snakemake_rapidrun_swarm tagshttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/tags2023-10-19T13:40:00Zhttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/tags/1.2.01.2.0mbrunohttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/tags/1.1.51.1.5<h2 data-sourcepos="1:1-1:37" dir="auto">
<a id="user-content-version-115-12th-december-2022" class="anchor" href="#version-115-12th-december-2022" aria-hidden="true"></a>VERSION 1.1.5 - 12th december 2022</h2>
<h3 data-sourcepos="2:1-2:9" dir="auto">
<a id="user-content-added" class="anchor" href="#added" aria-hidden="true"></a>Added</h3>
<ul data-sourcepos="3:1-6:0" dir="auto">
<li data-sourcepos="3:1-3:27">custom reference database</li>
<li data-sourcepos="4:1-4:39">rules taxonomic assignment custom ref</li>
<li data-sourcepos="5:1-6:0">
<code data-sourcepos="5:4-5:33">scripts/prepare_spygen_data.py</code> From SPYGEN Alice's file {marker}, {run} and {projet}, the program seek into corresponding marker .dat file the column tag to get the plaque position in order to attribute the right {sample} at demultiplexing step</li>
</ul>
<h3 data-sourcepos="7:1-7:11" dir="auto">
<a id="user-content-changed" class="anchor" href="#changed" aria-hidden="true"></a>Changed</h3>
<ul data-sourcepos="8:1-10:0" dir="auto">
<li data-sourcepos="8:1-8:46">configfile handles custom reference database</li>
<li data-sourcepos="9:1-10:0">Fix conda ram issue in envs/env_obitools.yaml</li>
</ul>
<h3 data-sourcepos="11:1-11:11" dir="auto">
<a id="user-content-removed" class="anchor" href="#removed" aria-hidden="true"></a>Removed</h3>
<ul data-sourcepos="12:1-12:34" dir="auto">
<li data-sourcepos="12:1-12:34">useless quality sequences steps</li>
</ul>2023-10-19T13:40:00Zmbrunohttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/tags/1.1.41.1.4<h2 data-sourcepos="2:1-2:33" dir="auto">
<a id="user-content-version-114-8th-april-2021" class="anchor" href="#version-114-8th-april-2021" aria-hidden="true"></a>VERSION 1.1.4 - 8th april 2021</h2>
<h3 data-sourcepos="4:1-4:9" dir="auto">
<a id="user-content-added" class="anchor" href="#added" aria-hidden="true"></a>Added</h3>
<ul data-sourcepos="5:1-9:0" dir="auto">
<li data-sourcepos="5:1-5:13">fastqc rule</li>
<li data-sourcepos="6:1-6:18">fastqc conda env</li>
<li data-sourcepos="7:1-7:31">documentation quickstart step</li>
<li data-sourcepos="8:1-9:0">resources test folder</li>
</ul>
<h3 data-sourcepos="10:1-10:11" dir="auto">
<a id="user-content-changed" class="anchor" href="#changed" aria-hidden="true"></a>Changed</h3>
<ul data-sourcepos="11:1-13:0" dir="auto">
<li data-sourcepos="11:1-11:28">name of results subfolders</li>
<li data-sourcepos="12:1-13:0">add fastqc item to configfiles</li>
</ul>
<h3 data-sourcepos="14:1-14:11" dir="auto">
<a id="user-content-removed" class="anchor" href="#removed" aria-hidden="true"></a>Removed</h3>
<ul data-sourcepos="15:1-15:25" dir="auto">
<li data-sourcepos="15:1-15:25">deprecated config files</li>
</ul>2021-04-08T19:18:26Zpeguerinpierre-edouard.guerin@cefe.cnrs.frhttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/tags/1.1.31.1.3<h2 data-sourcepos="1:1-1:47" dir="auto">
<a id="user-content-version-113-cascade-23th-february-2021" class="anchor" href="#version-113-cascade-23th-february-2021" aria-hidden="true"></a>VERSION 1.1.3 "Cascade" - 23th february 2021</h2>
<h3 data-sourcepos="2:1-2:9" dir="auto">
<a id="user-content-added" class="anchor" href="#added" aria-hidden="true"></a>Added</h3>
<ul data-sourcepos="3:1-12:0" dir="auto">
<li data-sourcepos="3:1-3:96">"spygen origine" format (one single <code data-sourcepos="3:40-3:43">.dat</code> file for one single <code data-sourcepos="3:67-3:72">.fastq</code> file) can be processed</li>
<li data-sourcepos="4:1-4:135">UNIT TEST <code data-sourcepos="4:14-4:61">01_settings/readwrite_rapidrun_demultiplexing.py</code> barcode_tags_duplicated.csv has exactly 2 columns (original, duplicated)</li>
<li data-sourcepos="5:1-5:88">TEST dataset to check in few seconds if the whole workflow works fine on RAPIDRUN case</li>
<li data-sourcepos="6:1-6:87">TEST dataset to check in few seconds if the whole workflow works fine on CLASSIC case</li>
<li data-sourcepos="7:1-7:101">copy and rename files generated from 19_otu_table and 24_table_assigned_sequences to results folder</li>
<li data-sourcepos="8:1-8:78">resources job: number of parallelized jobs are limited by the resource "job"</li>
<li data-sourcepos="9:1-9:132">
<code data-sourcepos="9:4-9:33">scripts/prepare_spygen_data.py</code> generates the all_samples.csv file from SPYGEN "standard" information file and {marker}.dat files</li>
<li data-sourcepos="10:1-10:32">TEST integrity of <code data-sourcepos="10:22-10:25">.dat</code> files</li>
<li data-sourcepos="11:1-11:2">
</li>
</ul>
<h3 data-sourcepos="13:1-13:11" dir="auto">
<a id="user-content-changed" class="anchor" href="#changed" aria-hidden="true"></a>Changed</h3>
<ul data-sourcepos="14:1-25:0" dir="auto">
<li data-sourcepos="14:1-14:43">all worklows are merged into a single one</li>
<li data-sourcepos="15:1-15:48">results subfolders are generated automatically</li>
<li data-sourcepos="16:1-16:46">unique <code data-sourcepos="16:11-16:17">scripts</code>, <code data-sourcepos="16:22-16:26">rules</code> and <code data-sourcepos="16:34-16:37">envs</code> folders</li>
<li data-sourcepos="17:1-17:85">Demultiplex: no_indel option cutadapt to prevent insertion between tags and primers</li>
<li data-sourcepos="18:1-18:71">Alternative workflow to perform taxonomic assignment wihtout <code data-sourcepos="18:65-18:70">ecotag</code>
</li>
<li data-sourcepos="19:1-19:31">Fix wildcards in CLASSIC mode</li>
<li data-sourcepos="20:1-20:83">convert <code data-sourcepos="20:12-20:51">scripts/scripts/OTU_contingency_table.py</code> code from python2 into python3</li>
<li data-sourcepos="21:1-21:51">update cutadapt version 2 to cutadapt version 3.2</li>
<li data-sourcepos="22:1-22:45">Fix SettingWithCopyWarning pandas dataframe</li>
<li data-sourcepos="23:1-23:41">factorisation folder results generation</li>
<li data-sourcepos="24:1-25:0">Fix data export</li>
</ul>
<h3 data-sourcepos="26:1-26:11" dir="auto">
<a id="user-content-removed" class="anchor" href="#removed" aria-hidden="true"></a>Removed</h3>
<ul data-sourcepos="27:1-30:61" dir="auto">
<li data-sourcepos="27:1-27:74">old folders and scripts 01_settings, 02_assembly, 03_demultiplex, etc...</li>
<li data-sourcepos="28:1-28:48">old preexisting subfolders into results folder</li>
<li data-sourcepos="29:1-29:40">
<code data-sourcepos="29:4-29:11">clean.sh</code> script which is now useless</li>
<li data-sourcepos="30:1-30:61">
<code data-sourcepos="30:4-30:12">rename.sh</code> script which is replaced by a rule in Snakefile</li>
</ul>2021-02-23T14:18:33Zpeguerinpierre-edouard.guerin@cefe.cnrs.frhttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/tags/1.1.11.1.1<h2 data-sourcepos="2:1-2:37" dir="auto">
<a id="user-content-version-111-8th-september-2020" class="anchor" href="#version-111-8th-september-2020" aria-hidden="true"></a>VERSION 1.1.1 - 8th september 2020</h2>
<h3 data-sourcepos="3:1-3:9" dir="auto">
<a id="user-content-added" class="anchor" href="#added" aria-hidden="true"></a>Added</h3>
<ul data-sourcepos="4:1-6:0" dir="auto">
<li data-sourcepos="4:1-4:11">data test</li>
<li data-sourcepos="5:1-6:0">tutorial</li>
</ul>
<h3 data-sourcepos="7:1-7:11" dir="auto">
<a id="user-content-changed" class="anchor" href="#changed" aria-hidden="true"></a>Changed</h3>
<ul data-sourcepos="8:1-8:283" dir="auto">
<li data-sourcepos="8:1-8:283">The demultiplexing method is more efficient. First it demultiplexes linked barcode tags. For each run, every linked barcode are seeked only once. Second it trimms primer 5' and 3' for each sample fastq files. Primer and barcode tags are processed in forward and reverse complement.</li>
</ul>2020-09-08T09:45:44Zpeguerinpierre-edouard.guerin@cefe.cnrs.frhttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/tags/1.1.01.1.0<h2 data-sourcepos="1:1-1:31" dir="auto">
<a id="user-content-version-110-1st-sep-2020" class="anchor" href="#version-110-1st-sep-2020" aria-hidden="true"></a>VERSION 1.1.0 - 1st sep 2020</h2>
<h3 data-sourcepos="2:1-2:9" dir="auto">
<a id="user-content-added" class="anchor" href="#added" aria-hidden="true"></a>Added</h3>
<ul data-sourcepos="3:1-6:0" dir="auto">
<li data-sourcepos="3:1-3:19">Conda v4.8.2 envs</li>
<li data-sourcepos="4:1-4:11">Autorship</li>
<li data-sourcepos="5:1-6:0">license MIT</li>
</ul>
<h3 data-sourcepos="7:1-7:11" dir="auto">
<a id="user-content-changed" class="anchor" href="#changed" aria-hidden="true"></a>Changed</h3>
<ul data-sourcepos="8:1-9:79" dir="auto">
<li data-sourcepos="8:1-8:66">new structure for distribution based on snakemake recommandation</li>
<li data-sourcepos="9:1-9:79">all_samples.tsv rapidrun input is now in a <code data-sourcepos="9:47-9:49">csv</code> format with <code data-sourcepos="9:65-9:65">;</code> as separator</li>
</ul>2020-09-01T14:19:45Zpeguerinpierre-edouard.guerin@cefe.cnrs.frhttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/tags/1.0.11.0.1V1.0.1<h2 data-sourcepos="2:1-2:32" dir="auto">
<a id="user-content-version-101-31th-aug-2020" class="anchor" href="#version-101-31th-aug-2020" aria-hidden="true"></a>VERSION 1.0.1 - 31th aug 2020</h2>
<h3 data-sourcepos="3:1-3:9" dir="auto">
<a id="user-content-added" class="anchor" href="#added" aria-hidden="true"></a>Added</h3>
<ul data-sourcepos="4:1-7:0" dir="auto">
<li data-sourcepos="4:1-4:54">blacklist runs or projects from 'rapidrun' .tsv file</li>
<li data-sourcepos="5:1-5:56">convert otu.table into otu.fasta at step 05_clustering</li>
<li data-sourcepos="6:1-7:0">step 06_assignment taxonomic assignment</li>
</ul>
<h3 data-sourcepos="8:1-8:11" dir="auto">
<a id="user-content-changed" class="anchor" href="#changed" aria-hidden="true"></a>Changed</h3>
<ul data-sourcepos="9:1-13:0" dir="auto">
<li data-sourcepos="9:1-9:31">configfile has blacklist keys</li>
<li data-sourcepos="10:1-10:47">configfile has reference database information</li>
<li data-sourcepos="11:1-11:44">final output is <code data-sourcepos="11:20-11:23">.csv</code> instead of <code data-sourcepos="11:38-11:43">.table</code>
</li>
<li data-sourcepos="12:1-13:0">script <code data-sourcepos="12:11-12:19">rename.sh</code> to automatically rename output files with a prefix</li>
</ul>
<h3 data-sourcepos="14:1-14:11" dir="auto">
<a id="user-content-removed" class="anchor" href="#removed" aria-hidden="true"></a>Removed</h3>
<ul data-sourcepos="15:1-15:28" dir="auto">
<li data-sourcepos="15:1-15:28">old rapidrun tables <code data-sourcepos="15:24-15:27">.rrr</code>
</li>
</ul>2020-08-31T08:46:14Zpeguerinpierre-edouard.guerin@cefe.cnrs.frhttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/tags/1.0.01.0.0version 1.0.0<h2 data-sourcepos="1:1-1:31" dir="auto">
<a id="user-content-version-100-6th-feb-2020" class="anchor" href="#version-100-6th-feb-2020" aria-hidden="true"></a>VERSION 1.0.0 - 6th feb 2020</h2>
<h3 data-sourcepos="2:1-2:9" dir="auto">
<a id="user-content-added" class="anchor" href="#added" aria-hidden="true"></a>Added</h3>
<ul data-sourcepos="3:1-4:0" dir="auto">
<li data-sourcepos="3:1-4:0">Complete workflow 04_cat_quality dedicated to generate .qual files</li>
</ul>
<h3 data-sourcepos="5:1-5:11" dir="auto">
<a id="user-content-changed" class="anchor" href="#changed" aria-hidden="true"></a>Changed</h3>
<ul data-sourcepos="6:1-7:0" dir="auto">
<li data-sourcepos="6:1-7:0">main.sh argument CONFIGFILE is constant</li>
</ul>
<h3 data-sourcepos="8:1-8:11" dir="auto">
<a id="user-content-removed" class="anchor" href="#removed" aria-hidden="true"></a>Removed</h3>
<ul data-sourcepos="9:1-10:0" dir="auto">
<li data-sourcepos="9:1-10:0">Files .qual are not generated anymore at demultiplexing step</li>
</ul>2020-02-06T12:59:32Zpeguerinpierre-edouard.guerin@cefe.cnrs.fr