Merge branch 'master' of https://github.com/metagenome-atlas/atlas

.github/workflows/stale.yml

@@ -0,0 +1,41 @@
+# This workflow warns and then closes issues and PRs that have had no activity for a specified amount of time.
+#
+# You can adjust the behavior by modifying this file.
+# For more information, see:
+# https://github.com/actions/stale
+name: Mark stale issues and pull requests
+
+on:
+  schedule:
+  - cron: '16 13 * * *'
+
+jobs:
+  stale:
+
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+
+    steps:
+    - uses: actions/stale@v7
+      with:
+        repo-token: ${{ secrets.GITHUB_TOKEN }}
+        stale-issue-message: |
+              There was no activity since some time. I hope your issue is solved in the mean time. 
+              This issue will automatically close soon if no further activity occurs. 
+              
+              Thank you for your contributions.
+        stale-pr-message: |
+            This PR is stale because it has not had any recent activity. 
+            This PR will automatically close soon if no further activity occurs. 
+            
+            Thank you for your contributions.
+        days-before-stale: 60
+        days-before-close: 15
+        stale-issue-label: stale
+        stale-pr-label: stale
+        exempt-issue-labels: 'keep,enhancement,bug,documentation,Feature-request,Known-issue'
+        exempt-pr-labels: ''
+        days-before-pr-stale: 1000
+        exempt-assignees: silask

atlas/workflow/envs/gtdbtk.yaml

@@ -3,4 +3,4 @@ channels:
 - bioconda
 - defaults
 dependencies:
-- gtdbtk >=2.1.1, < 3
+- gtdbtk =2.2

atlas/workflow/envs/tree.yaml

@@ -4,4 +4,3 @@ channels:
     - defaults
 dependencies:
     - ete3=3.1.2
-    - fasttree=2.1.8

atlas/workflow/rules/download.smk

@@ -204,8 +204,7 @@ rule extract_gtdb:
         "logs/download/gtdbtk_untar.log",
     shell:
         'tar -xzvf {input} -C "{GTDBTK_DATA_PATH}" --strip 1 2> {log}; '
-        'echo "Set the GTDBTK_DATA_PATH environment variable to {GTDBTK_DATA_PATH} " >> {log}; '
-        "conda env config vars set GTDBTK_DATA_PATH={GTDBTK_DATA_PATH} "
+
 
 
 rule checkm2_download_db:

atlas/workflow/rules/gtdbtk.smk

@@ -18,6 +18,7 @@ rule identify:
         extension="faa",
         gene_dir=lambda wc, input: os.path.abspath(os.path.dirname(input.genes_flag)),
     shell:
+        'export GTDBTK_DATA_PATH="{GTDBTK_DATA_PATH}" ; '
         "gtdbtk identify "
         "--genes --genome_dir {params.gene_dir} "
         " --out_dir {params.outdir} "
@@ -39,6 +40,7 @@ checkpoint align:
     params:
         outdir=gtdb_dir,
     shell:
+        'export GTDBTK_DATA_PATH="{GTDBTK_DATA_PATH}" ; '
         "gtdbtk align --identify_dir {params.outdir} --out_dir {params.outdir} "
         "--cpus {threads} &> {log[0]}"
 
@@ -63,6 +65,7 @@ rule classify:
         extension="fasta",
         mashdir = Path(GTDBTK_DATA_PATH)/"mash_db"
     shell:
+        'export GTDBTK_DATA_PATH="{GTDBTK_DATA_PATH}" ; '
         "gtdbtk classify --genome_dir {input.genome_dir} --align_dir {params.outdir} "
         " --mash_db {params.mashdir} "
         "--out_dir {params.outdir} "
@@ -83,20 +86,27 @@ rule combine_taxonomy:
         "../scripts/combine_taxonomy.py"
 
 
-rule fasttree:
+
+rule build_tree:
     input:
         f"{gtdb_dir}/align/{{msa}}.user_msa.fasta.gz",
     output:
-        temp("genomes/tree/{msa}.unrooted.nwk"),
+        temp("genomes/taxonomy/gtdb/{msa}.unrooted.tree"),
     log:
-        "logs/genomes/tree/FastTree_{msa}.log",
+        "logs/genomes/tree/{msa}.log",
+        "logs/genomes/tree/{msa}.err"
     threads: max(config["threads"], 3)
+    params:
+        outdir = lambda wc, output: Path(output[0]).parent
     conda:
-        "%s/tree.yaml" % CONDAENV
+        "../envs/gtdbtk.yaml"
     shell:
-        "export OMP_NUM_THREADS={threads}; "
-        "gunzip -c {input} | "
-        " FastTree > {output} 2> {log} "
+        'export GTDBTK_DATA_PATH="{GTDBTK_DATA_PATH}" ; '
+        "gtdbtk infer --msa_file {input} "
+        " --out_dir {params.outdir} "
+        " --prefix {wildcards.msa} "
+        " --cpus {threads} "
+        "--tmpdir {resources.tmpdir} > {log[0]} 2> {log[1]}"
 
 
 localrules:
@@ -105,13 +115,13 @@ localrules:
 
 rule root_tree:
     input:
-        tree="genomes/tree/{msa}.unrooted.nwk",
+        tree= rules.build_tree.output[0],
     wildcard_constraints:
         msa="((?!unrooted).)*",
     output:
         tree="genomes/tree/{msa}.nwk",
     conda:
-        "%s/tree.yaml" % CONDAENV
+        "../envs/tree.yaml"
     threads: 1
     resources:
         mem=config["simplejob_mem"],