"Project","temp","{name}.metaspades.contigs.kraken2.krona.meta"), name=pe_samples),
f2=expand(join(workpath,"Project","temp","{name}.metaspades.contigs.CAT.krona.meta"), name=pe_samples),
f3=expand(join(workpath,"Project","temp","{name}.metaspades_filtered.contigs.kraken2.krona.meta"), name=pe_samples),
output:
f1=join(workpath,"Project","temp","metaspades_kraken2.krona"),
f2=join(workpath,"Project","temp","metaspades_CAT.krona"),
f3=join(workpath,"Project","temp","metaspades_kraken2_filtered.krona"),
params:
rname='prepagg',
search=join(workpath,"Project","temp"),
threads: int(allocated("threads", "prep_aggregate_metaspades_gather", cluster))
container: config['images']['metavirs']
shell: """
# Create aggregated contig annotations
# Create aggregated contig annotations across all samples,
# Gather metaspades and kraken2 results
find {params.search} \\
-name '*.metaspades.contigs.kraken2.krona.meta' \\
-exec cat {{}} \\; \\
> {output.f1}
# Gather metaspades and CAT results
find {params.search} \\
-name '*.metaspades.contigs.CAT.krona.meta' \\
-exec cat {{}} \\; \\
> {output.f2}
# Gather filtered metaspades and kraken2 results
find {params.search} \\
-name '*.metaspades_filtered.contigs.kraken2.krona.meta' \\
-exec cat {{}} \\; \\
> {output.f3}
"""


Expand All @@ -1362,24 +1398,33 @@ rule prep_aggregate_megahit_gather:
input:
f1=expand(join(workpath,"Project","temp","{name}.megahit.contigs.kraken2.krona.meta"), name=samples),
f2=expand(join(workpath,"Project","temp","{name}.megahit.contigs.CAT.krona.meta"), name=samples),
f3=expand(join(workpath,"Project","temp","{name}.megahit_filtered.contigs.kraken2.krona.meta"), name=samples),
output:
f1=join(workpath,"Project","temp","megahit_kraken2.krona"),
f2=join(workpath,"Project","temp","megahit_CAT.krona"),
f3=join(workpath,"Project","temp","megahit_kraken2_filtered.krona"),
params:
rname='prepagg',
search=join(workpath,"Project","temp"),
threads: int(allocated("threads", "prep_aggregate_megahit_gather", cluster))
container: config['images']['metavirs']
shell: """
# Create aggregated contig annotations
# Create aggregated contig annotations across all samples,
# Gather megahit and kraken2 results
find {params.search} \\
-name '*.megahit.contigs.kraken2.krona.meta' \\
-exec cat {{}} \\; \\
> {output.f1}
# Gather megahit and CAT results
find {params.search} \\
-name '*.megahit.contigs.CAT.krona.meta' \\
-exec cat {{}} \\; \\
> {output.f2}
# Gather filtered megahit and kraken2 results
find {params.search} \\
-name '*.megahit_filtered.contigs.kraken2.krona.meta' \\
-exec cat {{}} \\; \\
> {output.f3}
"""


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