{% extends "base.html" %} {% block content %}

Sample: {{ project }}
Type: {{ type }}
Pipeline: {{ pipeline_name }}

Input
| Details
| FastQC

{{ dataset }}

Here are some basic statistics about the raw data. The A, C, G, T, N rows report the percentage of each bases in the overall sequences

{{ sample_stats }}
{% if sample_image_r1 %}
{% endif %} {% if sample_image_r2 %}
{% endif %}
{# ================================================================= PHIX #} {% if cfg['bwa_phix'] and cfg['bwa_phix']['do'] == True %}

Phix content
| Details
| FastQC

{{ phix_section }}

Reads statistics after/before Phix removal (mapped means wiith Phix).

The A, C, G, T, N rows report the percentage of each bases in the overall sequences

{{ phix_stats }}
{% endif %} {# ============================================================ ADAPTERS #} {% if cfg['adapter_removal'] and cfg['adapter_removal']['do'] %}

Adapters
| Cutadapt report
| Details
| FastQC

Reads statistics after trimming and adapter removal. Again, the A, C, G, T, N rows report the percentage of each bases in the overall sequences

{{ cutadapt_stats1 }} {{ cutadapt_stats2 }} {% endif %} {# ============================================================= OUTPUT #} {% if output %}

Output

{{ output }}
{% endif %} {# ============================================================ TAXONOMY #} {% if kraken_pie %}

Taxonomic content
Details

Overview of the Taxonomic content of the reads. Click on the image to get an interactive and more detailled visualisation.


{% endif %} {# ==================================================================== DAG #} {% if workflow %}

Workflow

{% include 'workflow.html' %}
{% endif %} {# ======================================================== software Details #} {% if snakemake_stats %}

Running Stats
collapse/expand

{% endif %} {% if dependencies %}

Dependencies
collapse/expand

Python dependencies (Pypi) {{ dependencies }}
Dependencies downloaded from bioconda requirements
{% endif %} {% endblock %}