Gtdb v9

atlas/atlas.py

@@ -7,7 +7,7 @@
 import click
 
 
-from snakemake.io import load_configfile
+from snakemake.common.configfile import load_configfile
 from .make_config import validate_config
 from .init.atlas_init import run_init  # , run_init_sra
 

atlas/make_config.py

@@ -1,6 +1,6 @@
 from .default_values import *
 from snakemake.utils import update_config as snakemake_update_config
-from snakemake.io import load_configfile
+from snakemake.common.configfile import load_configfile
 import tempfile
 import sys
 import os

atlasenv.yml

@@ -3,10 +3,10 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - python >=3.8, < 3.12
+  - python >=3.10, < 3.12
   - mamba
   - bbmap >= 39.01, <40
-  - snakemake-minimal >= 7.18.1, <7.26
+  - snakemake-minimal >= 8.12, <8.15
   - pygments
   - networkx
   - graphviz
@@ -16,3 +16,4 @@ dependencies:
   - ruamel.yaml >=0.17
   - cookiecutter
   - wget
+  -  snakemake-executor-plugin-slurm

workflow/rules/qc.smk

@@ -158,8 +158,7 @@ if not SKIP_QC:
                 dupesubs=config["duplicates_allow_substitutions"],
                 only_optical=("t" if config.get("duplicates_only_optical") else "f"),
             log:
-                sterr="{sample}/logs/QC/deduplicate.err",
-                stout="{sample}/logs/QC/deduplicate.log",
+                "{sample}/logs/QC/deduplicate.log",
             conda:
                 "%s/required_packages.yaml" % CONDAENV
             threads: config.get("threads", 1)
@@ -177,8 +176,7 @@ if not SKIP_QC:
                 " threads={threads} "
                 " pigz=t unpigz=t "
                 " -Xmx{resources.java_mem}G "
-                " 2> {log.sterr} "
-                " 1> {log.stout} "
+                " &> {log} "
 
     PROCESSED_STEPS.append("filtered")
 
@@ -229,8 +227,7 @@ if not SKIP_QC:
                 output.reads, key="out", allow_singletons=False
             ),
         log:
-            sterr="{sample}/logs/QC/quality_filter.err",
-            stout="{sample}/logs/QC/quality_filter.log",
+            "{sample}/logs/QC/quality_filter.log",
         conda:
             "%s/required_packages.yaml" % CONDAENV
         threads: config.get("threads", 1)
@@ -260,8 +257,7 @@ if not SKIP_QC:
             " prealloc={params.prealloc} "
             " pigz=t unpigz=t "
             " -Xmx{resources.java_mem}G "
-            " 2> {log.sterr} "
-            " 1> {log.stout} "
+            " &> {log} "
 
     # if there are no references, decontamination will be skipped
     if len(config.get("contaminant_references", {}).keys()) > 0: