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adapted vamb smk to use bingroups
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@SilasK
SilasK committed Jul 21, 2023
1 parent 3d84baf commit 1c16120
Showing 1 changed file with 52 additions and 34 deletions.
86 changes: 52 additions & 34 deletions workflow/rules/cobinning.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ rule filter_contigs:
input:
"{sample}/{sample}_contigs.fasta",
output:
temp("Cobinning/filtered_contigs/{sample}.fasta"),
temp("Intermediate/cobinning/filtered_contigs/{sample}.fasta"),
params:
min_length=config["cobining_min_contig_length"],
log:
Expand All @@ -29,19 +29,36 @@ rule filter_contigs:
" -Xmx{resources.java_mem}G 2> {log} "


localrules:
combine_contigs,


def get_filtered_contigs_of_bingroup(wildcards):


samples_of_group = sampleTable.query(f'BinGroup=="{wildcards.bingroup}"').index.tolist()

if len(samples_of_group) <= 5:
raise ValueError(f"Bin group {wildcards.bingroup} has {len(samples_of_group)} less than 5 samples."
"For cobinning we reccomend at least 5 samples per bin group."
)


return {
#Trigers rerun if contigs change
"flag": expand("{sample}/{sample}_contigs.fasta", sample=samples_of_group),
"fasta": ancient(expand(rules.filter_contigs.output[0], sample=samples_of_group)),
}




rule combine_contigs:
input:
#Trigers rerun if contigs change
flag=expand("{sample}/{sample}_contigs.fasta", sample=SAMPLES),
fasta=ancient(expand(rules.filter_contigs.output[0], sample=SAMPLES)),
unpack(get_filtered_contigs_of_bingroup),

output:
"Cobinning/combined_contigs.fasta.gz",
"Intermediate/cobinning/{bingroup}/combined_contigs.fasta.gz",
log:
"logs/cobinning/combine_contigs.log",
"logs/cobinning/{bingroup}/combine_contigs.log",
params:
seperator=config["cobinning_separator"],
samples=SAMPLES,
Expand All @@ -64,16 +81,16 @@ rule minimap_index:
input:
contigs=rules.combine_contigs.output,
output:
mmi=temp("Cobinning/combined_contigs.mmi"),
mmi=temp("Intermediate/cobinning/{bingroup}/combined_contigs.mmi"),
params:
index_size="12G",
resources:
mem=config["mem"], # limited num of fatnodes (>200g)
threads: 3
log:
"logs/cobinning/vamb/index.log",
"logs/cobinning/{bingroup}/minimap_index.log",
benchmark:
"logs/benchmarks/cobinning/mminimap_index.tsv"
"logs/benchmarks/cobinning/{bingroup}/mminimap_index.tsv"
conda:
"../envs/minimap.yaml"
shell:
Expand All @@ -84,13 +101,13 @@ rule samtools_dict:
input:
contigs=rules.combine_contigs.output,
output:
dict="Cobinning/combined_contigs.dict",
dict="Intermediate/cobinning/{bingroup}/combined_contigs.dict",
resources:
mem=config["simplejob_mem"],
ttime=config["runtime"]["simplejob"],
threads: 1
log:
"logs/cobinning/samtools_dict.log",
"logs/cobinning/{bingroup}/samtools_dict.log",
conda:
"../envs/minimap.yaml"
shell:
Expand All @@ -100,17 +117,17 @@ rule samtools_dict:
rule minimap:
input:
fq=get_quality_controlled_reads,
mmi="Cobinning/combined_contigs.mmi",
dict="Cobinning/combined_contigs.dict",
mmi="Intermediate/cobinning/{bingroup}/combined_contigs.mmi",
dict="Intermediate/cobinning/{bingroup}/combined_contigs.dict",
output:
bam=temp("Cobinning/mapping/{sample}.unsorted.bam"),
bam=temp("Intermediate/cobinning/{bingroup}/bams/{sample}.unsorted.bam"),
threads: config["threads"]
resources:
mem=config["mem"],
log:
"logs/cobinning/mapping/{sample}.minimap.log",
"logs/cobinning/{bingroup}/mapping/minimap/{sample}.log",
benchmark:
"logs/benchmarks/cobinning/mminimap/{sample}.tsv"
"logs/benchmarks/cobinning/{bingroup}/mminimap/{sample}.tsv"
conda:
"../envs/minimap.yaml"
shell:
Expand All @@ -122,17 +139,17 @@ ruleorder: sort_bam > minimap

rule sort_bam:
input:
"Cobinning/mapping/{sample}.unsorted.bam",
"Intermediate/cobinning/{bingroup}/bams/{sample}.unsorted.bam",
output:
"Cobinning/mapping/{sample}.sorted.bam",
"Intermediate/cobinning/{bingroup}/bams/{sample}.sorted.bam",
params:
prefix="Cobinning/mapping/tmp.{sample}",
prefix="Intermediate/cobinning/{bingroup}/bams/tmp.{sample}",
threads: 2
resources:
mem=config["simplejob_mem"],
time=int(config["runtime"]["simplejob"]),
log:
"logs/cobinning/mapping/{sample}.sortbam.log",
"logs/cobinning/{bingroup}/mapping/sortbam/{sample}.log",
conda:
"../envs/minimap.yaml"
shell:
Expand All @@ -143,9 +160,9 @@ rule summarize_bam_contig_depths:
input:
bam=expand(rules.sort_bam.output, sample=SAMPLES),
output:
"Cobinning/vamb/coverage.jgi.tsv",
"Intermediate/cobinning/{bingroup}/coverage.jgi.tsv",
log:
"logs/cobinning/vamb/combine_coverage.log",
"logs/cobinning/{bingroup}/combine_coverage.log",
conda:
"../envs/metabat.yaml"
threads: config["threads"]
Expand All @@ -163,32 +180,32 @@ localrules:

rule convert_jgi2vamb_coverage:
input:
"Cobinning/vamb/coverage.jgi.tsv",
rules.summarize_bam_contig_depths.output,
output:
"Cobinning/vamb/coverage.tsv",
"Intermediate/cobinning/{bingroup}/coverage.tsv",
log:
"logs/cobinning/vamb/convert_jgi2vamb_coverage.log",
"logs/cobinning/{bingroup}/convert_jgi2vamb_coverage.log",
threads: 1
script:
"../scripts/convert_jgi2vamb_coverage.py"


rule run_vamb:
input:
coverage="Cobinning/vamb/coverage.tsv",
coverage= "Intermediate/cobinning/{bingroup}/coverage.tsv",
fasta=rules.combine_contigs.output,
output:
directory("Cobinning/vamb/clustering"),
directory("Intermediate/cobinning/vamb_{bingroup}"),
conda:
"../envs/vamb.yaml"
threads: config["threads"]
resources:
mem=config["mem"],
time=config["runtime"]["long"],
log:
"logs/cobinning/vamb/run_vamb.log",
"logs/cobinning/run_vamb/{bingroup}.log",
benchmark:
"logs/benchmarks/vamb/run_vamb.tsv"
"logs/benchmarks/run_vamb/{bingroup}.tsv"
params:
mincontig=config["cobining_min_contig_length"], # min contig length for binning
minfasta=config["cobining_min_bin_size"], # min bin size for output
Expand All @@ -203,6 +220,7 @@ rule run_vamb:
"2> {log}"



vamb_cluster_attribution_path = "{sample}/binning/vamb/cluster_attribution.tsv"


Expand All @@ -212,10 +230,10 @@ localrules:

rule parse_vamb_output:
input:
rules.run_vamb.output,
expand(rules.run_vamb.output, bingroup = SampleTable.BinGroup.unique()),
output:
renamed_clusters="Cobinning/vamb/clusters.tsv.gz",
cluster_atributions=expand(vamb_cluster_attribution_path, sample=SAMPLES),
cluster_atributions= expand(vamb_cluster_attribution_path, sample=SAMPLES),
log:
"logs/cobinning/vamb_parse_output.log",
params:
Expand All @@ -231,7 +249,7 @@ rule parse_vamb_output:

rule vamb:
input:
"Cobinning/vamb/clustering",
#"Cobinning/vamb/clustering",
"Cobinning/vamb/clusters.tsv.gz",
expand("{sample}/binning/vamb/cluster_attribution.tsv", sample=SAMPLES),

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