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fischuufischuu
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dram mags added
1 parent 5b7c1a5 commit 9057c08

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+95
-52
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4 files changed

+95
-52
lines changed

‎workflow/rules/annotate/__main__.smk‎

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@@ -2,6 +2,7 @@ include: "bakta.smk"
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include: "quast.smk"
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include: "gtdbtk.smk"
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include: "dram.smk"
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include: "dram_mag.smk"
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include: "eggnog.smk"
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include: "checkm2.smk"
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include: "proteinortho.smk"
@@ -17,5 +18,6 @@ rule annotate:
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rules.annotate__checkm2__predict.output,
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rules.annotate__gtdbtk__classify.output,
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rules.annotate__dram.input,
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rules.annotate__dram_mags.input,
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rules.annotate__proteinortho.output,
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rules.annotate__phylophlan.output,

‎workflow/rules/annotate/dram.smk‎

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@@ -1,4 +1,4 @@
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rule _annotate__dram__annotate:
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rule annotate__dram__annotate:
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"""Annotate dereplicate genomes with DRAM"""
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input:
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dereplicated_genomes=DREP / "dereplicated_genomes.fa.gz",
@@ -43,56 +43,8 @@ rule _annotate__dram__annotate:
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--gtdb_taxonomy {input.gtdbtk_summary} \
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2>> {log} 1>&2
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"""
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#rule _annotate__dram__stack:
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# """Stack DRAM annotations"""
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# input:
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# annotation=DRAM / "annotations.tsv",
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# trnas=DRAM / "trnas.tsv",
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# rrnas=DRAM / "rrnas.tsv",
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# output:
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# tarball=DRAM / "annotate.tar.gz",
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# log:
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# DRAM / "annotate_stack.log",
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# conda:
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# "__environment__.yml"
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# container:
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# docker["dram"]
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# params:
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# config=config["dram-config"],
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# out_dir=DRAM,
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# tmp_dir=DRAM / "annotate",
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# threads: config["resources"]["cpu_per_task"]["multi_thread"]
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# resources:
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# cpu_per_task=config["resources"]["cpu_per_task"]["multi_thread"],
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# mem_per_cpu=config["resources"]["mem_per_cpu"]["quitehighmem"] // config["resources"]["cpu_per_task"]["multi_thread"],
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# time = config["resources"]["time"]["shortrun"],
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# partition = config["resources"]["partition"]["longrun"]
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# shell:
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# """
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#
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# for file in annotations trnas rrnas ; do
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# ( csvstack \
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# --tabs \
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# {params.tmp_dir}/*/$file.tsv \
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# | csvformat \
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# --out-tabs \
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# > {params.out_dir}/$file.tsv \
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# ) 2>> {log}
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# done
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#
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# tar \
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# --create \
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# --directory {params.out_dir} \
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# --file {output.tarball} \
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# --remove-files \
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# --use-compress-program="pigz --processes {threads}" \
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# --verbose \
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# annotate \
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# 2>> {log} 1>&2
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# """
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rule _annotate__dram__distill:
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rule annotate__dram__distill:
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"""Distill DRAM annotations."""
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input:
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annotations=DRAM / "annotate" / "annotations.tsv",
@@ -131,8 +83,7 @@ rule _annotate__dram__distill:
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rmdir {params.outdir_tmp} 2>> {log} 1>&2
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"""
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rule annotate__dram:
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"""Run DRAM on dereplicated genomes."""
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input:
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rules._annotate__dram__distill.output,
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rules.annotate__dram__distill.output,

‎workflow/rules/annotate/dram_mag.smk‎

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@@ -0,0 +1,89 @@
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# For now, I took the GTDBTK annotation out, as we get the taxonomic assignment also from the globlal run
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rule annotate__dram_mag__annotate:
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"""Annotate dereplicate genomes with DRAM"""
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input:
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contigs=MAGSCOT / "{assembly_id}.fa.gz",
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#gtdbtk_summary=GTDBTK / "gtdbtk.summary.tsv",
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dram_db=features["databases"]["dram"],
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output:
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annotation=DRAMMAG / "{assembly_id}" / "annotate" / "annotations_{assembly_id}.tsv",
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trnas=DRAMMAG / "{assembly_id}" / "annotate" / "trnas_{assembly_id}.tsv",
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rrnas=DRAMMAG / "{assembly_id}" / "annotate" / "rrnas_{assembly_id}.tsv",
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log:
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DRAM / "{assembly_id}" / "annotate_{assembly_id}.log",
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conda:
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"__environment__.yml"
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container:
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docker["dram"]
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params:
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config=config["dram-config"],
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min_contig_size=1500,
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out_dir=lambda wildcards: f"{DRAMMAG}/{wildcards.assembly_id}",
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tmp_dir=lambda wildcards: f"{DRAMMAG}/{wildcards.assembly_id}/annotate",
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threads: config["resources"]["cpu_per_task"]["multi_thread"]
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resources:
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cpu_per_task=config["resources"]["cpu_per_task"]["multi_thread"],
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mem_per_cpu=config["resources"]["mem_per_cpu"]["quitehighmem"] // config["resources"]["cpu_per_task"]["multi_thread"],
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time = config["resources"]["time"]["longrun"],
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nvme = config["resources"]["nvme"]["small"],
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partition = config["resources"]["partition"]["small"]
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shell:
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"""
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rm -rf {params.tmp_dir}
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echo "Hostname: $(hostname)" 2>> {log} 1>&2
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echo "Temporary directory: $TMPDIR" 2>> {log} 1>&2
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df -h 2>> {log} 1>&2
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DRAM.py annotate \
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--config_loc {params.config} \
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--input_fasta {input.contigs} \
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--output_dir {params.tmp_dir} \
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--threads {threads} \
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2>> {log} 1>&2
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"""
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rule annotate__dram_mag__distill:
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"""Distill DRAM annotations."""
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input:
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annotation=DRAMMAG / "{assembly_id}" / "annotate" / "annotations_{assembly_id}.tsv",
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trnas=DRAMMAG / "{assembly_id}" / "annotate" / "trnas_{assembly_id}.tsv",
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rrnas=DRAMMAG / "{assembly_id}" / "annotate" / "rrnas_{assembly_id}.tsv",
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dram_db=features["databases"]["dram"],
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output:
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genome=DRAMMAG / "{assembly_id}" / "genome_stats.tsv",
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metabolism=DRAMMAG / "{assembly_id}" / "metabolism_summary.xlsx",
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product_html=DRAMMAG / "{assembly_id}" / "product.html",
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product_tsv=DRAMMAG / "{assembly_id}" / "product.tsv",
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log:
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DRAMMAG / "{assembly_id}" / "distill.log2",
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conda:
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"__environment__.yml"
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container:
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docker["dram"]
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resources:
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mem_per_cpu=config["resources"]["mem_per_cpu"]["highmem"],
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time = config["resources"]["time"]["longrun"],
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params:
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config=config["dram-config"],
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outdir=lambda wildcards: f"{DRAMMAG}/{wildcards.assembly_id}",
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outdir_tmp=lambda wildcards: f"{DRAMMAG}/{wildcards.assembly_id}/distill",
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shell:
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"""
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DRAM.py distill \
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--config_loc {params.config} \
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--input_file {input.annotations} \
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--rrna_path {input.rrnas} \
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--trna_path {input.trnas} \
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--output_dir {params.outdir_tmp} \
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2> {log} 1>&2
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mv {params.outdir_tmp}/* {params.outdir}/ 2>> {log} 1>&2
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rmdir {params.outdir_tmp} 2>> {log} 1>&2
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"""
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rule annotate__dram_mags:
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"""Run Bakta over the dereplicated mags"""
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input:
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expand(DRAMMAG / "{assembly_id}" / "annotate" / "annotations_{assembly_id}.tsv", assembly_id=ASSEMBLIES),

‎workflow/rules/folders.smk‎

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@@ -55,6 +55,7 @@ GTDBTK = ANN / "gtdbtk/"
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QUAST = ANN / "quast/"
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CAMPER = ANN / "camper/"
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DRAM = ANN / "dram/"
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DRAMMAG = ANN / "dram_mags/"
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CHECKM = ANN / "checkm2"
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BAKTA = ANN / "bakta"
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BAKTAMAG = ANN / "bakta_mags"

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