check-my-sample-sheet 1.0.0__tar.gz

check_my_sample_sheet-1.0.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2024, Sequana Development Team (https://sequana.readthedocs.io)
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

check_my_sample_sheet-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: check-my-sample-sheet
+Version: 1.0.0
+Summary: Streamlit web application to validate Illumina sample sheets (bcl2fastq v1 and BCL Convert v2).
+License-Expression: BSD-3-Clause
+License-File: LICENSE
+Keywords: illumina,samplesheet,bcl2fastq,bcl-convert,sequana,ngs
+Author: Thomas Cokelaer
+Author-email: cokelaer@gmail.com
+Requires-Python: >=3.9,<4.0
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Dist: requests
+Requires-Dist: sequana (>=0.23.0)
+Requires-Dist: streamlit (>=1.28)
+Requires-Dist: streamlit-option-menu
+Project-URL: Documentation, https://github.com/sequana/webapp_samplesheet
+Project-URL: Homepage, https://github.com/sequana/webapp_samplesheet
+Project-URL: Repository, https://github.com/sequana/webapp_samplesheet
+Description-Content-Type: text/markdown
+
+# Check My Sample Sheet
+
+[![Tests](https://github.com/sequana/webapp_samplesheet/actions/workflows/tests.yml/badge.svg)](https://github.com/sequana/webapp_samplesheet/actions/workflows/tests.yml)
+[![Release](https://img.shields.io/github/v/release/sequana/webapp_samplesheet)](https://github.com/sequana/webapp_samplesheet/releases)
+[![License](https://img.shields.io/badge/license-BSD--3--Clause-blue.svg)](LICENSE)
+![Python](https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12-blue.svg)
+[![Streamlit App](https://img.shields.io/badge/Streamlit-Live%20Demo-FF4B4B?logo=streamlit&logoColor=white)](https://check-my-sample-sheet.streamlit.app/)
+![Visitors](https://api.visitorbadge.io/api/visitors?path=https%3A%2F%2Fcheck-my-sample-sheet.streamlit.app%2F&countColor=%23263759)
+
+This is a streamlit application that uses Sequana (github.com/sequana/sequana) **iem** modules to check Sample Sheets from Illumina sequencers. Both formats are supported and detected automatically:
+
+- **v1** (bcl2fastq): `[Data]` / `[Settings]` sections
+- **v2** (BCL Convert): `[BCLConvert_Data]` / `[BCLConvert_Settings]` sections
+
+Running demo is here: https://check-my-sample-sheet.streamlit.app/
+
+
+# General Information
+
+If you want to contribute to this web application, please provide PR here. Note, however, that the core of the application is within the Sequana project on https://github.com/sequana/sequana/, more specifically in the iem.py module.
+
+The sanity checks implemented are based on experience, the bcl2fastq documentation (v2.20) and the BCL Convert specification.
+
+# Installation
+
+From PyPI:
+
+    pip install check-my-sample-sheet
+
+Then launch the app (opens in your browser); extra arguments are forwarded to
+`streamlit run` (e.g. `--server.port 8502`):
+
+    check-my-sample-sheet
+
+# Local instance (from source)
+
+    git clone https://github.com/sequana/webapp_samplesheet
+    cd webapp_samplesheet
+
+    # install the dependencies (sequana, streamlit, ...)
+    pip install -r requirements.txt
+
+    # run the application locally in your browser
+    streamlit run check_my_sample_sheet/app.py
+
+# Running the tests
+
+    pip install -r requirements-dev.txt
+    pytest
+
+
+

check_my_sample_sheet-1.0.0/README.md

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+# Check My Sample Sheet
+
+[![Tests](https://github.com/sequana/webapp_samplesheet/actions/workflows/tests.yml/badge.svg)](https://github.com/sequana/webapp_samplesheet/actions/workflows/tests.yml)
+[![Release](https://img.shields.io/github/v/release/sequana/webapp_samplesheet)](https://github.com/sequana/webapp_samplesheet/releases)
+[![License](https://img.shields.io/badge/license-BSD--3--Clause-blue.svg)](LICENSE)
+![Python](https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12-blue.svg)
+[![Streamlit App](https://img.shields.io/badge/Streamlit-Live%20Demo-FF4B4B?logo=streamlit&logoColor=white)](https://check-my-sample-sheet.streamlit.app/)
+![Visitors](https://api.visitorbadge.io/api/visitors?path=https%3A%2F%2Fcheck-my-sample-sheet.streamlit.app%2F&countColor=%23263759)
+
+This is a streamlit application that uses Sequana (github.com/sequana/sequana) **iem** modules to check Sample Sheets from Illumina sequencers. Both formats are supported and detected automatically:
+
+- **v1** (bcl2fastq): `[Data]` / `[Settings]` sections
+- **v2** (BCL Convert): `[BCLConvert_Data]` / `[BCLConvert_Settings]` sections
+
+Running demo is here: https://check-my-sample-sheet.streamlit.app/
+
+
+# General Information
+
+If you want to contribute to this web application, please provide PR here. Note, however, that the core of the application is within the Sequana project on https://github.com/sequana/sequana/, more specifically in the iem.py module.
+
+The sanity checks implemented are based on experience, the bcl2fastq documentation (v2.20) and the BCL Convert specification.
+
+# Installation
+
+From PyPI:
+
+    pip install check-my-sample-sheet
+
+Then launch the app (opens in your browser); extra arguments are forwarded to
+`streamlit run` (e.g. `--server.port 8502`):
+
+    check-my-sample-sheet
+
+# Local instance (from source)
+
+    git clone https://github.com/sequana/webapp_samplesheet
+    cd webapp_samplesheet
+
+    # install the dependencies (sequana, streamlit, ...)
+    pip install -r requirements.txt
+
+    # run the application locally in your browser
+    streamlit run check_my_sample_sheet/app.py
+
+# Running the tests
+
+    pip install -r requirements-dev.txt
+    pytest
+
+

check_my_sample_sheet-1.0.0/check_my_sample_sheet/__init__.py

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+__version__ = "1.0.0"

check_my_sample_sheet-1.0.0/check_my_sample_sheet/__main__.py

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+"""Console entry point: launch the Streamlit sample sheet validator.
+
+Installed as the ``check-my-sample-sheet`` command (see pyproject.toml). Any
+extra arguments are forwarded to ``streamlit run`` (e.g. ``--server.port``).
+"""
+import sys
+from pathlib import Path
+
+from streamlit.web import cli as stcli
+
+
+def main():
+    app = str(Path(__file__).resolve().parent / "app.py")
+    sys.argv = ["streamlit", "run", app, *sys.argv[1:]]
+    sys.exit(stcli.main())
+
+
+if __name__ == "__main__":
+    main()

check_my_sample_sheet-1.0.0/check_my_sample_sheet/app.py

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+#
+#  This file is part of Sequana software
+#
+#  Copyright (c) 2023-2024 - Sequana Development Team
+#
+#  Distributed under the terms of the 3-clause BSD license.
+#  The full license is in the LICENSE file, distributed with this software.
+#
+#  website: https://github.com/sequana/webapp_samplesheet
+#  documentation: http://github.com/sequana/webapp_samplesheet/
+#
+##############################################################################
+
+import tempfile
+import time
+from collections import defaultdict
+from pathlib import Path
+
+import requests
+import streamlit as st
+from sequana.iem import SampleSheetFactory, get_sample_sheet_version
+from streamlit_option_menu import option_menu
+
+# directory holding this module, used to resolve packaged assets (imgs, examples)
+# regardless of the current working directory.
+HERE = Path(__file__).resolve().parent
+LOGO = str(HERE / "imgs" / "logo_256x256.png")
+
+st.set_page_config(
+    page_title="Check My Sample Sheet",
+    page_icon=LOGO,
+    layout="wide",
+    menu_items={"Report a bug": "https://github.com/sequana/webapp_samplesheet/issues/new/choose"},
+)
+
+version = "1.0.0"
+
+
+def print_checks(checks):
+    """
+    This function processes a list of checks and displays them in a Streamlit application.
+    Each check is represented as a dictionary with 'status' and 'msg' keys. The function
+    updates a color-coded progress bar based on the number of errors, warnings, and successes.
+    It also prints the messages associated with each check in the appropriate Streamlit function
+    (st.error, st.warning, st.success).
+
+    Parameters:
+    checks (list): A list of dictionaries, where each dictionary represents a check.
+                   The dictionary should have 'status' and 'msg' keys.
+
+    Returns:
+    dict: A dictionary containing the messages associated with each status (Error, Warning, Success).
+    """
+
+    # func to update colorbar
+    def colored_bar(success, warning, error, completed=0):
+        return f"""
+        <div style="display: flex; width: {completed}%; height: 30px; border: 1px solid black;">
+            <div style="width: {success}%; background-color: green;"></div>
+            <div style="width: {warning}%; background-color: yellow;"></div>
+            <div style="width: {error}%; background-color: red;"></div>
+        </div>
+        """
+
+    def add_legend(success, warning, error):
+        # finally add the legend
+        st.markdown(
+            f"""
+            <div style="display: flex; justify-content: space-between; width: 50%;">
+                 <div style="display: flex; align-items: center;">
+                     <div style="width: 20px; height: 20px; background-color: green; margin-right: 5px;"></div>
+                    <span>Success ({success})</span>
+                </div>
+                <div style="display: flex; align-items: center;">
+                     <div style="width: 20px; height: 20px; background-color: yellow; margin-right: 5px;"></div>
+                    <span>Warning ({warning})</span>
+                </div>
+                <div style="display: flex; align-items: center;">
+                    <div style="width: 20px; height: 20px; background-color: red; margin-right: 5px;"></div>
+                    <span>Error ({error})</span>
+                </div>
+            </div>
+            """,
+            unsafe_allow_html=True,
+        )
+
+    msgs = defaultdict(list)
+    emoji = {"Error": ":x:", "Success": ":white_check_mark:", "Warning": ":warning:"}
+
+    # Placeholder for the colored bar
+    bar_placeholder = st.empty()
+    bar_placeholder.markdown(colored_bar(0, 0, 0, 0), unsafe_allow_html=True)
+    # add_legend(0,0,0)
+
+    counter = {"Error": 0, "Warning": 0, "Success": 0}
+
+    N = len(checks)  # Number of checks
+    for i, check in enumerate(checks):
+        status = check["status"]
+        msg = check["msg"]
+
+        msgs[status].append(f"{status} {emoji[status]}. {msg}\n\n")
+        time.sleep(0.15)
+
+        counter[status] += 1
+
+        S = sum(counter.values())
+        success = counter["Success"] / S * 100
+        warning = counter["Warning"] / S * 100
+        error = counter["Error"] / S * 100
+
+        completed = min(round(100 * (S / float(N))), 100)
+        bar_placeholder.markdown(colored_bar(success, warning, error, completed), unsafe_allow_html=True)
+
+    # finally add the legend
+    _, col2, _ = st.columns([1, 4, 1])
+    with col2:
+        add_legend(counter["Success"], counter["Warning"], counter["Error"])
+
+    # prints all message
+    for error in msgs["Error"]:
+        st.error(error)
+    for warning in msgs["Warning"]:
+        st.warning(warning)
+    for success in msgs["Success"]:
+        st.success(success)
+    return dict(msgs)
+
+
+if "code_input" not in st.session_state:
+    st.session_state.code_input = ""
+
+# used to reset the file_uploader when an example is loaded: bumping this counter
+# changes the widget key, which forces Streamlit to drop any previously uploaded file.
+if "uploader_key" not in st.session_state:
+    st.session_state.uploader_key = 0
+
+
+def load_example(filename):
+    """Load example file from examples directory."""
+    examples_dir = Path(__file__).parent / "examples"
+    with open(examples_dir / filename, "r") as f:
+        return f.read()
+
+
+def set_example(filename):
+    """Callback to load example into the textarea session state.
+
+    Also resets the file_uploader (by bumping its key) so a previously uploaded
+    file does not silently take precedence over the loaded example.
+    """
+    st.session_state.code_input = load_example(filename)
+    st.session_state.uploader_key += 1
+
+
+def main():
+    st.sidebar.write("Provided by the [Sequana team](https://github.com/sequana/sequana)")
+    st.sidebar.image(LOGO)
+    st.title(f"Check My Sample Sheet (v{version})")
+
+    menu = ["Sample Sheet Validation (Illumina)", "Examples", "About", "How to cite"]
+
+    # 1. as sidebar menu
+    with st.sidebar:
+        choice = option_menu(
+            "Main Menu", menu, icons=["gear", "gear", "cloud-upload", ""], menu_icon="cast", default_index=0
+        )
+        st.markdown(
+            "**Resources:**\n\n"
+            "- [Source code](https://github.com/sequana/webapp_samplesheet)\n"
+            "- [Report a bug](https://github.com/sequana/webapp_samplesheet/issues/new/choose)\n"
+            "- [Sequana documentation](https://sequana.readthedocs.io)"
+        )
+
+    if choice == "Sample Sheet Validation (Illumina)":
+
+        st.markdown(
+            "This tool validates Illumina sample sheets. Both the **v1** format (bcl2fastq v2.20) and the "
+            "**v2** format (BCL Convert) are supported; the version is detected automatically. "
+            "It checks the structure, mandatory sections, sample identifiers, indexes, and more. "
+            "Provide a sample sheet below for validation, or load one of the examples to try the tool. "
+            "More examples are available in the **Examples** section of the menu."
+        )
+        st.subheader("Input Sample Sheet", divider="blue")
+
+        # create a 3-column layout
+        col1, col2, col3 = st.columns([4, 1, 4])
+        with col1:
+            data_file = st.file_uploader(
+                "Drop a sample sheet below and press the **Process** button. ",
+                type=["csv", "txt"],
+                key=f"uploader_{st.session_state.uploader_key}",
+            )
+        with col2:
+            # Centered "OR" text
+            st.markdown("<div style='text-align: center;'><br><br>OR</div>", unsafe_allow_html=True)
+
+        with col3:
+            code = st.text_area(
+                "Paste your sample sheet content here and press the **Process** button.", key="code_input"
+            )
+
+        st.subheader("Load an Example", divider="blue")
+        st.caption(
+            "Click a button to load a sample sheet into the text area above. "
+            "Examples 1, 2 and 4 are valid sheets; Example 3 is invalid and demonstrates how errors are reported. "
+            "Example 4 is a v2 (BCL Convert) sheet, the others are v1 (bcl2fastq)."
+        )
+        example_col1, example_col2, example_col3, example_col4 = st.columns(4)
+        with example_col1:
+            st.button("Example 1: Dual indexing (v1)", on_click=set_example, args=("sample_sheet.csv",))
+        with example_col2:
+            st.button("Example 2: Single index + Settings (v1)", on_click=set_example, args=("sample_sheet_settings_index.csv",))
+        with example_col3:
+            st.button("Example 3: Invalid (bad sample ID)", on_click=set_example, args=("Bad_SampleSheet_alphanum.csv",))
+        with example_col4:
+            st.button("Example 4: BCL Convert (v2)", on_click=set_example, args=("sample_sheet_v2_bclconvert.csv",))
+
+        if st.button(":gear: Process :gear:"):
+
+            try:
+                samplesheet = data_file.read().decode()
+                # st.experimental_rerun()
+            except:
+                samplesheet = code  # if there is no drag/drop data, we use the pasted code (if any)
+                data_file = None
+
+            try:
+                process_sample_sheet(data_file, samplesheet)
+            except Exception as err:
+                import urllib.parse
+
+                base_url = f"https://github.com/sequana/webapp_samplesheet/issues/new"
+
+                samplesheet = "\n".join(["    " + x for x in samplesheet.split("\n")])
+                params = {
+                    "title": "Automatic error from the check-my-sample-sheet website",
+                    "body": f"Dear developer(s),\n\nI encountered an unexpected error using the following sample sheet:\n\n{samplesheet}\n\nHere is the full error message:\n\n     {err}\n\nPlease let us know what you think might be the reason for the error.",
+                }
+                url = f"{base_url}?{urllib.parse.urlencode(params)}"
+                st.markdown(
+                    f'<div style="background-color: #ffcccc; padding: 10px; border-radius: 5px;"> Sorry, an unknown error occurred. Please create an issue <a href="{url}">here</a> to report it. A page will open; you will need to click on the "Submit new issue" button. </div>',
+                    unsafe_allow_html=True,
+                )
+
+                raise Exception(err)
+
+    elif choice == "Examples":
+        st.write("Below are several sample sheet examples, both valid and invalid, to illustrate the expected format.")
+        st.subheader("1 - Minimalist Example (only [Data] section)")
+        st.write(
+            "In this example, the sample sheet is simplified to keep only the [Data] section and the mandatory columns "
+            "(index and Sample_ID). Note that 'Sample_ID' is not strictly mandatory in bcl2fastq, but we make it "
+            "mandatory in this application as a design choice for better traceability."
+        )
+        st.code(
+            """[Data]
+Sample_ID,index
+ID1,TGACCA
+ID2,CATTTT"""
+        )
+
+        st.subheader("2 - [Data] section with dual indexing and no [Settings] section")
+        url = "https://raw.githubusercontent.com/sequana/webapp_samplesheet/main/examples/sample_sheet.csv"
+        r = requests.get(url, allow_redirects=True)
+        data = r.content.decode()
+        st.write(
+            "A more common example is shown below. The Illumina sample sheet uses sections enclosed in square brackets. "
+            "Up to four sections may appear: [Header], [Reads], [Settings] and [Data]. This example shows the [Header], "
+            "[Reads] and [Data] sections (the [Settings] section is missing). According to the Illumina specification, "
+            "all sections are optional, including [Data]. However, when [Data] is missing, all reads are stored as "
+            "undetermined, which is rarely useful. For this reason, we require the [Data] section in this application."
+        )
+        st.code(data, language="bash")
+
+        st.subheader("3 - [Data] section with single index and a [Settings] section")
+        url = (
+            "https://raw.githubusercontent.com/sequana/webapp_samplesheet/main/examples/sample_sheet_settings_index.csv"
+        )
+        r = requests.get(url, allow_redirects=True)
+        data = r.content.decode()
+        st.code(data, language="bash")
+
+        st.subheader("4 - Example of an erroneous sample sheet (invalid sample ID name)")
+        url = "https://raw.githubusercontent.com/sequana/webapp_samplesheet/main/examples/Bad_SampleSheet_alphanum.csv"
+        r = requests.get(url, allow_redirects=True)
+        data = r.content.decode()
+        st.code(data, language="bash")
+
+        st.subheader("5 - Example of an erroneous sample sheet (extra trailing semicolons)")
+        url = "https://raw.githubusercontent.com/sequana/webapp_samplesheet/main/examples/Bad_SampleSheet_extra_semicolons.csv"
+        r = requests.get(url, allow_redirects=True)
+        data = r.content.decode()
+        st.code(data, language="bash")
+
+    elif choice == "About":
+        st.subheader("About")
+        st.markdown(
+            "This application is part of the [Sequana Project](https://github.com/sequana), which is dedicated to NGS analysis. "
+            "Please see the [online documentation](https://sequana.readthedocs.io) as well as https://sequana.github.io for more information. "
+            "The code used in this application is based on the [IEM module](https://github.com/sequana/sequana) of the Sequana Python library. "
+            "It was developed based on the bcl2fastq documentation (v2.20) and is intended for users who want to demultiplex their data properly. "
+            "The source code for this web application is available on [GitHub](https://github.com/sequana/webapp_samplesheet)."
+            "\n\nThe different checks performed are described in this preprint: [Research Square](https://www.researchsquare.com/article/rs-5268893/v1)."
+        )
+        st.info(
+            "Application Author: Thomas Cokelaer\n\nIEM module provided by The Sequana Team\n\nOriginal beta testing: Laure Lemée, Etienne Kornobis, Rania Ouazahrou"
+        )
+    else:
+        st.subheader("How to cite?")
+        st.info("Check My Sample Sheet application (this website):\n\nLemée L. et al, [Research Square](https://www.researchsquare.com/article/rs-5268893/v1)")
+
+        st.info(
+            "The Sequana framework used to check the sample sheet:\n\nCokelaer T. et al, (2017), 'Sequana': a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI [doi:10.21105/joss.00352](https://joss.theoj.org/papers/10.21105/joss.00352)"
+        )
+
+
+def process_sample_sheet(data_file, samplesheet):
+    """
+    This function processes an uploaded sample sheet file and performs validation checks.
+    It saves the file locally, creates a SampleSheet object using the Sequana library,
+    and then validates the sample sheet. If errors are found, they are displayed in the
+    Streamlit application. The function also provides options to download the corrected
+    sample sheet file and view the data section as a CSV file.
+
+    Parameters:
+    data_file (FileIO): The uploaded sample sheet file.
+    samplesheet (str): The content of the sample sheet file.
+
+    Returns:
+    None
+    """
+    if data_file is not None:
+        file_details = {"Filename": data_file.name, "FileType": data_file.type, "FileSize": data_file.size}
+    else:
+        pass
+
+    if 1 == 1:
+
+        # read to save locally
+        # samplesheet = data_file.read().decode()
+
+        with tempfile.NamedTemporaryFile(delete=False, mode="w") as fout:
+            fout.write(samplesheet)
+            fout.close()
+            version = get_sample_sheet_version(fout.name)
+            iem = SampleSheetFactory(fout.name)
+
+        if version == "v2":
+            st.info(":information_source: Detected an Illumina **v2** sample sheet: validating against the **BCL Convert** specification.")
+        else:
+            st.info(":information_source: Detected an Illumina **v1** sample sheet: validating against the **bcl2fastq v2.20** specification.")
+
+        try:
+            # st.write(f"This sample sheet contains {len(iem.df)} samples")
+            iem.validate()
+        except SystemExit as err:
+            st.header("Validation Results", divider="blue")
+            msg = "Error(s) found. :sob: See the message below from Sequana for details."
+            st.error(msg)
+            st.info(err)
+        else:
+            st.header("Validation Results", divider="blue")
+            # emoji within div do not seem to work
+            msg = ":champagne: Your sample sheet looks correct. :champagne:"
+            st.success(msg)
+        # =============================================================== validation
+        st.subheader("Details about the checks", divider="blue")
+        checks = iem.checker()
+
+        msgs = print_checks(checks)
+
+        # =============================================================== original file
+        st.subheader("Original file", divider="blue")
+        st.code(samplesheet)
+
+        # =============================================================== corrected file
+        if len(msgs["Error"]):
+            st.subheader("Corrected file", divider="blue")
+            st.caption(
+                "The quick fix below removes extra trailing semicolons. Other types of errors are difficult to correct "
+                "automatically, so you will need to fix the file manually. We strongly recommend using the IEM software "
+                "from Illumina for that purpose. If you need to edit the file quickly, do not use Excel: although the "
+                "extension is usually .csv, an Illumina sample sheet is not a standard CSV file and Excel may corrupt it."
+            )
+            with tempfile.NamedTemporaryFile(delete=False, mode="w") as fout:
+                iem.quick_fix(fout.name)
+                fout.close()
+                with open(fout.name, "r") as fin:
+
+                    st.download_button(
+                        label="Download data as CSV",
+                        data=fin.read(),
+                        file_name="sample.csv",
+                        mime="text/csv",
+                    )
+
+        # =============================================================== data section
+        st.subheader("Data section", divider="blue")
+        st.caption(
+            "For convenience, the [Data] section is shown below as a parsed table. "
+            "Check that the values are consistent with your expectations (for example, that each index appears in a single column)."
+        )
+        df = iem.df.copy()
+        st.write(df)
+
+
+if __name__ == "__main__":
+    main()

check_my_sample_sheet-1.0.0/check_my_sample_sheet/examples/Bad_SampleSheet_alphanum.csv

@@ -0,0 +1,36 @@
+[Header]
+IEMFileVersion,5
+Investigator Name,tartampion
+Experiment Name,Daudet 
+Date,21/06/2024
+Workflow,GenerateFASTQ
+Application,NextSeq FASTQ Only
+Instrument Type,NextSeq/MiniSeq
+Assay,TruSeq DNA PCR-Free
+Index Adapters,"IDT-ILMN TruSeq DNA UD Indexes (96 Indexes)"
+Description,TEST_FILE
+Chemistry,Amplicon
+
+[Reads]
+151
+151
+
+[Settings]
+Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
+AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
+
+[Data]
+Sample_ID,Sample_Name,Sample_Plate,Sample_Well,Index_Plate_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description
+TagV1,,,,E01,UDI0005,ATCCACTG,UDI0005,ACGCACCT,B18249,
+TagV3,,,,F01,UDI0006,GCTTGTCA,UDI0006,GTATGTTC,B18249,
+TagV4,,,,G01,UDI0007,CAAGCTAG,UDI0007,CGCTATGT,B18249,
+TagV5,,,,H01,UDI0008,TGGATCGA,UDI0008,TATCGCAC,B18249,
+3D+LmeA14,,,,A02,UDI0009,AGTTCAGG,UDI0009,TCTGTTGG,B18249,
+3D+LmeA30,,,,B02,UDI0010,GACCTGAA,UDI0010,CTCACCAA,B18249,
+3D+LmeA56,,,,C02,UDI0011,TCTCTACT,UDI0011,GAACCGCG,B18249,
+3D+LmeA9,,,,D02,UDI0012,CTCTCGTC,UDI0012,AGGTTATA,B18249,
+3D+LmeA19,,,,E02,UDI0013,CCAAGTCT,UDI0013,TCATCCTT,B18249,
+3D+LmeA26,,,,F02,UDI0014,TTGGACTC,UDI0014,CTGCTTCC,B18249,
+3D+LmeA28,,,,G02,UDI0015,GGCTTAAG,UDI0015,GGTCACGA,B18249,
+3D+LmeA42,,,,H02,UDI0016,AATCCGGA,UDI0016,AACTGTAG,B18249,
+3D+LmeA55,,,,A03,UDI0017,TAATACAG,UDI0017,GTGAATAT,B18249,

check_my_sample_sheet-1.0.0/check_my_sample_sheet/examples/Bad_SampleSheet_extra_semicolons.csv

@@ -0,0 +1,17 @@
+[Header];;;;;;
+IEMFileVersion;4;;;
+Investigator Name;;;;
+Experiment Name;160104-SR-310v2-std;;
+Chemistry;Default;;;;
+;;;;;;;;;;
+[Reads];;;;;;;;
+315;;;;
+;;;
+[Settings];;;;
+Adapter;AGATCGGAAGAGCACACGTCTGAACTCCAGTCA;;;
+AdapterRead2;AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT;;;
+;;;
+[Data];;;
+Sample_ID;Sample_Name;I7_Index_ID;index;Sample_Project
+A;;NF01;CGATGT;
+B;;NF03;ACAGTG;

check_my_sample_sheet-1.0.0/check_my_sample_sheet/examples/case1.csv

@@ -0,0 +1,4 @@
+[Data]
+Sample_ID,index
+ID1,TGACCA
+ID2,CATTTT

check_my_sample_sheet-1.0.0/check_my_sample_sheet/examples/case2.csv

@@ -0,0 +1,7 @@
+[Settings]
+Adapter, ACGTACGTN
+
+[Data]
+Sample_ID,index
+ID1,TGACCa
+ID1,CATTTT

check_my_sample_sheet-1.0.0/check_my_sample_sheet/examples/case3.csv

@@ -0,0 +1,8 @@
+[Settings];;;;
+Adapter;AGATCGGAAGAGCACACGTCTGAACTCCAGTCA;;;
+AdapterRead2;AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT;;;
+;;;
+[Data];;;
+Sample_ID;Sample_Name;I7_Index_ID;index;Sample_Project
+A;;NF01;CGATGT;
+B;;NF03;ACAGTG;

check_my_sample_sheet-1.0.0/check_my_sample_sheet/examples/sample_sheet.csv

@@ -0,0 +1,21 @@
+[Header]
+Local Run Manager Analysis Id,43043
+Experiment Name,MyProject
+Date,2020-01-24
+Module,GenerateFASTQ - 2.0.0
+Workflow,GenerateFASTQ
+Library Prep Kit,Custom
+Description,200123-PE-MP-150
+Chemistry,Default
+
+[Reads]
+151
+151
+
+[Data]
+Sample_ID,Sample_Name,Description,index,I7_Index_ID,Sample_Project
+412,412,,TGACCA,TGACCA,B3202
+LMD666,LMD666,,CATTTT,CATTTT,B3202
+TaoP3,TaoP3,,ACAGTG,ACAGTG,B3202
+TaoP10,TaoP10,,GTGAAA,GTGAAA,B3202
+

check_my_sample_sheet-1.0.0/check_my_sample_sheet/examples/sample_sheet_settings_index.csv

@@ -0,0 +1,24 @@
+[Header]
+IEMFileVersion,4
+Investigator Name,
+Experiment Name,
+Date,8/23/2016
+Workflow,GenerateFASTQ
+Application,FASTQ Only
+Assay,NEXTFlex-PCRfree
+Description,
+Chemistry,Default
+
+[Reads]
+300
+300
+
+[Settings]
+Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
+AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
+
+[Data]
+Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
+ID1,,TEST,A01,NF02,TGACCA,,
+ID2,,TEST,A02,NF03,ACAGTG,,
+

check_my_sample_sheet-1.0.0/check_my_sample_sheet/examples/sample_sheet_v2_bclconvert.csv

@@ -0,0 +1,44 @@
+[Header],
+FileFormatVersion,2
+RunName,20260616_B21184-18S-PE-MPdbl-151-10-5M
+InstrumentPlatform,MiSeqi100Series
+IndexOrientation,Forward
+AnalysisLocation,Local
+
+[Reads]
+Read1Cycles,151
+Read2Cycles,151
+Index1Cycles,10
+Index2Cycles,10
+
+[Sequencing_Settings]
+LibraryPrepKits,NexteraXT
+
+[BCLConvert_Settings]
+SoftwareVersion,4.4.6
+AdapterRead1,CTGTCTCTTATACACATCT
+AdapterRead2,CTGTCTCTTATACACATCT
+OverrideCycles,R1:Y151;I1:I10;I2:I10;R2:Y151
+FastqCompressionFormat,dragen
+NoLaneSplitting,true
+GenerateFastqcMetrics,true
+
+[BCLConvert_Data]
+Sample_ID,Index,Index2
+1,AGGTCAGATA,CTACAAGATA
+2,CGACATCCGA,TACGTTCATT
+3,ATTCCATAAG,TGCCTGGTGG
+4,CACAATAGGA,TCCATCCGAG
+5,AACATCGCGC,GTCCACTTGT
+
+
+[Cloud_Settings]
+GeneratedVersion,1.25.0.202605080250
+
+[Cloud_Data]
+Sample_ID,ProjectName,LibraryName,LibraryPrepKitName,IndexAdapterKitName
+1,BXXXX,1_AGGTCAGATA_CTACAAGATA,NexteraXT,IlluminaDNARNAUDISetABCDTagmentation
+2,BXXXX,2_CGACATCCGA_TACGTTCATT,NexteraXT,IlluminaDNARNAUDISetABCDTagmentation
+3,BXXXX,3_ATTCCATAAG_TGCCTGGTGG,NexteraXT,IlluminaDNARNAUDISetABCDTagmentation
+4,BXXXX,4_CACAATAGGA_TCCATCCGAG,NexteraXT,IlluminaDNARNAUDISetABCDTagmentation
+5,BXXXX,5_AACATCGCGC_GTCCACTTGT,NexteraXT,IlluminaDNARNAUDISetABCDTagmentation

check_my_sample_sheet-1.0.0/pyproject.toml

@@ -0,0 +1,46 @@
+[project]
+name = "check-my-sample-sheet"
+version = "1.0.0"
+description = "Streamlit web application to validate Illumina sample sheets (bcl2fastq v1 and BCL Convert v2)."
+authors = [{ name = "Thomas Cokelaer", email = "cokelaer@gmail.com" }]
+license = "BSD-3-Clause"
+readme = "README.md"
+requires-python = ">=3.9,<4.0"
+keywords = ["illumina", "samplesheet", "bcl2fastq", "bcl-convert", "sequana", "ngs"]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = [
+    # sequana >= 0.23.0 ships BCLConvert / SampleSheetFactory / get_sample_sheet_version
+    "sequana>=0.23.0",
+    "streamlit>=1.28",
+    "streamlit-option-menu",
+    "requests",
+]
+
+[project.urls]
+homepage = "https://github.com/sequana/webapp_samplesheet"
+repository = "https://github.com/sequana/webapp_samplesheet"
+documentation = "https://github.com/sequana/webapp_samplesheet"
+
+[project.scripts]
+check-my-sample-sheet = "check_my_sample_sheet.__main__:main"
+
+[tool.poetry]
+packages = [{ include = "check_my_sample_sheet" }]
+include = ["check_my_sample_sheet/examples/*", "check_my_sample_sheet/imgs/*"]
+
+[tool.poetry.group.dev.dependencies]
+pytest = "*"
+pytest-cov = "*"
+
+[build-system]
+requires = ["poetry-core>=2.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.pytest.ini_options]
+addopts = "--cov=check_my_sample_sheet --cov-report=term-missing"
+testpaths = ["tests"]