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fix: align drep and CAT to using cohort instead of sample
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@rroutsong
rroutsong committed Jul 30, 2024
1 parent 4f382f0 commit 12ddc1c
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Showing 2 changed files with 27 additions and 36 deletions.
8 changes: 4 additions & 4 deletions workflow/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -90,9 +90,9 @@ rule all:
expand(join(top_binning_dir, "{name}", "figures", "binning_results.png"), name=samples),
# bin refinement
# ~~~~~~~~~~~~~~~
expand(join(top_refine_dir, "{name}", "dRep", "data_tables", "Widb.csv"), name=samples),
expand(join(top_refine_dir, "{name}", "dRep", "figures", "Winning_genomes.pdf"), name=samples),
expand(join(top_refine_dir, "{name}", "dRep", "log", "cluster_arguments.json"), name=samples),
expand(join(top_refine_dir, "dRep", "data_tables", "Widb.csv"), name=samples),
expand(join(top_refine_dir, "dRep", "figures", "Winning_genomes.pdf"), name=samples),
expand(join(top_refine_dir, "dRep", "log", "cluster_arguments.json"), name=samples),
# bin statistics
# ~~~~~~~~~~~~~~~
expand(join(top_refine_dir, "{name}", "RefinedBins_summmary.txt"), name=samples),
Expand All @@ -105,7 +105,7 @@ rule all:
join(top_refine_dir, "cumulative_stats_metawrap.txt"),
# contig annotation
# ~~~~~~~~~~~~~~~
expand(join(top_refine_dir, "{name}", "contig_annotation", "out.BAT.bin2classification.summary.txt"), name=samples),
expand(join(top_refine_dir, "contig_annotation", "out.BAT.bin2classification.summary.txt"), name=samples),
# BBMap mapping to MAGs
# ~~~~~~~~~~~~~~~
expand(join(top_mags_dir, "{name}", "index"), name=samples),
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55 changes: 23 additions & 32 deletions workflow/rules/DNA.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -524,20 +524,21 @@ rule derep_bins:
directory of consensus ensemble bins (deterministic output)
"""
input:
bin_breadcrumb = join(top_binning_dir, "{name}", "{name}_BINNING_COMPLETE"),
bins = expand(join(top_binning_dir, "{name}", "{name}_BINNING_COMPLETE"), name=samples),
output:
derep_genome_info = join(top_refine_dir, "{name}", "dRep", "data_tables", "Widb.csv"),
derep_winning_figure = join(top_refine_dir, "{name}", "dRep", "figures", "Winning_genomes.pdf"),
derep_args = join(top_refine_dir, "{name}", "dRep", "log", "cluster_arguments.json"),
derep_genome_dir = directory(join(top_refine_dir, "{name}", "dRep", "dereplicated_genomes")),
derep_genome_info = join(top_refine_dir, "dRep", "data_tables", "Widb.csv"),
derep_winning_figure = join(top_refine_dir, "dRep", "figures", "Winning_genomes.pdf"),
derep_args = join(top_refine_dir, "dRep", "log", "cluster_arguments.json"),
derep_genome_dir = directory(join(top_refine_dir, "dRep", "dereplicated_genomes")),
derep_dir = directory(join(top_refine_dir, "dRep")),
singularity: metawrap_container,
threads: int(cluster["derep_bins"].get("threads", default_threads)),
params:
rname = "derep_bins",
sid = "{name}",
tmpdir = config['options']['tmp_dir'],
derep_dir = join(top_refine_dir, "{name}", "dRep"),
metawrap_bins = join(top_binning_dir, "{name}", "metawrap_50_5_bins"),
bindir = join(top_binning_dir),
outto = join(top_refine_dir, "dRep"),
metawrap_dir_name = "metawrap_50_5_bins",
# -l LENGTH: Minimum genome length (default: 50000)
minimum_genome_length = "1000",
# -pa[--P_ani] P_ANI: ANI threshold to form primary (MASH) clusters (default: 0.9)
Expand All @@ -563,13 +564,8 @@ rule derep_bins:
dRep check_dependencies
# run drep
export DREP_BINS=$(ls {params.metawrap_bins}/* | tr '\\n' ' ')
printf "\ngenome list\n"
printf ${{DREP_BINS}}
printf "\n"
mkdir -p {params.derep_dir}
DREP_BINS=$(ls {params.bindir}/*/{params.metawrap_dir_name}/*.fa | tr '\\n' ' ')
mkdir -p {params.outto}
dRep dereplicate -d \
-g ${{DREP_BINS}} \
-p {threads} \
Expand All @@ -578,25 +574,23 @@ rule derep_bins:
-sa {params.ani_secondary_threshold} \
-nc {params.min_overlap} \
-cm {params.coverage_method} \
{params.derep_dir}
{params.outto}
"""


rule contig_annotation:
input:
derep_genome_info = join(top_refine_dir, "{name}", "dRep", "data_tables", "Widb.csv"),
derep_winning_figure = join(top_refine_dir, "{name}", "dRep", "figures", "Winning_genomes.pdf"),
derep_args = join(top_refine_dir, "{name}", "dRep", "log", "cluster_arguments.json"),
dRep_dir = join(top_refine_dir, "{name}", "dRep", "dereplicated_genomes"),
derep_genome_info = join(top_refine_dir, "dRep", "data_tables", "Widb.csv"),
derep_winning_figure = join(top_refine_dir, "dRep", "figures", "Winning_genomes.pdf"),
derep_args = join(top_refine_dir, "dRep", "log", "cluster_arguments.json"),
dRep_dir = join(top_refine_dir, "dRep", "dereplicated_genomes"),
output:
cat_bin2cls_filename = join(top_refine_dir, "{name}", "contig_annotation", "out.BAT.bin2classification.txt"),
cat_bin2cls_official = join(top_refine_dir, "{name}", "contig_annotation", "out.BAT.bin2classification.official_names.txt"),
cat_bin2cls_summary = join(top_refine_dir, "{name}", "contig_annotation", "out.BAT.bin2classification.summary.txt"),
cat_bin2cls_filename = join(top_refine_dir, "contig_annotation", "out.BAT.bin2classification.txt"),
cat_bin2cls_official = join(top_refine_dir, "contig_annotation", "out.BAT.bin2classification.official_names.txt"),
cat_bin2cls_summary = join(top_refine_dir, "contig_annotation", "out.BAT.bin2classification.summary.txt"),
params:
cat_dir = join(top_refine_dir, "{name}", "contig_annotation"),
dRep_dir = join(top_refine_dir, "{name}", "dRep", "dereplicated_genomes"),
cat_dir = join(top_refine_dir, "contig_annotation"),
rname = "contig_annotation",
sid = "{name}",
cat_db = "/data2/CAT", # from <root>/config/resources.json
tax_db = "/data2/CAT_tax", # from <root>/config/resourcs.json
diamond_exec = "/usr/bin/diamond",
Expand All @@ -606,7 +600,7 @@ rule contig_annotation:
"""
if [ ! -d "{params.cat_dir}" ]; then mkdir -p "{params.cat_dir}"; fi
cd {params.cat_dir} && CAT bins \
-b {params.dRep_dir} \
-b {input.dRep_dir} \
-d {params.cat_db} \
-t {params.tax_db} \
--path_to_diamond {params.diamond_exec} \
Expand Down Expand Up @@ -717,15 +711,12 @@ rule bbtools_index_map:

rule gtdbtk_classify:
input:
R1 = join(top_trim_dir, "{name}", "{name}_R1_trimmed.fastq"),
R2 = join(top_trim_dir, "{name}", "{name}_R2_trimmed.fastq"),
dRep_dir = join(top_refine_dir, "{name}", "dRep", "dereplicated_genomes"),
dRep_dir = join(top_refine_dir, "dRep", "dereplicated_genomes"),
output:
gtdbk_dir = directory(join(top_tax_dir, "{name}", "GTDBTK_classify_wf"))
gtdbk_dir = directory(join(top_tax_dir, "GTDBTK_classify_wf"))
threads: int(cluster["gtdbk_classify"].get("threads", default_threads)),
params:
rname = "gtdbk_classify",
sid = "{name}",
tmp_safe_dir = join(config['options']['tmp_dir'], 'gtdbtk_classify'),
GTDBTK_DB = "/data2/GTDBTK_DB",
singularity: metawrap_container,
Expand Down

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