MAINT: add threads/jobs primitives

q2_quality_control/_filter.py

@@ -10,6 +10,7 @@
 import shutil
 import tempfile
 
+from qiime2.plugin import get_available_cores
 from q2_types.feature_data import DNAFASTAFormat
 from q2_types.bowtie2 import Bowtie2IndexDirFmt
 from q2_types.per_sample_sequences import (
@@ -42,8 +43,12 @@
 }
 
 
-def bowtie2_build(sequences: DNAFASTAFormat,
-                  n_threads: str = 1) -> Bowtie2IndexDirFmt:
+def bowtie2_build(
+    sequences: DNAFASTAFormat, n_threads: int = 1
+) -> Bowtie2IndexDirFmt:
+    if n_threads == 0:
+        n_threads = get_available_cores()
+
     database = Bowtie2IndexDirFmt()
     build_cmd = ['bowtie2-build', '--threads', str(n_threads),
                  str(sequences), str(database.path / 'db')]
@@ -52,15 +57,18 @@ def bowtie2_build(sequences: DNAFASTAFormat,
 
 
 def filter_reads(
-        demultiplexed_sequences: CasavaOneEightSingleLanePerSampleDirFmt,
-        database: Bowtie2IndexDirFmt,
-        n_threads: int = _filter_defaults['n_threads'],
-        mode: str = _filter_defaults['mode'],
-        sensitivity: str = _filter_defaults['sensitivity'],
-        ref_gap_open_penalty: str = _filter_defaults['ref_gap_open_penalty'],
-        ref_gap_ext_penalty: str = _filter_defaults['ref_gap_ext_penalty'],
-        exclude_seqs: str = _filter_defaults['exclude_seqs']) \
-            -> CasavaOneEightSingleLanePerSampleDirFmt:
+    demultiplexed_sequences: CasavaOneEightSingleLanePerSampleDirFmt,
+    database: Bowtie2IndexDirFmt,
+    n_threads: int = _filter_defaults['n_threads'],
+    mode: str = _filter_defaults['mode'],
+    sensitivity: str = _filter_defaults['sensitivity'],
+    ref_gap_open_penalty: str = _filter_defaults['ref_gap_open_penalty'],
+    ref_gap_ext_penalty: str = _filter_defaults['ref_gap_ext_penalty'],
+    exclude_seqs: str = _filter_defaults['exclude_seqs']
+) -> CasavaOneEightSingleLanePerSampleDirFmt:
+    if n_threads == 0:
+        n_threads = get_available_cores()
+
     filtered_seqs = CasavaOneEightSingleLanePerSampleDirFmt()
     df = demultiplexed_sequences.manifest
     fastq_paths = [record[1:] for record in df.itertuples()]

q2_quality_control/plugin_setup.py

@@ -8,7 +8,7 @@
 import importlib
 import q2_quality_control
 from qiime2.plugin import (Str, Plugin, Choices, Range, Float, Int, Bool,
-                           MetadataColumn, Visualization,
+                           Threads, MetadataColumn, Visualization,
                            Categorical, Citations, TypeMap,
                            TypeMatch, Metadata, Collection)
 from q2_types.feature_data import FeatureData, Sequence, Taxonomy
@@ -66,7 +66,7 @@
 filter_output = {'filtered_sequences': 'The resulting filtered sequences.'}
 
 filter_parameters = {
-    'n_threads': Int % Range(1, None),
+    'n_threads': Threads,
     'mode': Str % Choices(['local', 'global']),
     'sensitivity': Str % Choices([
         'very-fast', 'fast', 'sensitive', 'very-sensitive']),
@@ -100,7 +100,7 @@
                 'perc_identity': Float % Range(0.0, 1.0, inclusive_end=True),
                 'evalue': Float,
                 'perc_query_aligned': Float,
-                'threads': Int % Range(1, None),
+                'threads': Threads,
                 'left_justify': P_left_justify,
                 },
     outputs=[('sequence_hits', FeatureData[Sequence]),
@@ -118,7 +118,7 @@
             'Percent of query sequence that must align to reference in order '
             'to be accepted as a hit.'),
         'threads': (
-            'Number of jobs to execute. Only applies to vsearch method.'),
+            'Number of threads to use. Only applies to vsearch method.'),
         'left_justify': ('Reject match if the pairwise alignment begins with '
                          'gaps'),
     },
@@ -294,11 +294,11 @@
 plugin.methods.register_function(
     function=bowtie2_build,
     inputs={'sequences': FeatureData[Sequence]},
-    parameters={'n_threads': Int % Range(1, None)},
+    parameters={'n_threads': Threads},
     outputs=[('database', Bowtie2Index)],
     input_descriptions={
         'sequences': 'Reference sequences used to build bowtie2 index.'},
-    parameter_descriptions={'n_threads': 'Number of threads to launch'},
+    parameter_descriptions={'n_threads': 'Number of threads to launch.'},
     output_descriptions={'database': 'Bowtie2 index.'},
     name='Build bowtie2 index from reference sequences.',
     description='Build bowtie2 index from reference sequences.',

q2_quality_control/quality_control.py

@@ -22,7 +22,7 @@
 def exclude_seqs(query_sequences: DNAFASTAFormat,
                  reference_sequences: DNAFASTAFormat, method: str = 'blast',
                  perc_identity: float = 0.97, evalue: float = None,
-                 perc_query_aligned: float = 0.97, threads: str = 1,
+                 perc_query_aligned: float = 0.97, threads: int = 1,
                  left_justify: bool = False,
                  ) -> (pd.Series, pd.Series):