perf: autobump bio/trinity (#634)

Automatic update of bio/trinity.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>

bio/trinity/environment.yaml

@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - trinity ==2.8.4
+  - trinity =2.13.2

bio/trinity/meta.yaml

@@ -1,9 +1,12 @@
 name: trinity
 description: |
   Generate transcriptome assembly with Trinity
+url: https://github.com/trinityrnaseq/trinityrnaseq/
 authors:
   - Tessa Pierce
 input:
   - fastq files
 output:
-  - fasta containing assembly
+  - fas: fasta containing assembly
+  - map: gene transcripts map
+  - dir: folder for intermediate results

bio/trinity/test/Snakefile

@@ -2,19 +2,17 @@
 rule trinity:
     input:
         left=["reads/reads.left.fq.gz", "reads/reads2.left.fq.gz"],
-        right=["reads/reads.right.fq.gz", "reads/reads2.right.fq.gz"]
+        right=["reads/reads.right.fq.gz", "reads/reads2.right.fq.gz"],
     output:
-        "trinity_out_dir/Trinity.fasta"
+        dir=temp(directory("trinity_out_dir/")),
+        fas="trinity_out_dir.Trinity.fasta",
+        map="trinity_out_dir.Trinity.fasta.gene_trans_map",
     log:
-        'logs/trinity/trinity.log'
+        'logs/trinity/trinity.log',
     params:
-        extra=""
+        extra="",
     threads: 4
-    # optional specification of memory usage of the JVM that snakemake will respect with global
-    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
-    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
-    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
     resources:
-        mem_gb=10
+        mem_gb=10,
     wrapper:
         "master/bio/trinity"

bio/trinity/wrapper.py

@@ -5,10 +5,10 @@
 __email__ = "ntpierce@gmail.com"
 __license__ = "MIT"
 
-from os import path
 from snakemake.shell import shell
 
 extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 # Previous wrapper reserved 10 Gigabytes by default. This behaviour is
 # preserved below:
 max_memory = "10G"
@@ -57,21 +57,17 @@
 if not seqtype:
     if "fq" in left[0] or "fastq" in left[0]:
         seqtype = "fq"
-    elif "fa" in left[0] or "fasta" in left[0]:
+    elif "fa" in left[0] or "fas" in left[0] or "fasta" in left[0]:
         seqtype = "fa"
     else:  # assertion is redundant - warning or error instead?
         assert (
             seqtype is not None
         ), "cannot infer 'fq' or 'fa' seqtype from input files. Please specify 'fq' or 'fa' in 'seqtype' parameter"
 
-outdir = path.dirname(snakemake.output[0])
-assert "trinity" in outdir, "output directory name must contain 'trinity'"
-
-log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
 shell(
     "Trinity {input_cmd} --CPU {snakemake.threads} "
     " --max_memory {max_memory} --seqType {seqtype} "
-    " --output {outdir} {snakemake.params.extra} "
+    " --output {snakemake.output.dir} {snakemake.params.extra} "
     " {log}"
 )

test.py

@@ -3502,7 +3502,7 @@ def test_trinity():
             "snakemake",
             "--cores",
             "1",
-            "trinity_out_dir/Trinity.fasta",
+            "trinity_out_dir.Trinity.fasta",
             "--use-conda",
             "-F",
         ],