.coveragerc

-[run]
-branch = True
-omit =
-    */tests*
-    */__init__.py
-    q2_cutadapt/_version.py
-    versioneer.py
-
-[report]
-omit =
-    */tests*
-    */__init__.py
-    q2_cutadapt/_version.py
-    versioneer.py

.gitattributes

-q2_cutadapt/_version.py export-subst
+q2cli/_version.py export-subst

.gitignore

@@ -63,8 +63,3 @@ target/
 
 # vi
 .*.swp
-
-# other
-*~
-
-.DS_store

.travis.yml

@@ -14,12 +14,12 @@ install:
   - wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py36-linux-conda.yml
   - conda env create -q -n test-env --file qiime2-latest-py36-linux-conda.yml
   - source activate test-env
-  - conda install -q pytest-cov
-  - pip install flake8 coveralls
+  - conda install -q nose
+  - pip install -q flake8
   - pip install -q https://github.com/qiime2/q2lint/archive/master.zip
   - make install
 script:
   - make lint
-  - make test-cov
-after_success:
-  - coveralls
+  - make test
+  - QIIMETEST= source tab-qiime
+  - QIIMETEST= qiime info

LICENSE

 BSD 3-Clause License
 
-Copyright (c) 2017-2019, QIIME 2 development team.
+Copyright (c) 2016-2019, QIIME 2 development team.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

MANIFEST.in

 include versioneer.py
-include q2_cutadapt/_version.py
+include q2cli/_version.py

Makefile

-.PHONY: all lint test test-cov install dev clean distclean
+.PHONY: all lint test install dev clean distclean
 
 PYTHON ?= python
+PREFIX ?= $(CONDA_PREFIX)
 
 all: ;
 
@@ -9,16 +10,17 @@ lint:
 	flake8
 
 test: all
-	py.test
-
-test-cov: all
-	py.test --cov=q2_cutadapt
+	QIIMETEST= nosetests
 
 install: all
-	$(PYTHON) setup.py install
+	$(PYTHON) setup.py install && \
+	mkdir -p $(PREFIX)/etc/conda/activate.d && \
+	cp hooks/50_activate_q2cli_tab_completion.sh $(PREFIX)/etc/conda/activate.d/
 
 dev: all
-	pip install -e .
+	pip install -e . && \
+	mkdir -p $(PREFIX)/etc/conda/activate.d && \
+	cp hooks/50_activate_q2cli_tab_completion.sh $(PREFIX)/etc/conda/activate.d/
 
 clean: distclean
 

README.md

-# q2-cutadapt
+# q2cli
+A [click-based](http://click.pocoo.org/) command line interface for [QIIME 2](https://github.com/qiime2/qiime2).
 
-[![Build Status](https://travis-ci.org/qiime2/q2-cutadapt.svg?branch=master)](https://travis-ci.org/qiime2/q2-cutadapt) [![Coverage Status](https://coveralls.io/repos/github/qiime2/q2-cutadapt/badge.svg?branch=master)](https://coveralls.io/github/qiime2/q2-cutadapt?branch=master)
+## Installation and getting help
 
-This is a QIIME 2 plugin. For details on QIIME 2 and tutorials demonstrating how to use this plugin, see the [QIIME 2 documentation](https://qiime2.org/).
+Visit https://qiime2.org to learn more about q2cli and the QIIME 2 project.
+
+## Enabling tab completion
+
+### Bash
+
+To enable tab completion in Bash, run the following command or add it to your `.bashrc`/`.bash_profile`:
+
+```bash
+source tab-qiime
+```
+
+### ZSH
+
+To enable tab completion in ZSH, run the following commands or add them to your `.zshrc`:
+
+```bash
+autoload bashcompinit && bashcompinit && source tab-qiime
+```

bin/tab-qiime

+#!/usr/bin/env bash
+
+# Bash completion script that defers to a cached completion script representing
+# the state of the current QIIME 2 deployment.
+#
+# This script is intended to be executed on the command-line or in
+# .bashrc/.bash_profile:
+#
+#     source tab-qiime
+#
+
+_qiime_completion()
+{
+  # Attempt to find the cached completion script. If q2cli isn't installed, or
+  # is an incompatible version, don't attempt completion.
+  local completion_path="$(python -c "import q2cli.util; print(q2cli.util.get_completion_path())" 2> /dev/null)"
+
+  if [[ $? != 0 ]]; then
+    unset COMPREPLY
+    return 0
+  fi
+
+  # If the completion script exists, attempt completion by invoking the script
+  # in a subshell, supplying COMP_WORDS and COMP_CWORD. Capture the output as
+  # the completion reply. If the completion script failed, don't attempt
+  # completion.
+  if [[ -f "$completion_path" ]] ; then
+    COMPREPLY=( $(COMP_WORDS="${COMP_WORDS[*]}" COMP_CWORD="${COMP_CWORD}" "$completion_path" 2> /dev/null) )
+
+    if [[ $? != 0 ]]; then
+      unset COMPREPLY
+      return 0
+    fi
+  else
+    unset COMPREPLY
+    return 0
+  fi
+
+  return 0
+}
+
+# Enable default readline and bash completion behavior when `_qiime_completion`
+# doesn't have a reply.
+complete -F _qiime_completion -o default -o bashdefault qiime
+
+# Execute a `qiime` command (any command will do) so that tab-completion will
+# work out-of-the-box (e.g. with a fresh installation of q2cli). Running a
+# command will create or refresh the cache if necessary, which contains the
+# actual completion script.
+#
+# Ignore stdout to avoid displaying help text to users enabling tab-completion.
+# stderr displays the note about cache refreshing, as that can take a few
+# moments to complete.
+qiime > /dev/null

ci/recipe/meta.yaml

@@ -3,7 +3,7 @@
 {% set release = '.'.join(version.split('.')[:2]) %}
 
 package:
-  name: q2-cutadapt
+  name: q2cli
   version: {{ version }}
 
 source:
@@ -11,6 +11,8 @@ source:
 
 build:
   script: make install
+  entry_points:
+    - qiime=q2cli.__main__:qiime
 
 requirements:
   host:
@@ -19,17 +21,16 @@ requirements:
 
   run:
     - python  {{ python }}
-    - cutadapt
-    - pigz
-    - pandas
-    - numpy
+    - pip
+    - click
     - qiime2 {{ release }}.*
-    - q2-types {{ release }}.*
 
 test:
   imports:
-    - q2_cutadapt
-    - qiime2.plugins.cutadapt
+    - q2cli
+
+  commands:
+    - QIIMETEST= qiime --help
 
 about:
   home: https://qiime2.org

debian/changelog

+q2-cutadapt (2019.7.0-1) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  TODO: Needs most probably qiime (>= 2019.7.0)
+
+ -- Andreas Tille <tille@debian.org>  Fri, 02 Aug 2019 23:13:39 +0200
+
 q2-cutadapt (2019.4.0-1) unstable; urgency=medium
 
   * Initial release (Closes: #931249)

debian/compat

-12

debian/control

 Source: q2-cutadapt
-Section: science
-Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Liubov Chuprikova <chuprikovalv@gmail.com>
-Build-Depends: debhelper (>= 12~),
+Section: science
+Priority: optional
+Build-Depends: debhelper-compat (= 12),
                dh-python,
                python3,
                python3-setuptools,
@@ -11,7 +11,7 @@ Build-Depends: debhelper (>= 12~),
                python3-pandas,
                cutadapt (>= 2.3),
                q2-types
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/q2-cutadapt
 Vcs-Git: https://salsa.debian.org/med-team/q2-cutadapt.git
 Homepage: https://qiime2.org/

debian/rules

@@ -13,5 +13,6 @@ export PYBUILD_BEFORE_INSTALL=rm -rvf {build_dir}/q2-cutadapt.egg-* {build_dir}/
 	dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	dh_auto_test -- -s custom --test-args="cd {build_dir}; py.test-3 --cov=q2_cutadapt"
-
+endif

hooks/50_activate_q2cli_tab_completion.sh

+if [ -n "${ZSH_VERSION-}" ]; then
+  autoload bashcompinit && bashcompinit && source tab-qiime
+elif [ -n "${BASH_VERSION-}" ]; then
+  source tab-qiime
+fi

q2_cutadapt/_demux.py

-# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2019, QIIME 2 development team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file LICENSE, distributed with this software.
-# ----------------------------------------------------------------------------
-
-import gzip
-import os
-import subprocess
-import tempfile
-
-import qiime2
-from q2_types.per_sample_sequences import (
-    CasavaOneEightSingleLanePerSampleDirFmt,
-    FastqGzFormat,
-)
-from q2_types.multiplexed_sequences import (
-    MultiplexedSingleEndBarcodeInSequenceDirFmt,
-    MultiplexedPairedEndBarcodeInSequenceDirFmt,
-)
-
-import pandas as pd
-import numpy as np
-
-
-def run_command(cmd, verbose=True):
-    print('Running external command line application. This may print '
-          'messages to stdout and/or stderr.')
-    print('The command being run is below. This command cannot '
-          'be manually re-run as it will depend on temporary files that '
-          'no longer exist.')
-    print('\nCommand:', end=' ')
-    print(' '.join(cmd), end='\n\n')
-    subprocess.run(cmd, check=True)
-
-
-def _build_demux_command(seqs_dir_fmt, barcode_fhs, per_sample_dir_fmt,
-                         untrimmed_dir_fmt, error_rate):
-    cmd = ['cutadapt',
-           '--front', 'file:%s' % barcode_fhs['fwd'].name,
-           '--error-rate', str(error_rate),
-           # {name} is a cutadapt convention for interpolating the sample id
-           # into the filename.
-           '-o', os.path.join(str(per_sample_dir_fmt), '{name}.1.fastq.gz'),
-           '--untrimmed-output',
-           os.path.join(str(untrimmed_dir_fmt), 'forward.fastq.gz'),
-           ]
-    if isinstance(seqs_dir_fmt, MultiplexedPairedEndBarcodeInSequenceDirFmt):
-        # PAIRED-END
-        if barcode_fhs['rev'] is not None:
-            # Dual indices
-            cmd += [
-                '--pair-adapters',
-                '-G', 'file:%s' % barcode_fhs['rev'].name,
-            ]
-        cmd += [
-            '-p', os.path.join(str(per_sample_dir_fmt), '{name}.2.fastq.gz'),
-            '--untrimmed-paired-output',
-            os.path.join(str(untrimmed_dir_fmt), 'reverse.fastq.gz'),
-            str(seqs_dir_fmt.forward_sequences.view(FastqGzFormat)),
-            str(seqs_dir_fmt.reverse_sequences.view(FastqGzFormat)),
-            ]
-    else:
-        # SINGLE-END
-        cmd += [str(seqs_dir_fmt.file.view(FastqGzFormat))]
-    return cmd
-
-
-def _rename_files(seqs_dir_fmt, per_sample_dir_fmt, barcode_series):
-    read_directions = [1]
-    if isinstance(seqs_dir_fmt, MultiplexedPairedEndBarcodeInSequenceDirFmt):
-        # PAIRED-END
-        read_directions.append(2)
-
-    for (sample_id, barcode_id) in barcode_series.iteritems():
-        for read_direction in read_directions:
-            out_fp = per_sample_dir_fmt.sequences.path_maker(
-                sample_id=sample_id, barcode_id=barcode_id,
-                lane_number=1, read_number=read_direction)
-            src = os.path.join(str(per_sample_dir_fmt),
-                               '%s.%d.fastq.gz' % (sample_id,
-                                                   read_direction))
-            if os.path.isfile(src):
-                os.rename(src, str(out_fp))
-
-
-def _write_barcode_fasta(barcode_series, barcode_fasta):
-    with open(barcode_fasta.name, 'w') as fh:
-        for (sample_id, barcode) in barcode_series.iteritems():
-            fh.write('>%s\n%s\n' % (sample_id, barcode))
-
-
-def _write_empty_fastq_to_mux_barcode_in_seq_fmt(seqs_dir_fmt):
-    fastq = FastqGzFormat()
-    with gzip.open(str(fastq), 'w') as fh:
-        fh.write(b'')
-    # PAIRED-END
-    if isinstance(seqs_dir_fmt, MultiplexedPairedEndBarcodeInSequenceDirFmt):
-        seqs_dir_fmt.forward_sequences.write_data(fastq, FastqGzFormat)
-        seqs_dir_fmt.reverse_sequences.write_data(fastq, FastqGzFormat)
-    # SINGLE-END
-    else:
-        seqs_dir_fmt.file.write_data(fastq, FastqGzFormat)
-
-
-def _demux(seqs, forward_barcodes, reverse_barcodes, error_tolerance,
-           mux_fmt, batch_size):
-    fwd_barcode_name = forward_barcodes.name
-    forward_barcodes = forward_barcodes.drop_missing_values()
-    barcodes = forward_barcodes.to_series().to_frame()
-    if reverse_barcodes is not None:
-        barcode_pairs = set()
-        samples_w_missing_barcodes = set()
-        samples_w_dup_barcode_pairs = set()
-        rev_barcode_name = reverse_barcodes.name
-        rev_barcodes = reverse_barcodes.to_series()
-        # 'sort = false' below prevents a warning about future behavior changes
-        # by selecting the future behavior explicitly
-        barcodes = pd.concat([barcodes, rev_barcodes], axis=1, sort=False)
-
-        for sample_id, f_barcode, r_barcode in barcodes.itertuples():
-            if pd.isnull(f_barcode) or pd.isnull(r_barcode):
-                samples_w_missing_barcodes.add(sample_id)
-            if (f_barcode, r_barcode) in barcode_pairs:
-                samples_w_dup_barcode_pairs.add(sample_id)
-            barcode_pairs.add((f_barcode, r_barcode))
-
-        if samples_w_missing_barcodes:
-            raise ValueError('The following samples do not have both '
-                             'forward and reverse barcodes: %s'
-                             % ', '.join(sorted(samples_w_missing_barcodes)))
-        if samples_w_dup_barcode_pairs:
-            raise ValueError('The following samples have duplicate barcode'
-                             ' pairs: %s' %
-                             ', '.join(sorted(samples_w_dup_barcode_pairs)))
-
-    per_sample_sequences = CasavaOneEightSingleLanePerSampleDirFmt()
-    n_samples = len(barcodes)
-    if batch_size > n_samples:
-        raise ValueError('The batch_size (%d) cannot be greater than the '
-                         'number of samples (%d).' % (
-                             batch_size, n_samples))
-    batch_size = n_samples if batch_size == 0 else batch_size
-    batches = np.arange(n_samples) // batch_size
-    previous_untrimmed = seqs
-    for _, barcode_batch in barcodes.groupby(batches):
-        current_untrimmed = mux_fmt()
-        _write_empty_fastq_to_mux_barcode_in_seq_fmt(current_untrimmed)
-        open_fhs = {'fwd': tempfile.NamedTemporaryFile(), 'rev': None}
-        _write_barcode_fasta(barcode_batch[fwd_barcode_name], open_fhs['fwd'])
-        if reverse_barcodes is not None:
-            open_fhs['rev'] = tempfile.NamedTemporaryFile()
-            _write_barcode_fasta(barcode_batch[rev_barcode_name],
-                                 open_fhs['rev'])
-        cmd = _build_demux_command(previous_untrimmed, open_fhs,
-                                   per_sample_sequences,
-                                   current_untrimmed, error_tolerance)
-        run_command(cmd)
-        open_fhs['fwd'].close()
-        if reverse_barcodes is not None:
-            open_fhs['rev'].close()
-        previous_untrimmed = current_untrimmed
-        # Only use the forward barcode in the renamed files
-    _rename_files(seqs, per_sample_sequences, barcodes[fwd_barcode_name])
-
-    muxed = len(list(per_sample_sequences.sequences.iter_views(FastqGzFormat)))
-    if muxed == 0:
-        raise ValueError('No samples were demultiplexed.')
-    return per_sample_sequences, previous_untrimmed
-
-
-def demux_single(seqs: MultiplexedSingleEndBarcodeInSequenceDirFmt,
-                 barcodes: qiime2.CategoricalMetadataColumn,
-                 error_rate: float = 0.1,
-                 batch_size: int = 0) -> \
-                    (CasavaOneEightSingleLanePerSampleDirFmt,
-                     MultiplexedSingleEndBarcodeInSequenceDirFmt):
-    mux_fmt = MultiplexedSingleEndBarcodeInSequenceDirFmt
-    return _demux(seqs, barcodes, None, error_rate, mux_fmt, batch_size)
-
-
-def demux_paired(seqs: MultiplexedPairedEndBarcodeInSequenceDirFmt,
-                 forward_barcodes: qiime2.CategoricalMetadataColumn,
-                 reverse_barcodes: qiime2.CategoricalMetadataColumn = None,
-                 error_rate: float = 0.1,
-                 batch_size: int = 0) -> \
-                    (CasavaOneEightSingleLanePerSampleDirFmt,
-                     MultiplexedPairedEndBarcodeInSequenceDirFmt):
-    mux_fmt = MultiplexedPairedEndBarcodeInSequenceDirFmt
-    return _demux(seqs, forward_barcodes, reverse_barcodes, error_rate,
-                  mux_fmt, batch_size)

q2_cutadapt/_trim.py

-# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2019, QIIME 2 development team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file LICENSE, distributed with this software.
-# ----------------------------------------------------------------------------
-
-import os
-
-import subprocess
-import pandas as pd
-
-from q2_types.per_sample_sequences import (
-    CasavaOneEightSingleLanePerSampleDirFmt,
-    SingleLanePerSampleSingleEndFastqDirFmt,
-    SingleLanePerSamplePairedEndFastqDirFmt,
-)
-
-
-def run_commands(cmds, verbose=True):
-    print('Running external command line application. This may print '
-          'messages to stdout and/or stderr.')
-    print('The commands to be run are below. These commands cannot '
-          'be manually re-run as they will depend on temporary files that '
-          'no longer exist.')
-    for cmd in cmds:
-        print('\nCommand:', end=' ')
-        print(' '.join(cmd), end='\n\n')
-        subprocess.run(cmd, check=True)
-
-
-_trim_defaults = {
-    'cores': 1,
-    'adapter_f': None,
-    'adapter_r': None,
-    'front_f': None,
-    'front_r': None,
-    'anywhere_f': None,
-    'anywhere_r': None,
-    'error_rate': 0.1,
-    'indels': True,
-    'times': 1,
-    'overlap': 3,
-    'match_read_wildcards': False,
-    'match_adapter_wildcards': True,
-    'minimum_length': 1,
-    'discard_untrimmed': False,
-}
-
-
-def _build_trim_command(f_read, r_read, trimmed_seqs,
-                        cores=_trim_defaults['cores'],
-                        adapter_f=_trim_defaults['adapter_f'],
-                        front_f=_trim_defaults['front_f'],
-                        anywhere_f=_trim_defaults['anywhere_f'],
-                        adapter_r=_trim_defaults['adapter_r'],
-                        front_r=_trim_defaults['front_r'],
-                        anywhere_r=_trim_defaults['anywhere_r'],
-                        error_rate=_trim_defaults['error_rate'],
-                        indels=_trim_defaults['indels'],
-                        times=_trim_defaults['times'],
-                        overlap=_trim_defaults['overlap'],
-                        match_read_wildcards=_trim_defaults[
-                            'match_read_wildcards'],
-                        match_adapter_wildcards=_trim_defaults[
-                            'match_adapter_wildcards'],
-                        minimum_length=_trim_defaults['minimum_length'],
-                        discard_untrimmed=_trim_defaults['discard_untrimmed'],
-                        ):
-    cmd = [
-        'cutadapt',
-        '--cores', str(cores),
-        '--error-rate', str(error_rate),
-        '--times', str(times),
-        '--overlap', str(overlap),
-        '--minimum-length', str(minimum_length),
-        '-o', str(trimmed_seqs.path / os.path.basename(f_read)),
-    ]
-
-    if r_read is not None:
-        cmd += ['-p', str(trimmed_seqs.path / os.path.basename(r_read))]
-
-    if adapter_f is not None:
-        for adapter in adapter_f:
-            cmd += ['--adapter', adapter]
-    if front_f is not None:
-        for adapter in front_f:
-            cmd += ['--front', adapter]
-    if anywhere_f is not None:
-        for adapter in anywhere_f:
-            cmd += ['--anywhere', adapter]
-
-    if adapter_r is not None:
-        for adapter in adapter_r:
-            cmd += ['-A', adapter]  # cutadapt doesn't have a long-form flag
-    if front_r is not None:
-        for adapter in front_r:
-            cmd += ['-G', adapter]  # cutadapt doesn't have a long-form flag
-    if anywhere_r is not None:
-        for adapter in anywhere_r:
-            cmd += ['-B', adapter]  # cutadapt doesn't have a long-form flag
-
-    if not indels:
-        cmd += ['--no-indels']
-    if match_read_wildcards:
-        cmd += ['--match-read-wildcards']
-    if not match_adapter_wildcards:
-        cmd += ['--no-match-adapter-wildcards']
-    if discard_untrimmed:
-        cmd += ['--discard-untrimmed']
-
-    cmd += [f_read]
-
-    if r_read is not None:
-        cmd += [r_read]
-
-    return cmd
-
-
-def trim_single(demultiplexed_sequences:
-                SingleLanePerSampleSingleEndFastqDirFmt,
-                cores: int = _trim_defaults['cores'],
-                adapter: str = _trim_defaults['adapter_f'],
-                front: str = _trim_defaults['front_f'],
-                anywhere: str = _trim_defaults['anywhere_f'],
-                error_rate: float = _trim_defaults['error_rate'],
-                indels: bool = _trim_defaults['indels'],
-                times: int = _trim_defaults['times'],
-                overlap: int = _trim_defaults['overlap'],
-                match_read_wildcards:
-                bool = _trim_defaults['match_read_wildcards'],
-                match_adapter_wildcards:
-                bool = _trim_defaults['match_adapter_wildcards'],
-                minimum_length: int = _trim_defaults['minimum_length'],
-                discard_untrimmed:
-                bool = _trim_defaults['discard_untrimmed']) -> \
-                    CasavaOneEightSingleLanePerSampleDirFmt:
-    trimmed_sequences = CasavaOneEightSingleLanePerSampleDirFmt()
-    cmds = []
-    df = demultiplexed_sequences.manifest.view(pd.DataFrame)
-    for _, fwd in df.itertuples():
-        cmd = _build_trim_command(fwd, None,
-                                  trimmed_sequences, cores, adapter, front,
-                                  anywhere, None, None, None, error_rate,
-                                  indels, times, overlap, match_read_wildcards,
-                                  match_adapter_wildcards, minimum_length,
-                                  discard_untrimmed)
-        cmds.append(cmd)
-
-    run_commands(cmds)
-    return trimmed_sequences
-
-
-def trim_paired(demultiplexed_sequences:
-                SingleLanePerSamplePairedEndFastqDirFmt,
-                cores: int = _trim_defaults['cores'],
-                adapter_f: str = _trim_defaults['adapter_f'],
-                front_f: str = _trim_defaults['front_f'],
-                anywhere_f: str = _trim_defaults['anywhere_f'],
-                adapter_r: str = _trim_defaults['adapter_r'],
-                front_r: str = _trim_defaults['front_r'],
-                anywhere_r: str = _trim_defaults['anywhere_r'],
-                error_rate: float = _trim_defaults['error_rate'],
-                indels: bool = _trim_defaults['indels'],
-                times: int = _trim_defaults['times'],
-                overlap: int = _trim_defaults['overlap'],
-                match_read_wildcards:
-                bool = _trim_defaults['match_read_wildcards'],
-                match_adapter_wildcards:
-                bool = _trim_defaults['match_adapter_wildcards'],
-                minimum_length: int = _trim_defaults['minimum_length'],
-                discard_untrimmed:
-                bool = _trim_defaults['discard_untrimmed']) -> \
-                    CasavaOneEightSingleLanePerSampleDirFmt:
-    trimmed_sequences = CasavaOneEightSingleLanePerSampleDirFmt()
-    cmds = []
-    df = demultiplexed_sequences.manifest.view(pd.DataFrame)
-    for _, fwd, rev in df.itertuples():
-        cmd = _build_trim_command(fwd, rev, trimmed_sequences, cores,
-                                  adapter_f, front_f,
-                                  anywhere_f, adapter_r, front_r, anywhere_r,
-                                  error_rate, indels, times, overlap,
-                                  match_read_wildcards,
-                                  match_adapter_wildcards, minimum_length,
-                                  discard_untrimmed)
-        cmds.append(cmd)
-
-    run_commands(cmds)
-    return trimmed_sequences

q2_cutadapt/citations.bib

-@article{martin2011cutadapt,
-  title={Cutadapt removes adapter sequences from high-throughput sequencing reads},
-  author={Martin, Marcel},
-  journal={EMBnet. journal},
-  volume={17},
-  number={1},
-  pages={pp--10},
-  year={2011},
-  doi={10.14806/ej.17.1.200}
-}

q2_cutadapt/plugin_setup.py

-# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2019, QIIME 2 development team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file LICENSE, distributed with this software.
-# ----------------------------------------------------------------------------
-
-from qiime2.plugin import (
-    Plugin,
-    Citations,
-    MetadataColumn,
-    Categorical,
-    Float,
-    Range,
-    Int,
-    List,
-    Str,
-    Bool,
-)
-from q2_types.multiplexed_sequences import (
-    MultiplexedSingleEndBarcodeInSequence,
-    MultiplexedPairedEndBarcodeInSequence,
-)
-from q2_types.sample_data import SampleData
-from q2_types.per_sample_sequences import (
-    SequencesWithQuality,
-    PairedEndSequencesWithQuality,
-)
-
-import q2_cutadapt
-import q2_cutadapt._demux
-import q2_cutadapt._trim
-
-
-plugin = Plugin(
-    name='cutadapt',
-    version=q2_cutadapt.__version__,
-    website='https://github.com/qiime2/q2-cutadapt',
-    package='q2_cutadapt',
-    description='This QIIME 2 plugin uses cutadapt to work with '
-                'adapters (e.g. barcodes, primers) in sequence data.',
-    short_description='Plugin for removing adapter sequences, primers, and '
-                      'other unwanted sequence from sequence data.',
-    citations=Citations.load('citations.bib', package='q2_cutadapt')
-)
-
-plugin.methods.register_function(
-    function=q2_cutadapt._trim.trim_single,
-    inputs={
-        'demultiplexed_sequences': SampleData[SequencesWithQuality],
-    },
-    parameters={
-        'cores': Int % Range(1, None),
-        'adapter': List[Str],
-        'front': List[Str],
-        'anywhere': List[Str],
-        'error_rate': Float % Range(0, 1, inclusive_start=True,
-                                    inclusive_end=True),
-        'indels': Bool,
-        'times': Int % Range(1, None),
-        'overlap': Int % Range(1, None),
-        'match_read_wildcards': Bool,
-        'match_adapter_wildcards': Bool,
-        'minimum_length': Int % Range(1, None),
-        'discard_untrimmed': Bool,
-    },
-    outputs=[
-        ('trimmed_sequences', SampleData[SequencesWithQuality]),
-    ],
-    input_descriptions={
-        'demultiplexed_sequences': 'The single-end sequences to be trimmed.',
-    },
-    parameter_descriptions={
-        'cores': 'Number of CPU cores to use.',
-        'adapter': 'Sequence of an adapter ligated to the 3\' end. The '
-                   'adapter and any subsequent bases are trimmed. If a `$` '
-                   'is appended, the adapter is only found if it is at the '
-                   'end of the read. If your sequence of interest is "framed" '
-                   'by a 5\' and a 3\' adapter, use this parameter to define '
-                   'a "linked" primer - see https://cutadapt.readthedocs.io '
-                   'for complete details.',
-        'front': 'Sequence of an adapter ligated to the 5\' end. The adapter '
-                 'and any preceding bases are trimmed. Partial matches at the '
-                 '5\' end are allowed. If a `^` character is prepended, the '
-                 'adapter is only found if it is at the beginning of the '
-                 'read.',
-        'anywhere': 'Sequence of an adapter that may be ligated to the 5\' or '
-                    '3\' end. Both types of matches as described under '
-                    '`adapter` and `front` are allowed. If the first base of '
-                    'the read is part of the match, the behavior is as with '
-                    '`front`, otherwise as with `adapter`. This option is '
-                    'mostly for rescuing failed library preparations - do '
-                    'not use if you know which end your adapter was ligated '
-                    'to.',
-        'error_rate': 'Maximum allowed error rate.',
-        'indels': 'Allow insertions or deletions of bases when matching '
-                  'adapters.',
-        'times': 'Remove multiple occurrences of an adapter if it is '
-                 'repeated, up to `times` times.',
-        'overlap': 'Require at least `overlap` bases of overlap between read '
-                   'and adapter for an adapter to be found.',
-        'match_read_wildcards': 'Interpret IUPAC wildcards (e.g., N) in '
-                                'reads.',
-        'match_adapter_wildcards': 'Interpret IUPAC wildcards (e.g., N) in '
-                                   'adapters.',
-        'minimum_length': 'Discard reads shorter than specified value. Note, '
-                          'the cutadapt default of 0 has been overridden, '
-                          'because that value produces empty sequence '
-                          'records.',
-        'discard_untrimmed': 'Discard reads in which no adapter was found.',
-    },
-    output_descriptions={
-        'trimmed_sequences': 'The resulting trimmed sequences.',
-    },
-    name='Find and remove adapters in demultiplexed single-end sequences.',
-    description='Search demultiplexed single-end sequences for adapters and '
-                'remove them. The parameter descriptions in this method are '
-                'adapted from the official cutadapt docs - please see those '
-                'docs at https://cutadapt.readthedocs.io for complete '
-                'details.',
-)
-
-plugin.methods.register_function(
-    function=q2_cutadapt._trim.trim_paired,
-    inputs={
-        'demultiplexed_sequences': SampleData[PairedEndSequencesWithQuality],
-    },
-    parameters={
-        'cores': Int % Range(1, None),
-        'adapter_f': List[Str],
-        'front_f': List[Str],
-        'anywhere_f': List[Str],
-        'adapter_r': List[Str],
-        'front_r': List[Str],
-        'anywhere_r': List[Str],
-        'error_rate': Float % Range(0, 1, inclusive_start=True,
-                                    inclusive_end=True),
-        'indels': Bool,
-        'times': Int % Range(1, None),
-        'overlap': Int % Range(1, None),
-        'match_read_wildcards': Bool,
-        'match_adapter_wildcards': Bool,
-        'minimum_length': Int % Range(1, None),
-        'discard_untrimmed': Bool,
-    },
-    outputs=[
-        ('trimmed_sequences', SampleData[PairedEndSequencesWithQuality]),
-    ],
-    input_descriptions={
-        'demultiplexed_sequences': 'The paired-end sequences to be trimmed.',
-    },
-    parameter_descriptions={
-        'cores': 'Number of CPU cores to use.',
-        'adapter_f': 'Sequence of an adapter ligated to the 3\' end. The '
-                     'adapter and any subsequent bases are trimmed. If a `$` '
-                     'is appended, the adapter is only found if it is at the '
-                     'end of the read. Search in forward read. If your '
-                     'sequence of interest is "framed" by a 5\' and a 3\' '
-                     'adapter, use this parameter to define a "linked" primer '
-                     '- see https://cutadapt.readthedocs.io for complete '
-                     'details.',
-        'front_f': 'Sequence of an adapter ligated to the 5\' end. The '
-                   'adapter and any preceding bases are trimmed. Partial '
-                   'matches at the 5\' end are allowed. If a `^` character '
-                   'is prepended, the adapter is only found if it is at the '
-                   'beginning of the read. Search in forward read.',
-        'anywhere_f': 'Sequence of an adapter that may be ligated to the 5\' '
-                      'or 3\' end. Both types of matches as described under '
-                      '`adapter` and `front` are allowed. If the first base '
-                      'of the read is part of the match, the behavior is as '
-                      'with `front`, otherwise as with `adapter`. This option '
-                      'is mostly for rescuing failed library preparations - '
-                      'do not use if you know which end your adapter was '
-                      'ligated to. Search in forward read.',
-        'adapter_r': 'Sequence of an adapter ligated to the 3\' end. The '
-                     'adapter and any subsequent bases are trimmed. If a `$` '
-                     'is appended, the adapter is only found if it is at the '
-                     'end of the read. Search in reverse read. If your '
-                     'sequence of interest is "framed" by a 5\' and a 3\' '
-                     'adapter, use this parameter to define a "linked" primer '
-                     '- see https://cutadapt.readthedocs.io for complete '
-                     'details.',
-        'front_r': 'Sequence of an adapter ligated to the 5\' end. The '
-                   'adapter and any preceding bases are trimmed. Partial '
-                   'matches at the 5\' end are allowed. If a `^` character '
-                   'is prepended, the adapter is only found if it is at the '
-                   'beginning of the read. Search in reverse read.',
-        'anywhere_r': 'Sequence of an adapter that may be ligated to the 5\' '
-                      'or 3\' end. Both types of matches as described under '
-                      '`adapter` and `front` are allowed. If the first base '
-                      'of the read is part of the match, the behavior is as '
-                      'with `front`, otherwise as with `adapter`. This '
-                      'option is mostly for rescuing failed library '
-                      'preparations - do not use if you know which end your '
-                      'adapter was ligated to. Search in reverse read.',
-        'error_rate': 'Maximum allowed error rate.',
-        'indels': 'Allow insertions or deletions of bases when matching '
-                  'adapters.',
-        'times': 'Remove multiple occurrences of an adapter if it is '
-                 'repeated, up to `times` times.',
-        'overlap': 'Require at least `overlap` bases of overlap between read '
-                   'and adapter for an adapter to be found.',
-        'match_read_wildcards': 'Interpret IUPAC wildcards (e.g., N) in '
-                                'reads.',
-        'match_adapter_wildcards': 'Interpret IUPAC wildcards (e.g., N) in '
-                                   'adapters.',
-        'minimum_length': 'Discard reads shorter than specified value. Note, '
-                          'the cutadapt default of 0 has been overridden, '
-                          'because that value produces empty sequence '
-                          'records.',
-        'discard_untrimmed': 'Discard reads in which no adapter was found.',
-    },
-    output_descriptions={
-        'trimmed_sequences': 'The resulting trimmed sequences.',
-    },
-    name='Find and remove adapters in demultiplexed paired-end sequences.',
-    description='Search demultiplexed paired-end sequences for adapters and '
-                'remove them. The parameter descriptions in this method are '
-                'adapted from the official cutadapt docs - please see those '
-                'docs at https://cutadapt.readthedocs.io for complete '
-                'details.',
-)
-
-plugin.methods.register_function(
-    function=q2_cutadapt._demux.demux_single,
-    inputs={
-        'seqs': MultiplexedSingleEndBarcodeInSequence,
-    },
-    parameters={
-        'barcodes': MetadataColumn[Categorical],
-        'error_rate': Float % Range(0, 1, inclusive_start=True,
-                                    inclusive_end=True),
-        'batch_size': Int % Range(0, None),
-    },
-    outputs=[
-        ('per_sample_sequences', SampleData[SequencesWithQuality]),
-        ('untrimmed_sequences', MultiplexedSingleEndBarcodeInSequence),
-    ],
-    input_descriptions={
-        'seqs': 'The single-end sequences to be demultiplexed.',
-    },
-    parameter_descriptions={
-        'barcodes': 'The sample metadata column listing the per-sample '
-                    'barcodes.',
-        'error_rate': 'The level of error tolerance, specified as the maximum '
-                      'allowable error rate. The default value specified by '
-                      'cutadapt is 0.1 (=10%), which is greater than '
-                      '`demux emp-*`, which is 0.0 (=0%).',
-        'batch_size': 'The number of samples cutadapt demultiplexes '
-                      'concurrently. Demultiplexing in smaller batches will '
-                      'yield the same result with marginal speed loss, and '
-                      'may solve "too many files" errors related to sample '
-                      'quantity. Set to "0" to process all samples at once.'
-    },
-    output_descriptions={
-        'per_sample_sequences': 'The resulting demultiplexed sequences.',
-        'untrimmed_sequences': 'The sequences that were unmatched to '
-                               'barcodes.',
-    },
-    name='Demultiplex single-end sequence data with barcodes in-sequence.',
-    description='Demultiplex sequence data (i.e., map barcode reads to '
-                'sample ids). Barcodes are expected to be located within the '
-                'sequence data (versus the header, or a separate barcode '
-                'file).',
-)
-
-plugin.methods.register_function(
-    function=q2_cutadapt._demux.demux_paired,
-    inputs={
-        'seqs': MultiplexedPairedEndBarcodeInSequence,
-    },
-    parameters={
-        'forward_barcodes': MetadataColumn[Categorical],
-        'reverse_barcodes': MetadataColumn[Categorical],
-        'error_rate': Float % Range(0, 1, inclusive_start=True,
-                                    inclusive_end=True),
-        'batch_size': Int % Range(0, None),
-    },
-    outputs=[
-        ('per_sample_sequences', SampleData[PairedEndSequencesWithQuality]),
-        ('untrimmed_sequences', MultiplexedPairedEndBarcodeInSequence),
-    ],
-    input_descriptions={
-        'seqs': 'The paired-end sequences to be demultiplexed.',
-    },
-    parameter_descriptions={
-        'forward_barcodes': 'The sample metadata column listing the '
-                            'per-sample barcodes for the forward reads.',
-        'reverse_barcodes': 'The sample metadata column listing the '
-                            'per-sample barcodes for the reverse reads.',
-        'error_rate': 'The level of error tolerance, specified as the maximum '
-                      'allowable error rate.',
-        'batch_size': 'The number of samples cutadapt demultiplexes '
-                      'concurrently. Demultiplexing in smaller batches will '
-                      'yield the same result with marginal speed loss, and '
-                      'may solve "too many files" errors related to sample '
-                      'quantity. Set to "0" to process all samples at once.'
-    },
-    output_descriptions={
-        'per_sample_sequences': 'The resulting demultiplexed sequences.',
-        'untrimmed_sequences': 'The sequences that were unmatched to '
-                               'barcodes.',
-    },
-    name='Demultiplex paired-end sequence data with barcodes in-sequence.',
-    description='Demultiplex sequence data (i.e., map barcode reads to '
-                'sample ids). Barcodes are expected to be located within the '
-                'sequence data (versus the header, or a separate barcode '
-                'file).',
-)