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desc for deprecated software (#3339)
* adding the software desction to the GUI for deprecated software * clean docs * add workflow not active message * Update qiita_pet/support_files/doc/source/processingdata/qp-fastp-minimap2.rst Co-authored-by: Daniel McDonald <[email protected]> --------- Co-authored-by: Charles Cowart <[email protected]> Co-authored-by: Daniel McDonald <[email protected]>
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qiita_pet/handlers/artifact_handlers/base_handlers.py

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@@ -228,6 +228,7 @@ def artifact_summary_get_request(user, artifact_id):
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'processing_parameters': proc_params.values,
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'command_active': cmd.active,
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'software_deprecated': sw.deprecated,
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'software_description': sw.description
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}
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else:
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processing_info = {}

qiita_pet/handlers/artifact_handlers/tests/test_base_handlers.py

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@@ -243,6 +243,12 @@ def test_artifact_summary_get_request(self):
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private_download_button % 2),
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'processing_info': {
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'command_active': True, 'software_deprecated': False,
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'software_description': ('Quantitative Insights Into '
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'Microbial Ecology (QIIME) is an '
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'open-source bioinformatics '
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'pipeline for performing '
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'microbiome analysis from raw DNA '
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'sequencing data'),
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'command': 'Split libraries FASTQ',
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'processing_parameters': {
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'max_barcode_errors': '1.5', 'sequence_max_n': '0',

qiita_pet/handlers/software.py

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@@ -146,7 +146,7 @@ def _default_parameters_parsing(node):
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workflows.append(
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{'name': w.name, 'id': w.id, 'data_types': w.data_type,
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'description': w.description,
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'description': w.description, 'active': w.active,
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'parameters_sample': wparams['sample'],
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'parameters_prep': wparams['prep'],
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'nodes': nodes, 'edges': edges})

qiita_pet/support_files/doc/source/processingdata/processing-recommendations.rst

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@@ -77,6 +77,12 @@ subsequent meta-analyses. We currently provide the several options for your conv
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- auto-detect adapters and **rat** + phix filtering. Includes Norway rat (*Rattus norvegicus*) reference `GCF_000001895.5 (Rnor_6.0) <https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000001895.5/>`_. `GCF_000001895.5 fna <https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/895/GCA_000001895.4_Rnor_6.0/GCA_000001895.4_Rnor_6.0_genomic.fna.gz>`_
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- auto-detect adapters only filtering. Only includes the two adapter sequences noted above.
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For more information about the versions in this plugin, visit:
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.. toctree::
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qp-fastp-minimap2.rst
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Note that the command produces up to 6 output artifacts based on the aligner and database selected:
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- Alignment Profile: contains the raw alignment file and the no rank classification BIOM table
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Adapter and host filtering
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==========================
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At the end of August 2023, we discovered that the parameters used by
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qp-fastp-minimap2 did not trigger application of adapter filtering. By default,
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fastp performs autodetection of adapters and filtering for single-end data. By
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default, fastp does not perform these operations on paired-end data. This behavior
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was not expected by us. It was discovered when manually assessing replicated
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sequences, which on examination by BLAST against NT reported to be adapters.
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Adapter filtering for paired-end data with fastp requires specifying either the
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exact adapters to remove (i.e., no autodetection), or to explicitly specify “--detect_adapter_for_pe”. Qiita previously indicated to users that the
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qp-fastp-minimap2 plugin was performing adapter autodetection and filtering.
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However, because this flag was not specified, that behavior did not occur.
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In the metagenomic dataset the adapters were discovered in, we observed a few
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sequences with high replication, with assignments to a few genomes in RS210.
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The coverage of those genomes, using all metagenomic short reads, was constrained
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to very specific regions. The replicated sequences exhibited high identity to
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known adapters. As such, we suspect the replicated sequences we observed were
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adapters. We suspect the observed genomes either suffer from adapter contamination
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themselves, or the constructs used in the samples we examined were derived from
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real organisms. Although we cannot differentiate this definitively in the data
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we examined, in either case these short reads are likely artifactual.
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For the dataset we examined, removal of these false positives was important
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for the biological interpretation of the results. However, whether the removal
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is important likely depends on the dataset and question.
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qp-fastp-minimap2 has been updated to perform adapter filtering on paired-end data.
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The fastp autodetection is compile-time limited to `the first 256k sequences <https://github.com/OpenGene/fastp/blob/7784d047fdf0a8df4211967156f5c97920c6d2e8/src/evaluator.cpp#L410-L417>`_.
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Because of this, we opted for a more conservative approach of not relying on
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autodetection and instead we now test all adapters that fastp is aware of. Specifically,
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we now provide fastp a known adapters FASTA which is a serialized representation
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of their `known adapter list <https://github.com/OpenGene/fastp/blob/7784d047fdf0a8df4211967156f5c97920c6d2e8/src/knownadapters.h#L11>`_.
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The new command is named: `Adapter and host filtering v2023.12`.

qiita_pet/templates/artifact_ajax/artifact_summary.html

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{% if processing_info['software_deprecated'] %}
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<div class="alert alert-danger" role="alert">
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Danger, the software that generated this artifact was produced by a software version with a known bug and the results are wrong, please re-run with the newer version.
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{% raw processing_info['software_description'] %}
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</div>
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{% elif not processing_info['command_active'] %}
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<div class="alert alert-warning" role="alert">

qiita_pet/templates/workflows.html

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@@ -87,6 +87,11 @@ <h5>Hover on the spheres to get more information</h5>
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<div class="row">
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<div class="col-sm-7" style="background-color: #DCDCDC; height: 650px" id="workflow_{{i}}"></div>
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<div class="col-sm-5">
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{% if not w['active'] %}
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<h3 style="color:red">
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~~ NOT ACTIVE ~~
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</h3>
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{% end %}
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<h4>
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Application: {{', '.join(w['data_types'])}} ->
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{% if w['parameters_sample'] or w['parameters_prep'] %}

qiita_pet/test/test_software.py

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@@ -175,7 +175,7 @@ def test_retrive_workflows(self):
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{'name': 'FASTQ upstream workflow', 'id': 1, 'data_types': ['16S', '18S'],
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'description': 'This accepts html <a href="https://qiita.ucsd.edu">Qiita!'
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'</a><br/><br/><b>BYE!</b>',
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'parameters_sample': {}, 'parameters_prep': {},
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'active': True, 'parameters_sample': {}, 'parameters_prep': {},
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'nodes': [
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['params_1', 1, 'Split libraries FASTQ', 'Defaults', {
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'max_bad_run_length': '3', 'min_per_read_length_fraction': '0.75',
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['params_2', 'output_params_2_OTU table | BIOM']]},
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{'name': 'FASTA upstream workflow', 'id': 2, 'data_types': ['18S'],
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'description': 'This is another description',
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'parameters_sample': {}, 'parameters_prep': {},
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'active': False, 'parameters_sample': {}, 'parameters_prep': {},
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'nodes': [
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['params_3', 2, 'Split libraries', 'Defaults with Golay 12 barcodes', {
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'min_seq_len': '200', 'max_seq_len': '1000',
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['params_4', 'output_params_4_OTU table | BIOM']]},
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{'name': 'Per sample FASTQ upstream workflow', 'id': 3,
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'data_types': ['ITS'], 'description': None,
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'parameters_sample': {}, 'parameters_prep': {},
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'active': True, 'parameters_sample': {}, 'parameters_prep': {},
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'nodes': [
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['params_5', 1, 'Split libraries FASTQ', 'per sample FASTQ defaults', {
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'max_bad_run_length': '3', 'min_per_read_length_fraction': '0.75',

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