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Collapse FALCO and FASTQC sections, move FALCO/FASTQC sections together

This commit is contained in:
James Fellows Yates 2023-03-06 10:37:09 +01:00
parent 1f1c63bb51
commit 9ed384e0f2

View file

@ -51,37 +51,23 @@ sp:
top_modules:
- "fastqc":
name: "FastQC (pre-Trimming)"
name: "FastQC / Falco (pre-Trimming)"
path_filters:
- "*raw*"
path_filters_exclude:
- "*falco*"
- "*processed*"
extra: "If used in this run, Falco is a drop-in replacement for FastQC producing the same output, written by Guilherme de Sena Brandine and Andrew D. Smith."
- "fastqc":
name: "Falco (pre-Trimming)"
name: "FastQC / Falco (post-Trimming)"
path_filters:
- "*raw*"
- "*[falco]*"
path_filters_exclude:
- "*processed*"
path_filters_exclude:
- "*raw*"
extra: "If used in this run, Falco is a drop-in replacement for FastQC producing the same output, written by Guilherme de Sena Brandine and Andrew D. Smith."
- "fastp"
- "adapterRemoval"
- "porechop":
extra: ": if you get the error message 'Error - was not able to plot data.' this means that porechop did not detect any adapters and therefore no statistics generated."
- "fastqc":
name: "FastQC (post-Trimming)"
path_filters:
- "*processed*"
path_filters_exclude:
- "*falco*"
- "*raw*"
- "fastqc":
name: "Falco (post-Trimming)"
path_filters:
- "*processed*"
- "*falco*"
path_filters_exclude:
- "*raw*"
- "bbduk"
- "prinseqplusplus"
- "filtlong"
@ -121,19 +107,20 @@ top_modules:
#It is not possible to set placement for custom kraken and centrifuge columns.
table_columns_placement:
FastQC (pre-Trimming):
FastQC / Falco (pre-Trimming):
total_sequences: 100
avg_sequence_length: 110
median_sequence_length: 120
percent_duplicates: 130
percent_gc: 140
percent_fails: 150
Falco (pre-Trimming):
FastQC / Falco (post-Trimming):
total_sequences: 200
avg_sequence_length: 210
percent_duplicates: 220
percent_gc: 230
percent_fails: 240
median_sequence_length: 220
percent_duplicates: 230
percent_gc: 240
percent_fails: 250
fastp:
pct_adapter: 300
pct_surviving: 310
@ -157,19 +144,6 @@ table_columns_placement:
Middle Split Percent: 460
Filtlong:
Target bases: 500
FastQC (post-Trimming):
total_sequences: 600
avg_sequence_length: 610
median_sequence_length: 620
percent_duplicates: 630
percent_gc: 640
percent_fails: 650
Falco (post-Trimming):
total_sequences: 700
avg_sequence_length: 710
percent_duplicates: 720
percent_gc: 730
percent_fails: 740
BBDuk:
Input reads: 800
Total Removed bases percent: 810
@ -221,25 +195,18 @@ table_columns_placement:
"Number of ext-mOTUs": 1880
table_columns_visible:
FastQC (pre-Trimming):
FastQC / Falco (pre-Trimming):
total_sequences: True
avg_sequence_length: True
percent_duplicates: True
percent_gc: True
percent_fails: False
Falco (pre-Trimming):
FastQC / Falco (post-Trimming):
total_sequences: True
avg_sequence_length: True
percent_duplicates: True
percent_gc: True
percent_duplicates: False
percent_gc: False
percent_fails: False
fastp:
pct_adapter: True
pct_surviving: True
pct_duplication: False
after_filtering_gc_content: False
after_filtering_q30_rate: False
after_filtering_q30_bases: False
porechop:
Input reads: False
Start Trimmed:
@ -248,6 +215,13 @@ table_columns_visible:
End Trimmed Percent: True
Middle Split: False
Middle Split Percent: True
fastp:
pct_adapter: True
pct_surviving: True
pct_duplication: False
after_filtering_gc_content: False
after_filtering_q30_rate: False
after_filtering_q30_bases: False
Filtlong:
Target bases: True
Adapter Removal:
@ -255,18 +229,6 @@ table_columns_visible:
percent_aligned: True
percent_collapsed: True
percent_discarded: False
FastQC (post-Trimming):
total_sequences: True
avg_sequence_length: True
percent_duplicates: False
percent_gc: False
percent_fails: False
Falco (post-Trimming):
total_sequences: True
avg_sequence_length: True
percent_duplicates: False
percent_gc: False
percent_fails: False
BBDuk:
Input reads: False
Total Removed bases Percent: False
@ -294,25 +256,13 @@ table_columns_visible:
motus: False
table_columns_name:
FastQC (pre-Trimming):
FastQC / Falco (pre-Trimming):
total_sequences: "Nr. Input Reads"
avg_sequence_length: "Length Input Reads"
percent_gc: "% GC Input Reads"
percent_duplicates: "% Dups Input Reads"
percent_fails: "% Failed Input Reads"
Falco (pre-Trimming):
total_sequences: "Nr. Input Reads"
avg_sequence_length: "Length Input Reads"
percent_gc: "% GC Input Reads"
percent_duplicates: "% Dups Input Reads"
percent_fails: "% Failed Input Reads"
FastQC (post-Trimming):
total_sequences: "Nr. Processed Reads"
avg_sequence_length: "Length Processed Reads"
percent_gc: "% GC Processed Reads"
percent_duplicates: "% Dups Processed Reads"
percent_fails: "% Failed Processed Reads"
Falco (post-Trimming):
FastQC / Falco (post-Trimming):
total_sequences: "Nr. Processed Reads"
avg_sequence_length: "Length Processed Reads"
percent_gc: "% GC Processed Reads"
@ -330,7 +280,8 @@ extra_fn_clean_exts:
- ".bbduk"
- ".unmapped"
- "_filtered"
- "_processed"
- type: remove
pattern: "_falco"
section_comments:
general_stats: "By default, all read count columns are displayed as millions (M) of reads."