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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - defaults | ||
| dependencies: | ||
| - kmcp=0.8.2 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,163 @@ | ||
| if len(KMCP_DBS) > 0: | ||
| rule profiling_kmcp_search: | ||
| input: | ||
| reads = profiling_input_with_short_reads, | ||
| db_dir = lambda wildcards: config["params"]["profiling"]["kmcp"]["database"][wildcards.kmcp_db] | ||
| output: | ||
| os.path.join(config["output"]["profiling"], | ||
| "search/kmcp/{sample}/{sample}.kmcp_search@{kmcp_db}.tsv.gz") | ||
| conda: | ||
| config["envs"]["kmcp"] | ||
| log: | ||
| os.path.join(config["output"]["profiling"], | ||
| "logs/kmcp/search/{sample}.kmcp_search@{kmcp_db}.log") | ||
| benchmark: | ||
| os.path.join(config["output"]["profiling"], | ||
| "benchmark/kmcp/search/{sample}.kmcp_search@{kmcp_db}.benchmark.txt") | ||
| params: | ||
| reads_mode = config["params"]["profiling"]["kmcp"]["search"]["reads_mode"], | ||
| reads_layout = 1 if IS_PE else 0, | ||
| min_query_len = config["params"]["profiling"]["kmcp"]["search"]["min_query_len"], | ||
| min_query_cov = config["params"]["profiling"]["kmcp"]["search"]["min_query_cov"], | ||
| external_opts = config["params"]["profiling"]["kmcp"]["search"]["external_opts"] | ||
| priority: | ||
| 20 | ||
| threads: | ||
| config["params"]["profiling"]["threads"] | ||
| shell: | ||
| ''' | ||
| if [ {params.reads_layout} -eq 1 ] && [ "{params.reads_mode}" == "Paired-end" ] | ||
| then | ||
| kmcp search \ | ||
| --threads {threads} \ | ||
| --load-whole-db \ | ||
| --db-dir {input.db_dir} \ | ||
| --min-query-len {params.min_query_len} \ | ||
| --min-query-cov {params.min_query_cov} \ | ||
| {params.external_opts} \ | ||
| -1 {input.reads[0]} \ | ||
| -2 {input.reads[1]} \ | ||
| --out-file {output} \ | ||
| --log {log} | ||
| else | ||
| kmcp search \ | ||
| --threads {threads} \ | ||
| --load-whole-db \ | ||
| --db-dir {input.db_dir} \ | ||
| --min-query-len {params.min_query_len} \ | ||
| --min-query-cov {params.min_query_cov} \ | ||
| {input.reads} \ | ||
| --out-file {output} \ | ||
| --log {log} | ||
| fi | ||
| ''' | ||
|
|
||
|
|
||
| rule profiling_kmcp_search_merge: | ||
| input: | ||
| expand(os.path.join(config["output"]["profiling"], | ||
| "search/kmcp/{{sample}}/{{sample}}.kmcp_search@{kmcp_db}.tsv.gz"), | ||
| kmcp_db=KMCP_DBS) | ||
| output: | ||
| os.path.join(config["output"]["profiling"], | ||
| "search/kmcp/{sample}/{sample}.kmcp_search@all.tsv.gz") | ||
| conda: | ||
| config["envs"]["kmcp"] | ||
| log: | ||
| os.path.join(config["output"]["profiling"], | ||
| "logs/kmcp/search_merge/{sample}.kmcp_search_merge.log") | ||
| benchmark: | ||
| os.path.join(config["output"]["profiling"], | ||
| "benchmark/kmcp/search_merge/{sample}.kmcp_search_merge.benchmark.txt") | ||
| shell: | ||
| ''' | ||
| kmcp merge \ | ||
| {input} \ | ||
| --out-file {output} \ | ||
| --log {log} | ||
| ''' | ||
|
|
||
|
|
||
| KMCP_PROFILING_MODE = { | ||
| "pathogen_detection": 0, | ||
| "higher_recall": 1, | ||
| "high_recall": 2, | ||
| "default": 3, | ||
| "high_precision": 4, | ||
| "higher_precision": 5 | ||
| } | ||
|
|
||
|
|
||
| rule profiling_kmcp_profile: | ||
| input: | ||
| search = os.path.join(config["output"]["profiling"], | ||
| "search/kmcp/{sample}/{sample}.kmcp_search@all.tsv.gz"), | ||
| taxid = KMCP_TAXIDMAP, | ||
| taxdump = config["params"]["profiling"]["kmcp"]["database"]["ncbi_taxdump"] | ||
| output: | ||
| default_profile = os.path.join(config["output"]["profiling"], | ||
| "profile/kmcp/{sample}/{sample}.kmcp.default_format.profile.{profiling_mode}.tsv.gz"), | ||
| metaphlan_profile = os.path.join(config["output"]["profiling"], | ||
| "profile/kmcp/{sample}/{sample}.kmcp.metaphlan_format.profile.{profiling_mode}.tsv.gz"), | ||
| cami_profile = os.path.join(config["output"]["profiling"], | ||
| "profile/kmcp/{sample}/{sample}.kmcp.CAMI_format.profile.{profiling_mode}.tsv.gz"), | ||
| binning_result = os.path.join(config["output"]["profiling"], | ||
| "profile/kmcp/{sample}/{sample}.kmcp.binning.{profiling_mode}.gz") | ||
| conda: | ||
| config["envs"]["kmcp"] | ||
| log: | ||
| os.path.join(config["output"]["profiling"], | ||
| "logs/kmcp/profile/{sample}.kmcp_profile_{profiling_mode}.log") | ||
| benchmark: | ||
| os.path.join(config["output"]["profiling"], | ||
| "benchmark/kmcp/profile/{sample}.kmcp_profile_{profiling_mode}.benchmark.txt") | ||
| params: | ||
| profiling_mode = lambda wildcards: KMCP_PROFILING_MODE[wildcards.profiling_mode], | ||
| min_query_cov = config["params"]["profiling"]["kmcp"]["profile"]["min_query_cov"], | ||
| min_chunks_reads = config["params"]["profiling"]["kmcp"]["profile"]["min_chunks_reads"], | ||
| min_chunks_fraction = config["params"]["profiling"]["kmcp"]["profile"]["min_chunks_fraction"], | ||
| max_chunks_depth_stdev = config["params"]["profiling"]["kmcp"]["profile"]["max_chunks_depth_stdev"], | ||
| min_uniq_reads = config["params"]["profiling"]["kmcp"]["profile"]["min_uniq_reads"], | ||
| min_hic_ureads = config["params"]["profiling"]["kmcp"]["profile"]["min_hic_ureads"], | ||
| min_hic_ureads_qcov = config["params"]["profiling"]["kmcp"]["profile"]["min_hic_ureads_qcov"], | ||
| min_hic_ureads_prop = config["params"]["profiling"]["kmcp"]["profile"]["min_hic_ureads_prop"], | ||
| external_opts = config["params"]["profiling"]["kmcp"]["profile"]["external_opts"] | ||
| shell: | ||
| ''' | ||
| kmcp profile \ | ||
| {input.search} \ | ||
| --taxid-map {input.taxid} \ | ||
| --taxdump {input.taxdump} \ | ||
| --level species \ | ||
| --mode {params.profiling_mode} \ | ||
| --min-query-cov {params.min_query_cov} \ | ||
| --min-chunks-reads {params.min_chunks_reads} \ | ||
| --min-chunks-fraction {params.min_chunks_fraction} \ | ||
| --max-chunks-depth-stdev {params.max_chunks_depth_stdev} \ | ||
| --min-uniq-reads {params.min_uniq_reads} \ | ||
| --min-hic-ureads {params.min_hic_ureads} \ | ||
| --min-hic-ureads-qcov {params.min_hic_ureads_qcov} \ | ||
| --min-hic-ureads-prop {params.min_hic_ureads_prop} \ | ||
| {params.external_opts} \ | ||
| --out-prefix {output.default_profile} \ | ||
| --metaphlan-report {output.metaphlan_profile} \ | ||
| --cami-report {output.cami_profile} \ | ||
| --binning-result {output.binning_result} \ | ||
| --log {log} | ||
| ''' | ||
|
|
||
|
|
||
| rule profiling_kmcp_all: | ||
| input: | ||
| expand([ | ||
| os.path.join(config["output"]["profiling"], | ||
| "profile/kmcp/{sample}/{sample}.kmcp.{profile_format}.profile.{profiling_mode}.tsv.gz"), | ||
| os.path.join(config["output"]["profiling"], | ||
| "profile/kmcp/{sample}/{sample}.kmcp.binning.{profiling_mode}.gz")], | ||
| sample=SAMPLES_ID_LIST, | ||
| profile_format=["default_format", "metaphlan_format", "CAMI_format"], | ||
| profiling_mode=list(KMCP_PROFILING_MODE.keys())) | ||
|
|
||
| else: | ||
| rule profiling_kmcp_all: | ||
| input: |
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