From 36e56128ff717559211be4f3345243b6af9af5b3 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 19 Jul 2024 13:34:53 +1200 Subject: [PATCH 1/2] Created summary presence/absence tables for NCBI FCS modules --- CHANGELOG.md | 3 ++ .../templates/ncbi_fcs_adaptor/dropdown.html | 1 + .../ncbi_fcs_adaptor/ncbi_fcs_adaptor.html | 4 ++- .../ncbi_fcs_adaptor/report_contents.html | 9 +++--- .../ncbi_fcs_adaptor/summary_contents.html | 32 +++++++++++++++++++ .../templates/ncbi_fcs_gx/dropdown.html | 1 + .../templates/ncbi_fcs_gx/ncbi_fcs_gx.html | 6 ++-- .../ncbi_fcs_gx/report_contents.html | 9 +++--- .../ncbi_fcs_gx/summary_contents.html | 32 +++++++++++++++++++ 9 files changed, 83 insertions(+), 14 deletions(-) create mode 100644 bin/report_modules/templates/ncbi_fcs_adaptor/summary_contents.html create mode 100644 bin/report_modules/templates/ncbi_fcs_gx/summary_contents.html diff --git a/CHANGELOG.md b/CHANGELOG.md index 94edf630..4022d699 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,9 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` +1. Created summary presence/absence tables for NCBI FCS modules [#88](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/88) + ### `Fixed` 1. Fixed a bug where `intron_length_distribution` was used instead of `cds_length_distribution` when creating the CDS Length Distribution Graph [#95](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/95) +2. Fixed a bug where 'Subsequent pipeline modules are skipped.' was printed in the `report.html` even when `contamination_stops_pipeline` was set to false ### `Dependencies` diff --git a/bin/report_modules/templates/ncbi_fcs_adaptor/dropdown.html b/bin/report_modules/templates/ncbi_fcs_adaptor/dropdown.html index 9f21bc26..fda13538 100644 --- a/bin/report_modules/templates/ncbi_fcs_adaptor/dropdown.html +++ b/bin/report_modules/templates/ncbi_fcs_adaptor/dropdown.html @@ -1,6 +1,7 @@
+ {% set str_hap = 'hap' %} {% for item in range(all_stats_dicts["NCBI_FCS_GX"]|length) %}
- {% include 'ncbi_fcs_gx/dropdown.html' %} {% include 'ncbi_fcs_gx/report_contents.html' %} + {% include 'ncbi_fcs_gx/dropdown.html' %} + {% include 'ncbi_fcs_gx/summary_contents.html' %} + {% include 'ncbi_fcs_gx/report_contents.html' %}
diff --git a/bin/report_modules/templates/ncbi_fcs_gx/report_contents.html b/bin/report_modules/templates/ncbi_fcs_gx/report_contents.html index c99c5622..a7d6f27d 100644 --- a/bin/report_modules/templates/ncbi_fcs_gx/report_contents.html +++ b/bin/report_modules/templates/ncbi_fcs_gx/report_contents.html @@ -1,9 +1,8 @@ -{% set vars = {'is_first': True} %} {% for item in range(all_stats_dicts["NCBI_FCS_GX"]|length) %} {% set active_text = -'display: block' if vars.is_first else 'display: none' %} +{% for item in range(all_stats_dicts["NCBI_FCS_GX"]|length) %}
@@ -11,7 +10,7 @@
{%if all_stats_dicts['NCBI_FCS_GX'][item]['did_detect_contamination'] %}
-

Contamination detected. Subsequent pipeline modules are skipped.

+

Contamination detected.{%if all_stats_dicts['PARAMS_DICT']['contamination_stops_pipeline'] %} Subsequent pipeline modules are skipped.{% endif %}

{{ all_stats_dicts['NCBI_FCS_GX'][item]['report_table_html'] }}
@@ -46,4 +45,4 @@
-{% if vars.update({'is_first': False}) %} {% endif %} {% endfor %} +{% endfor %} diff --git a/bin/report_modules/templates/ncbi_fcs_gx/summary_contents.html b/bin/report_modules/templates/ncbi_fcs_gx/summary_contents.html new file mode 100644 index 00000000..706a6d5d --- /dev/null +++ b/bin/report_modules/templates/ncbi_fcs_gx/summary_contents.html @@ -0,0 +1,32 @@ +
+
+
+
Summary
+
+ +
+
+ + + + + + + + + {% for item in range(all_stats_dicts["NCBI_FCS_GX"]|length) %} + + + + + {% endfor %} + +
AssemblyContaminated?
+ {{ all_stats_dicts['NCBI_FCS_GX'][item]['hap'] }} + + {%if all_stats_dicts['NCBI_FCS_GX'][item]['did_detect_contamination'] %}Yes!{% else %}No{% endif %} +
+
+
+
+
From c9e791d6e97052195b2639820fa1edc05c000f98 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 19 Jul 2024 13:54:29 +1200 Subject: [PATCH 2/2] Fixed linting --- .nf-core.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.nf-core.yml b/.nf-core.yml index d18bcef6..f9b5f934 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -21,7 +21,6 @@ lint: - manifest.homePage multiqc_config: False template_strings: False - multiqc_config: False nf_core_version: 2.14.1 repository_type: pipeline template: