update to v0.8.0

ohmeta · Jun 7, 2020 · 245964d · 245964d
1 parent 9e263b8
commit 245964d
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Showing 4 changed files with 6 additions and 8 deletions.
diff --git a/metapi/__about__.py b/metapi/__about__.py
@@ -1,4 +1,4 @@
 #!/usr/bin/env python3
 
-__version__ = '0.7.10'
+__version__ = '0.8.0'
 __author__ = "Jie Zhu"
diff --git a/metapi/config.yaml b/metapi/config.yaml
@@ -152,15 +152,14 @@ params:
     batch_num: 500
 
   classify:
+    threads: 8
     kraken2:
       do: True
       database: /path/to/kraken2/database
-      threads: 8
       use_mpa_style: False
       report_zero_counts: True
     gtdbtk:
       do: True
-      threads: 8
 
   dereplicate:
     drep:
@@ -177,7 +176,6 @@ params:
     threads: 8
     metaphlan2:
       do: False
-      threads: 8
       bowtie2db: "/path/to/metaphlan_databases"
       index: "latest"
       bowtie2_presets: "very-sensitive"
@@ -203,7 +201,6 @@ params:
       index_prefix: /path/to/bowtie2_index_prefix
     humann2:
       do: False
-      threads: 8
       remove_temp_output: True
       normalize_method: "relab"
       regroup_method: "sum"

diff --git a/metapi/rules/classify.smk b/metapi/rules/classify.smk
@@ -22,7 +22,7 @@ if config["params"]["classify"]["kraken2"]["do"]:
                 if config["params"]["classify"]["kraken2"]["report_zero_counts"] \
                    else ""
         threads:
-            config["params"]["classify"]["kraken2"]["threads"]
+            config["params"]["classify"]["threads"]
         run:
             shell(
                 '''
@@ -85,7 +85,7 @@ if config["params"]["classify"]["gtdbtk"]["do"]:
         params:
             bin_suffix = "fa"
         threads:
-            config["params"]["classify"]["gtdbtk"]["threads"]
+            config["params"]["classify"]["threads"]
         shell:
             '''
             gtdbtk classify_wf \

diff --git a/metapi/rules/profiling.smk b/metapi/rules/profiling.smk
@@ -581,4 +581,5 @@ rule profiling_all:
         rules.profiling_jgi_all.input,
         rules.profiling_humann2_all.input,
 
-        rules.rmhost_all.input
+        rules.rmhost_all.input,
+        rules.qcreport_all.input