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genotoul-bioinfo
ng6
Commits
11250b33
Commit
11250b33
authored
Jul 25, 2019
by
Maxime Manno
🍜
Browse files
Merge branch 'ng6_ontqc-update' into 'master'
Add N10 read lenght to the ont_qc run status See merge request
!27
parents
ce861266
a141658d
Changes
2
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ui/nG6/pi1/analyzes/Run_stats.tpl
View file @
11250b33
...
...
@@ -386,6 +386,10 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<li><strong>
N90 read length
</strong>
:
90% of all bases come from reads longer than this value.
</li>
</li>
<li><strong>
N10 read length
</strong>
:
10% of all bases come from reads longer than this value.
</li>
<li><strong>
Mean read quality
</strong>
:
The mean quality (qscore ONT) for this Flow Cell.
</li>
...
...
workflows/ont_qc/components/run_stats.py
View file @
11250b33
...
...
@@ -73,6 +73,7 @@ class Run_stats (Analysis):
if
parts
[
0
]
==
"mean_read_length"
:
stats
[
"mean_read_length"
]
=
parts
[
1
]
if
parts
[
0
]
==
"N50_read_length"
:
stats
[
"N50_read_length"
]
=
parts
[
1
]
if
parts
[
0
]
==
"N90_read_length"
:
stats
[
"N90_read_length"
]
=
parts
[
1
]
if
parts
[
0
]
==
"N10_read_length"
:
stats
[
"N10_read_length"
]
=
parts
[
1
]
if
parts
[
0
]
==
"mean_read_quality"
:
stats
[
"mean_read_quality"
]
=
parts
[
1
]
if
parts
[
0
]
==
"mean_yield_per_sec"
:
stats
[
"mean_yield_per_sec"
]
=
parts
[
1
]
if
parts
[
0
]
==
"longread1"
:
stats
[
"longread1"
]
=
parts
[
1
]
...
...
@@ -86,6 +87,7 @@ class Run_stats (Analysis):
if
parts
[
0
]
==
"mean_read_length_Q7"
:
stats
[
"mean_read_length_Q7"
]
=
parts
[
1
]
if
parts
[
0
]
==
"N50_read_length_Q7"
:
stats
[
"N50_read_length_Q7"
]
=
parts
[
1
]
if
parts
[
0
]
==
"N90_read_length_Q7"
:
stats
[
"N90_read_length_Q7"
]
=
parts
[
1
]
if
parts
[
0
]
==
"N10_read_length_Q7"
:
stats
[
"N10_read_length_Q7"
]
=
parts
[
1
]
if
parts
[
0
]
==
"mean_read_quality_Q7"
:
stats
[
"mean_read_quality_Q7"
]
=
parts
[
1
]
if
parts
[
0
]
==
"mean_yield_per_sec_Q7"
:
stats
[
"mean_yield_per_sec_Q7"
]
=
parts
[
1
]
if
parts
[
0
]
==
"longread1_Q7"
:
stats
[
"longread1_Q7"
]
=
parts
[
1
]
...
...
@@ -99,6 +101,7 @@ class Run_stats (Analysis):
if
parts
[
0
]
==
"mean_read_length_Q9"
:
stats
[
"mean_read_length_Q9"
]
=
parts
[
1
]
if
parts
[
0
]
==
"N50_read_length_Q9"
:
stats
[
"N50_read_length_Q9"
]
=
parts
[
1
]
if
parts
[
0
]
==
"N90_read_length_Q9"
:
stats
[
"N90_read_length_Q9"
]
=
parts
[
1
]
if
parts
[
0
]
==
"N10_read_length_Q9"
:
stats
[
"N10_read_length_Q9"
]
=
parts
[
1
]
if
parts
[
0
]
==
"mean_read_quality_Q9"
:
stats
[
"mean_read_quality_Q9"
]
=
parts
[
1
]
if
parts
[
0
]
==
"mean_yield_per_sec_Q9"
:
stats
[
"mean_yield_per_sec_Q9"
]
=
parts
[
1
]
if
parts
[
0
]
==
"longread1_Q9"
:
stats
[
"longread1_Q9"
]
=
parts
[
1
]
...
...
@@ -165,6 +168,7 @@ class Run_stats (Analysis):
"mean_read_length"
,
"N50_read_length"
,
"N90_read_length"
,
"N10_read_length"
,
"mean_read_quality"
,
"mean_yield_per_sec"
,
"longread1"
,
...
...
@@ -183,6 +187,7 @@ class Run_stats (Analysis):
"mean_read_length_Q7"
,
"N50_read_length_Q7"
,
"N90_read_length_Q7"
,
"N10_read_length_Q7"
,
"mean_read_quality_Q7"
,
"mean_yield_per_sec_Q7"
,
"longread1_Q7"
,
...
...
@@ -201,6 +206,7 @@ class Run_stats (Analysis):
"mean_read_length_Q9"
,
"N50_read_length_Q9"
,
"N90_read_length_Q9"
,
"N10_read_length_Q9"
,
"mean_read_quality_Q9"
,
"mean_yield_per_sec_Q9"
,
"longread1_Q9"
,
...
...
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