Merge pull request #18 from NBISweden/develop

Develop

.test/config/binning.yaml

@@ -117,11 +117,11 @@ annotation:
   # run tRNAscan-SE?
   tRNAscan: False
   # run infernal for rRNA identification?
-  infernal: True
+  infernal: False
   # run eggnog-mapper to infer KEGG orthologs, pathways and modules?
   eggnog: False
   # run PFAM-scan to infer protein families from PFAM?
-  pfam: True
+  pfam: False
   # run Resistance gene identifier?
   rgi: False
   # run taxonomic annotation of assembled contigs (using tango + sourmash)?
@@ -231,7 +231,7 @@ bowtie2:
 # what type of read-based classification to do
 classification:
   # run kraken2 read classifier?
-  kraken: True
+  kraken: False
   # run centrifuge to classify reads
   centrifuge: False
   # run metaphlan profiler?

.test/config/kraken.yaml

@@ -91,7 +91,7 @@ remove_duplicates: True
 
 assembly:
   # run Megahit assembler?
-  megahit: True
+  megahit: False
   # Use Metaspades instead of Megahit for assembly?
   metaspades: False
 

.test/config/metabat.yaml

@@ -117,11 +117,11 @@ annotation:
   # run tRNAscan-SE?
   tRNAscan: False
   # run infernal for rRNA identification?
-  infernal: True
+  infernal: False
   # run eggnog-mapper to infer KEGG orthologs, pathways and modules?
   eggnog: False
   # run PFAM-scan to infer protein families from PFAM?
-  pfam: True
+  pfam: False
   # run Resistance gene identifier?
   rgi: False
   # run taxonomic annotation of assembled contigs (using tango + sourmash)?
@@ -208,7 +208,7 @@ bowtie2:
 # what type of read-based classification to do
 classification:
   # run kraken2 read classifier?
-  kraken: True
+  kraken: False
   # run centrifuge to classify reads
   centrifuge: False
   # run metaphlan profiler?

config/config.yaml

@@ -45,7 +45,7 @@ trimmomatic:
     # ["TruSeq2-SE", "TruSeq3-SE"]
     adapter: "TruSeq3-SE"
     # parameters for trimming adapters on single-end samples
-    se_adapter_params: "2:30:15"
+    adapter_params: "2:30:15"
     # parameters for trimming prior to adapter removal on single-end samples
     pre_adapter_params: ""
     # parameters for trimming after adapter removal on single-end samples
@@ -59,7 +59,7 @@ cutadapt:
   # reverse adapter sequence to trim with cutadapt
   rev_adapter_sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
   # maximum allowed error rate as value between 0 and 1 (no. of errors divided by length of matching region)
-  error_rate: 0.1 #Maximum allowed error rate as value between 0 and 1
+  error_rate: 0.1
 
 # parameters for sortmerna
 sortmerna:
@@ -220,6 +220,12 @@ fastani:
   kmer_size: 16
   # fragment length used to calculate ANI
   frag_len: 3000
+  # minimum number of aligned fragments to consider a pair of genomes for clustering
+  minfrags: 100
+  # minimum estimated completeness for bins to include in clustering
+  min_completeness: 50
+  # maximum estimated contamination for bins to include in clustering
+  max_contamination: 10
 
 # parameters for bowtie2
 bowtie2:

workflow/Snakefile

@@ -31,7 +31,7 @@ def all_input(wildcards):
         # get annotation input
         wanted_input += annotation_input(config, assemblies)
         # get binning input
-        wanted_input += binning_input(config, assemblies)
+        wanted_input += binning_input(config)
 
     wanted_input += classify_input(config)
 

workflow/rules/binning.smk

@@ -30,7 +30,7 @@ localrules:
 
 rule bin:
     input:
-        binning_input(config, assemblies),
+        binning_input(config),
         opj(config["paths"]["results"], "report", "binning", "bin_report.pdf")
 
 ##### target rule for running checkm analysis #####
@@ -746,7 +746,9 @@ rule generate_fastANI_lists:
         temp(opj(config["paths"]["results"], "binning", "fastANI", "refList")),
         temp(opj(config["paths"]["results"], "binning", "fastANI", "queryList"))
     params:
-        outdir = lambda wildcards, output: os.path.abspath(os.path.dirname(output[0]))
+        outdir = lambda wildcards, output: os.path.abspath(os.path.dirname(output[0])),
+        completeness = config["fastani"]["min_completeness"],
+        contamination = config["fastani"]["max_contamination"]
     message:
         "Generating input lists for fastANI"
     script:
@@ -788,15 +790,16 @@ rule cluster_genomes:
     conda:
         "../envs/fastani.yml"
     params:
-        thresh = config["fastani"]["threshold"]
+        thresh = config["fastani"]["threshold"],
+        minfrags = config["fastani"]["minfrags"]
     script:
         "../scripts/binning_utils.py"
 
 ##### rule to generate summary plots
 
 rule binning_report:
     input:
-        binning_input(config, assemblies, report=True)
+        binning_input(config, report=True)
     output:
         report(opj(config["paths"]["results"], "report", "binning", "bin_report.pdf"),
                category="Binning", caption="../report/binning.rst")

workflow/rules/classification.smk

@@ -338,7 +338,8 @@ rule metaphlan2krona:
         files = get_all_files(samples, opj(config["paths"]["results"], "metaphlan"), ".krona"),
         db = opj("resources", "krona", "taxonomy.tab")
     output:
-        opj(config["paths"]["results"], "report", "metaphlan", "metaphlan.html")
+        opj(config["paths"]["results"], "report", "metaphlan",
+                   "metaphlan.html")
     log:
         opj(config["paths"]["results"], "report", "metaphlan", "krona.log")
     conda:
@@ -356,7 +357,8 @@ rule plot_metaphlan:
     input:
         opj(config["paths"]["results"], "report", "metaphlan", "metaphlan.tsv")
     output:
-        opj(config["paths"]["results"], "report", "metaphlan", "metaphlan.pdf")
+        opj(config["paths"]["results"], "report", "metaphlan",
+                   "metaphlan.pdf")
     params:
         rank=config["metaphlan"]["plot_rank"]
     conda:
@@ -390,6 +392,9 @@ rule classifier2krona:
     output:
         opj(config["paths"]["results"], "{classifier}",
             "{sample}_{unit}_{seq_type}.html")
+    log:
+        opj(config["paths"]["results"], "{classifier}",
+            "{sample}_{unit}_{seq_type}.krona.log")
     params:
         tax="resources/krona"
     conda:
@@ -398,9 +403,8 @@ rule classifier2krona:
         "docker://continuumio/miniconda3:4.8.2"
     shell:
         """
-        ktImportTaxonomy -t 5 -m 3 \
-            -tax {params.tax} -o {output[0]} \
-            {input[0]},{wildcards.sample}_{wildcards.unit}
+        ktImportTaxonomy -t 5 -m 3 -tax {params.tax} -o {output[0]} \
+            {input[0]},{wildcards.sample}_{wildcards.unit} > {log} 2>&1
         """
 
 rule all2krona:
@@ -411,7 +415,8 @@ rule all2krona:
                                     "{classifier}"), ".html"),
         t=opj("resources", "krona", "taxonomy.tab")
     output:
-        opj(config["paths"]["results"], "report", "{classifier}", "{classifier}.krona.html")
+        opj(config["paths"]["results"], "report", "{classifier}",
+                   "{classifier}.krona.html")
     log:
         opj(config["paths"]["results"], "report", "{classifier}", "{classifier}.krona.log")
     params:

workflow/rules/common.smk

@@ -13,7 +13,7 @@ singularity: "docker://continuumio/miniconda3:4.8.2"
 
 if os.path.exists("config/config.yaml"):
     configfile: "config/config.yaml"
-validate(config, schema="../schemas/config.schema.yaml")
+validate(config, schema="../schemas/config.schema.yaml", set_default=True)
 
 ##### generate preprocess/postprocess strings #####
 from scripts.common import prepost_string