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Fix issues and improvements from first release

Merged Jules Sabban requested to merge dev_Jules into master
17 files
+ 732
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@@ -15,6 +15,24 @@ show_analysis_time: False
## Number formatting
thousandsSep_format: " "
## General Statistics table
table_columns_visible:
Duplicats: False
ContaminationSearch - RNA: True
samtools: False
ReadsStats:
percent_duplicates: False
percent_fails: False
AlignmentStat:
avg_gc: False
1_x_pc: True
5_x_pc: True
10_x_pc: True
50_x_pc: False
mapped_reads: False
total_reads: True
general_error_rate: True
## Sample name formatting
extra_fn_clean_exts:
- "_filtered"
@@ -33,18 +51,13 @@ report_section_order:
order: -1000
summary:
order: -1001
module_order:
- fastqc:
name: "ReadsStats"
#info: "Analysis performed with FastQC, which is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge"
href: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
target: "FastQC"
- qualimap:
name: "AlignmentStat"
#info: "Analysis performed with QualiMap"
href: "http://qualimap.bioinfo.cipf.es/"
target: "QualiMap"
- samtools:
- fastp:
name: "Duplicats"
@@ -54,6 +67,19 @@ module_order:
name: "ContaminationSearch"
#info: "This section shows the module with different files"
target: "FastQ-Screen"
- sortmerna:
name: "ContaminationSearch - rRNA"
target: "SortMeRNA"
- qualimap:
name: "AlignmentStat"
#info: "Analysis performed with QualiMap"
href: "http://qualimap.bioinfo.cipf.es/"
target: "QualiMap"
- salmon:
name: "AlignmentStat"
href: "https://combine-lab.github.io/salmon/"
target: "Salmon"
# Pattern
sp:
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