adding Woltka v0.1.6, pairends

.github/workflows/qiita-plugin-ci.yml

@@ -76,8 +76,8 @@ jobs:
         shell: bash -l {0}
         run: |
           conda config --add channels bioconda
-          conda create --yes -n qp-woltka-0.1.4 python=3.9 biom-format bowtie2
-          conda activate qp-woltka-0.1.4
+          conda create --yes -n qp-woltka python=3.9 biom-format bowtie2
+          conda activate qp-woltka
           # bowtie2==2.5.0 is what's installed in main qiita so making sure we keep
           # using the same version for consistency; note that we will need to force
           conda install --yes -c bioconda bowtie2==2.5.0
@@ -87,7 +87,7 @@ jobs:
           pip --quiet install -U pip pip nose flake8
           pip --quiet install https://github.com/qiita-spots/qiita_client/archive/master.zip
 
-          export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
+          export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
           export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
           export QC_WOLTKA_DB_DP=$PWD/qp_woltka/databases/woltka/
           export QC_WOLTKA_SYNDNA_DB_DP=$PWD/qp_woltka/databases/synDNA
@@ -101,7 +101,7 @@ jobs:
 
           export ENVIRONMENT="source /home/runner/.profile; conda activate qp-woltka; export QC_WOLTKA_DB_DP=$PWD/qp_woltka/databases/woltka/; export QC_WOLTKA_SYNDNA_DB_DP=$PWD/qp_woltka/databases/synDNA"
 
-          configure_woltka --env-script 'source /home/runner/.profile; conda activate qp-woltka-0.1.4; export QC_WOLTKA_DB_DP=$PWD/qp_woltka/databases/woltka/; export QC_WOLTKA_SYNDNA_DB_DP=$PWD/qp_woltka/databases/synDNA; export ENVIRONMENT="source /home/runner/.profile; conda activate qp-woltka-0.1.4; export QC_WOLTKA_DB_DP=$PWD/qp_woltka/databases/woltka/; export QC_WOLTKA_SYNDNA_DB_DP=$PWD/qp_woltka/databases/synDNA"' --server-cert $QIITA_SERVER_CERT
+          configure_woltka --env-script 'source /home/runner/.profile; conda activate qp-woltka; export QC_WOLTKA_DB_DP=$PWD/qp_woltka/databases/woltka/; export QC_WOLTKA_SYNDNA_DB_DP=$PWD/qp_woltka/databases/synDNA; export ENVIRONMENT="source /home/runner/.profile; conda activate qp-woltka; export QC_WOLTKA_DB_DP=$PWD/qp_woltka/databases/woltka/; export QC_WOLTKA_SYNDNA_DB_DP=$PWD/qp_woltka/databases/synDNA"' --ca-cert $QIITA_ROOTCA_CERT
 
           echo "Available Qiita plugins"
           ls ~/.qiita_plugins/
@@ -110,7 +110,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate qiita
-          export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
+          export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
           export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
           sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev/#g" `pwd`/qiita-dev/qiita_core/support_files/config_test.cfg > ${QIITA_CONFIG_FP}
 
@@ -141,10 +141,10 @@ jobs:
         env:
           COVER_PACKAGE: ${{ matrix.cover_package }}
         run: |
-          conda activate qp-woltka-0.1.4
-          export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
+          conda activate qp-woltka
+          export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
           export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
-          export ENVIRONMENT="source /home/runner/.profile; conda activate qp-woltka-0.1.4; export QC_WOLTKA_DB_DP=$PWD/qp_woltka/databases/woltka/; export QC_WOLTKA_SYNDNA_DB_DP=$PWD/qp_woltka/databases/synDNA"
+          export ENVIRONMENT="source /home/runner/.profile; conda activate qp-woltka; export QC_WOLTKA_DB_DP=$PWD/qp_woltka/databases/woltka/; export QC_WOLTKA_SYNDNA_DB_DP=$PWD/qp_woltka/databases/synDNA"
           export QC_WOLTKA_DB_DP=$PWD/qp_woltka/databases/woltka/
           export QC_WOLTKA_SYNDNA_DB_DP=$PWD/qp_woltka/databases/synDNA
           export PYTHONWARNINGS="ignore:Certificate for localhost has no \`subjectAltName\`"

qp_woltka/__init__.py

@@ -27,7 +27,6 @@
     }
 outputs = {
     # taxonomic
-    'Alignment Profile': 'BIOM',
     'Per genome Predictions': 'BIOM',
     'Per gene Predictions': 'BIOM',
     # functional
@@ -37,7 +36,8 @@
     }
 dflt_param_set = generate_woltka_dflt_params()
 woltka_cmd = QiitaCommand(
-    'Woltka v0.1.4', "Functional and Taxonomic Predictions", woltka,
+    'Woltka v0.1.4, pairends + suppress singleton & discordant',
+    "Functional and Taxonomic Predictions", woltka,
     req_params, opt_params, outputs, dflt_param_set)
 plugin.register_command(woltka_cmd)
 

qp_woltka/support_files/files_list.tsv

@@ -0,0 +1,3 @@
+filename_1	filename_2	record_count
+/tmp/folder/S22205_S104_L001_R1_001.fastq.gz	/tmp/folder/S22205_S104_L001_R2_001.fastq.gz	1000000
+/tmp/folder/S22282_S102_L001_R1_001.fastq.gz	/tmp/folder/S22282_S102_L001_R2_001.fastq.gz	1000000

qp_woltka/support_files/summary.html

@@ -0,0 +1,36 @@
+<table border="1" class="dataframe">
+  <thead>
+    <tr style="text-align: right;">
+      <th>filename</th>
+      <th>md5</th>
+      <th>file_type</th>
+      <th>reads</th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <td>S22205_S104_L001_R1_001.fastq.gz</td>
+      <td>9dcfb0c77674fdada176262963196db0</td>
+      <td>raw_forward_seqs</td>
+      <td>1000000</td>
+    </tr>
+    <tr>
+      <td>S22282_S102_L001_R1_001.fastq.gz</td>
+      <td>9dcfb0c77674fdada176262963196db0</td>
+      <td>raw_forward_seqs</td>
+      <td>1000000</td>
+    </tr>
+    <tr>
+      <td>S22205_S104_L001_R2_001.fastq.gz</td>
+      <td>9dcfb0c77674fdada176262963196db0</td>
+      <td>raw_reverse_seqs</td>
+      <td>1000000</td>
+    </tr>
+    <tr>
+      <td>S22282_S102_L001_R2_001.fastq.gz</td>
+      <td>9dcfb0c77674fdada176262963196db0</td>
+      <td>raw_reverse_seqs</td>
+      <td>1000000</td>
+    </tr>
+  </tbody>
+</table>

qp_woltka/tests/test_util.py

@@ -9,13 +9,9 @@
 from unittest import main, TestCase
 from os import environ
 from os.path import join
-from tempfile import TemporaryDirectory
-import gzip
-import io
-import pandas as pd
 
 from qp_woltka.util import (
-    get_dbs, generate_woltka_dflt_params, mux, demux, search_by_filename,
+    get_dbs, generate_woltka_dflt_params, search_by_filename,
     merge_ranges, coverage_percentage)
 
 
@@ -38,41 +34,6 @@ def test_generate_woltka_dflt_params(self):
 
         self.assertDictEqual(obs, exp)
 
-    def test_mux(self):
-        f1 = b"@foo\nATGC\n+\nIIII\n"
-        f2 = b"@bar\nAAAA\n+\nIIII\n"
-        exp = b"@foo@@@foofile\nATGC\n+\nIIII\n@bar@@@barfile\nAAAA\n+\nIIII\n"
-        with TemporaryDirectory() as d:
-            f1fp = join(d, 'foofile.fastq')
-            f2fp = join(d, 'barfile.fastq')
-            ofp = join(d, 'output')
-            with gzip.open(f1fp, 'wb') as fp:
-                fp.write(f1)
-            with gzip.open(f2fp, 'wb') as fp:
-                fp.write(f2)
-            with open(ofp, 'wb') as output:
-                mux([f1fp, f2fp], output)
-            with open(ofp, 'rb') as result:
-                obs = result.read()
-
-        self.assertEqual(obs, exp)
-
-    def test_demux(self):
-        prep = pd.DataFrame([['sample_foo', 'foofile'],
-                             ['sample_bar', 'barfile']],
-                            columns=['sample_name', 'run_prefix'])
-        input_ = io.BytesIO(b"foo@@@foofile_R1\tATGC\t+\tIIII\nbar@@@"
-                            b"barfile_R2\tAAAA\t+\tIIII\n")
-        expfoo = b"foo\tATGC\t+\tIIII\n"
-        expbar = b"bar\tAAAA\t+\tIIII\n"
-        with TemporaryDirectory() as d:
-            demux(input_, d.encode('ascii'), prep)
-            foo = open(join(d, 'sample_foo.sam'), 'rb').read()
-            bar = open(join(d, 'sample_bar.sam'), 'rb').read()
-
-        self.assertEqual(foo, expfoo)
-        self.assertEqual(bar, expbar)
-
     def test_search_by_filename(self):
         lookup = {'foo_bar': 'baz',
                   'foo': 'bar'}