Commit 4b82b6aa authored by Mattia Forneris's avatar Mattia Forneris

Merge branch 'final_branch' into 'master'

trying new tables format

See merge request !4
parents b064efec 8e47d2ad
......@@ -414,108 +414,91 @@ summary {
<table>
<thead>
<tr class="header">
<th>Software</th>
<th>version</th>
<th>conda install command</th>
<th></th>
<th align="left">Software</th>
<th align="left">version</th>
<th align="center">conda install command</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>fastqc</td>
<td>0.11.5</td>
<td>conda install -c bioconda fastqc</td>
<td></td>
<td align="left">fastqc</td>
<td align="left">0.11.5</td>
<td align="center">conda install -c bioconda fastqc</td>
</tr>
<tr class="even">
<td>multiqc</td>
<td>1.6</td>
<td>conda install -c bioconda multiqc</td>
<td></td>
<td align="left">multiqc</td>
<td align="left">1.6</td>
<td align="center">conda install -c bioconda multiqc</td>
</tr>
<tr class="odd">
<td>trimgalore</td>
<td>0.5.0</td>
<td>conda install -c bioconda trim-galore</td>
<td></td>
<td align="left">trimgalore</td>
<td align="left">0.5.0</td>
<td align="center">conda install -c bioconda trim-galore</td>
</tr>
<tr class="even">
<td>bwa</td>
<td>0.7.17</td>
<td>conda install -c bioconda bwa</td>
<td></td>
<td align="left">bwa</td>
<td align="left">0.7.17</td>
<td align="center">conda install -c bioconda bwa</td>
</tr>
<tr class="odd">
<td>samtools</td>
<td>1.9</td>
<td>conda install -c bioconda samtools</td>
<td></td>
<td align="left">samtools</td>
<td align="left">1.9</td>
<td align="center">conda install -c bioconda samtools</td>
</tr>
<tr class="even">
<td>picard</td>
<td>2.16.0</td>
<td>conda install -c bioconda picard</td>
<td></td>
<td align="left">picard</td>
<td align="left">2.16.0</td>
<td align="center">conda install -c bioconda picard</td>
</tr>
<tr class="odd">
<td>gatk</td>
<td>4.1.0.0</td>
<td>Dowload from <a href="https://software.broadinstitute.org/gatk/download/index">GATK website</a></td>
<td></td>
<td align="left">gatk</td>
<td align="left">4.1.0.0</td>
<td align="center">Dowload from <a href="https://software.broadinstitute.org/gatk/download/index">GATK website</a></td>
</tr>
<tr class="even">
<td>vcftools</td>
<td>0.1.14</td>
<td>conda install -c bioconda vcftools</td>
<td></td>
<td align="left">vcftools</td>
<td align="left">0.1.14</td>
<td align="center">conda install -c bioconda vcftools</td>
</tr>
<tr class="odd">
<td>tabix</td>
<td>1.9</td>
<td>conda install -c bioconda tabix</td>
<td></td>
<td align="left">tabix</td>
<td align="left">1.9</td>
<td align="center">conda install -c bioconda tabix</td>
</tr>
<tr class="even">
<td>bgzip</td>
<td>1.9</td>
<td>conda install -c bioconda htslib</td>
<td></td>
<td align="left">bgzip</td>
<td align="left">1.9</td>
<td align="center">conda install -c bioconda htslib</td>
</tr>
<tr class="odd">
<td>bcftools</td>
<td>1.9</td>
<td>conda install -c bioconda bcftools</td>
<td></td>
<td align="left">bcftools</td>
<td align="left">1.9</td>
<td align="center">conda install -c bioconda bcftools</td>
</tr>
<tr class="even">
<td>snpeff</td>
<td>4.3T</td>
<td>Dowload from <a href="http://snpeff.sourceforge.net/">SnpEff website</a></td>
<td></td>
<td align="left">snpeff</td>
<td align="left">4.3T</td>
<td align="center">Dowload from <a href="http://snpeff.sourceforge.net/">SnpEff website</a></td>
</tr>
<tr class="odd">
<td>snpsift</td>
<td>4.3T</td>
<td>Dowload from <a href="http://snpeff.sourceforge.net/">SnpEff website</a></td>
<td></td>
<td align="left">snpsift</td>
<td align="left">4.3T</td>
<td align="center">Dowload from <a href="http://snpeff.sourceforge.net/">SnpEff website</a></td>
</tr>
<tr class="even">
<td>bedtools</td>
<td>2.26.0</td>
<td>conda install -c bioconda bedtools</td>
<td></td>
<td align="left">bedtools</td>
<td align="left">2.26.0</td>
<td align="center">conda install -c bioconda bedtools</td>
</tr>
<tr class="odd">
<td>plink</td>
<td>1.90b3</td>
<td>conda install -c bioconda plink</td>
<td></td>
<td align="left">plink</td>
<td align="left">1.90b3</td>
<td align="center">conda install -c bioconda plink</td>
</tr>
<tr class="even">
<td>rscript</td>
<td>3.4.3</td>
<td>Dowload from <a href="https://cran.uni-muenster.de/">R website</a></td>
<td></td>
<td align="left">rscript</td>
<td align="left">3.4.3</td>
<td align="center">Dowload from <a href="https://cran.uni-muenster.de/">R website</a></td>
</tr>
</tbody>
</table>
......
......@@ -43,7 +43,7 @@ Theis software is necessary to run the pipeline. In general, you need an [Anacon
The table below lists the software necessary to run the pipeline, the version used in this pipeline and the conda command to install the software (simply run in a shell to install). If you want to install a specific version of the softare use '=='. E.g. to install version 0.11.5 of fastqc run 'conda install -c bioconda fastqc==0.11.5'
| Software | version | conda install command |
|---|---|---|---|
|:---|:---|:---:|
| fastqc | 0.11.5 | conda install -c bioconda fastqc |
| multiqc | 1.6 | conda install -c bioconda multiqc |
| trimgalore | 0.5.0 | conda install -c bioconda trim-galore |
......
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