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genotoul-bioinfo
ng6
Commits
14d919ed
Commit
14d919ed
authored
Apr 10, 2019
by
Maxime Manno
🍜
Browse files
Add new version of ONT run stats analysis : new graph, new visu.
old runs are still ok
parent
e0889190
Changes
4
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ui/nG6/pi1/analyzes/Run_stats.tpl
View file @
14d919ed
...
...
@@ -16,6 +16,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
*}
{
extends
file
=
'AnalysisTemplate.tpl'
}
{
block
name
=
params
}
{
assign
var
=
"params"
value
=
" "
|
explode
:
$analyse.params
}
{
foreach
from
=
$analyse_results
key
=
sample
item
=
sample_results
}
...
...
@@ -48,18 +49,39 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
block
name
=
results_title
}
Reports
{/
block
}
{
block
name
=
results
}
{
assign
var
=
"analyse_results_sorted"
value
=
$analyse_results
[
"ONT_sample"
]|@
ksort
}
{* find if user is CTD *}
<input
type=
"hidden"
id=
"user_login"
value=
"
{
$user_login
}
"
/>
{
if
$user_login
==
"CTD"
}
{
assign
var
=
"isCTD"
value
=
true
}
{
else
}
{
assign
var
=
"isCTD"
value
=
false
}
{/
if
}
{
assign
var
=
"template_status"
value
=
$analyse_results
[
"metrics"
].
analyse_info
.
template_status
}
{
assign
var
=
"metrics"
value
=
$analyse_results
[
"metrics"
]
}
{
assign
var
=
"basic"
value
=
$analyse_results
[
"ONT_sample"
].
basic
}
{
assign
var
=
"quality"
value
=
$analyse_results
[
"ONT_sample"
].
quality
}
{
assign
var
=
"plots"
value
=
$analyse_results
[
"ONT_sample"
].
plots
}
{
assign
var
=
"plots_barcode"
value
=
$analyse_results
[
"ONT_sample"
].
plots_barcode
}
{
if
$template_status
==
"2.0"
}
{
assign
var
=
"sample_name"
value
=
$analyse_results
[
"metrics"
].
analyse_info
.
Sample_name
}
{
assign
var
=
"rawdata"
value
=
$analyse_results
[
$sample_name
].
rawdata
}
{
assign
var
=
'rawdata_headers'
value
=
','
|
explode
:
$metrics
[
'rawdata'
].
headers
}
{
assign
var
=
'rawdata_count'
value
=
$rawdata_headers
|@
count
}
{
assign
var
=
"Q7"
value
=
$analyse_results
[
$sample_name
].
Q7
}
{
assign
var
=
'Q7_headers'
value
=
','
|
explode
:
$metrics
[
'Q7'
].
headers
}
{
assign
var
=
'Q7_count'
value
=
$Q7_headers
|@
count
}
{
assign
var
=
"Q9"
value
=
$analyse_results
[
$sample_name
].
Q9
}
{
assign
var
=
'Q9_headers'
value
=
','
|
explode
:
$metrics
[
'Q9'
].
headers
}
{
assign
var
=
'Q9_count'
value
=
$Q9_headers
|@
count
}
{
else
}
{
assign
var
=
"sample_name"
value
=
"ONT_sample"
}
{
assign
var
=
"basic"
value
=
$analyse_results
[
$sample_name
].
basic
}
{
assign
var
=
"quality"
value
=
$analyse_results
[
$sample_name
].
quality
}
{
assign
var
=
'basic_headers'
value
=
','
|
explode
:
$metrics
[
'basic'
].
headers
}
{
assign
var
=
'quality_headers'
value
=
','
|
explode
:
$metrics
[
'quality'
].
headers
}
{
assign
var
=
'quality_count'
value
=
$quality_headers
|@
count
}
{
assign
var
=
'basic_count'
value
=
$basic_headers
|@
count
}
{/
if
}
{
assign
var
=
'basic_headers'
value
=
','
|
explode
:
$metrics
[
'basic'
].
headers
}
{
assign
var
=
'basic_count'
value
=
$basic_headers
|@
count
}
{
assign
var
=
'quality_headers'
value
=
','
|
explode
:
$metrics
[
'quality'
].
headers
}
{
assign
var
=
'quality_count'
value
=
$quality_headers
|@
count
}
{
assign
var
=
"analyse_results_sorted"
value
=
$analyse_results
[
$sample_name
]|@
ksort
}
{
assign
var
=
"plots"
value
=
$analyse_results
[
$sample_name
].
plots
}
{
assign
var
=
"plots_barcode"
value
=
$analyse_results
[
$sample_name
].
plots_barcode
}
{
assign
var
=
'plots_headers'
value
=
','
|
explode
:
$metrics
[
'plots'
].
headers
}
{
assign
var
=
'plots_count'
value
=
$plots_headers
|@
count
}
...
...
@@ -72,10 +94,9 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
assign
var
=
'barcode_name_sample'
value
=
','
|
explode
:
$metrics
[
'barcode'
].
names
|@
ksort
}
{
assign
var
=
'barcode_name_count'
value
=
$barcode_name_sample
|@
count
}
{*debug*}
<legend>
Analyse results report - Sample name :
{
$sample_name
}
</legend>
<legend>
Analyse results report - Sample name :
{
$descriptions.sample_1
}
</legend>
{
if
$template_status
!=
"2.0"
}
{
assign
var
=
'data_col'
value
=
2
}
<div
class=
"row"
>
{
if
$metrics
[
'basic'
]
}
...
...
@@ -88,6 +109,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
if
(
$head
==
'median_yield_per_sec'
)
}
<td><label>
{
$head
|
replace
:
'_'
:
' '
}
</label></td>
<td>
{($basic.$head)|number_format:2:',':' '}
</td>
{
elseif
$head
==
'nb_actif_channel'
}
{
else
}
<td><label>
{
$head
|
replace
:
'_'
:
' '
}
</label></td>
<td>
{($basic.$head)|number_format:0:',':' '}
</td>
...
...
@@ -152,16 +174,142 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
</div>
{/
if
}
</div>
{
else
}
{
assign
var
=
'data_col'
value
=
2
}
<div
class=
"row"
>
{
if
$metrics
[
'rawdata'
]
}
<div
class=
"col-md-4 col-lg-4"
>
<table
id=
"ont_table_rawdata"
class=
"table table-striped table-bordered dataTable"
>
<thead><tr><th
colspan=
"2"
><h4>
Rawdata metrics report
</h4></thead></tr></th>
<tbody>
{
foreach
from
=
$rawdata_headers
key
=
k
item
=
head
}
<tr>
{
if
(
$head
==
'mean_read_quality'
)
}
<td><label>
{
$head
|
replace
:
'_'
:
' '
}
</label></td>
<td>
{($rawdata.$head)|number_format:2:',':' '}
</td>
{
else
}
<td><label>
{
$head
|
replace
:
'_'
:
' '
}
</label></td>
<td>
{($rawdata.$head)|number_format:0:',':' '}
</td>
{/
if
}
</tr>
{
$data_col
=
$data_col
+
1
}
{/
foreach
}
</body>
</table>
</div>
{/
if
}
{
if
$metrics
[
'Q7'
]
and
$metrics
[
'Q7'
]
}
<div
class=
"col-md-4 col-lg-4"
>
<table
id=
"ont_table_filtered"
class=
"table table-striped table-bordered dataTable"
>
<thead><tr><th
colspan=
"2"
><h4>
Filtered Q7 metrics report
</h4></thead></tr></th>
<tbody>
{
foreach
from
=
$Q7_headers
key
=
k
item
=
head
}
<tr>
{
if
(
$head
==
'mean_read_quality_Q7'
)
}
<td><label>
{
$head
|
replace
:
'_'
:
' '
}
</label></td>
<td>
{($Q7.$head)|number_format:2:',':' '}
</td>
{
elseif
(
$head
==
'N50_read_length_Q7'
)
}
<td><label>
N50 read length Q7
</label></td>
<td>
{($Q7.$head)|number_format:0:',':' '}
{
elseif
$head
|
strstr
:
"nb_reads_Q7"
}
<td><label>
{
$head
|
replace
:
'_'
:
' '
}
</label></td>
<td>
{($Q7.$head)|number_format:0:',':' '} ({($Q7.$head / $rawdata.nb_reads*100)|number_format:2:',':' '}%)
</td>
{
elseif
$head
|
strstr
:
"total_bases_Q7"
}
<td><label>
{
$head
|
replace
:
'_'
:
' '
}
</label></td>
<td>
{($Q7.$head)|number_format:0:',':' '} ({($Q7.$head / $rawdata.total_bases*100)|number_format:2:',':' '}%)
</td>
{
else
}
<td><label>
{
$head
|
replace
:
'_'
:
' '
}
</label></td>
<td>
{($Q7.$head)|number_format:0:',':' '}
{/
if
}
</tr>
{
$data_col
=
$data_col
+
1
}
{/
foreach
}
</tbody>
<thead><tr><th
colspan=
"2"
><h4>
Filtered Q9 metrics report
</h4></thead></tr></th>
<tbody>
{
foreach
from
=
$Q9_headers
key
=
k
item
=
head
}
<tr>
{
if
(
$head
==
'mean_read_quality_Q9'
)
}
<td><label>
{
$head
|
replace
:
'_'
:
' '
}
</label></td>
<td>
{($Q9.$head)|number_format:2:',':' '}
</td>
{
elseif
(
$head
==
'N50_read_length_Q9'
)
}
<td><label>
N50 read length Q9
</label></td>
<td>
{($Q9.$head)|number_format:0:',':' '}
{
elseif
$head
|
strstr
:
"nb_reads_Q9"
}
<td><label>
{
$head
|
replace
:
'_'
:
' '
}
</label></td>
<td>
{($Q9.$head)|number_format:0:',':' '} ({($Q9.$head / $rawdata.nb_reads*100)|number_format:2:',':' '}%)
</td>
{
elseif
$head
|
strstr
:
"total_bases_Q9"
}
<td><label>
{
$head
|
replace
:
'_'
:
' '
}
</label></td>
<td>
{($Q9.$head)|number_format:0:',':' '} ({($Q9.$head / $rawdata.total_bases*100)|number_format:2:',':' '}%)
</td>
{
else
}
<td><label>
{
$head
|
replace
:
'_'
:
' '
}
</label></td>
<td>
{($Q9.$head)|number_format:0:',':' '}
{/
if
}
</tr>
{
$data_col
=
$data_col
+
1
}
{/
foreach
}
</tbody>
</table>
</div>
{/
if
}
{
if
$metrics
[
'plots'
]
}
<div
class=
"col-md-3 col-lg-3"
>
<table
id=
"ont_table_plot"
class=
"table table-striped table-bordered dataTable"
>
<thead><tr><th
colspan=
"2"
><h4>
Plots report
</h4></h4></thead></tr></th>
<tbody>
{
foreach
from
=
$plots_headers
key
=
k
item
=
head
}
<tr>
{
if
(
$head
==
'cumulyield'
)
}
<td><label>
Cumulate Yield per second
</label></td>
<td><a
class=
"imglink"
href=
"
{
$plots
.
$head
}
"
><i
class=
"glyphicon glyphicon-picture"
></i></a></td>
{
elseif
(
$head
==
'distriblength'
)
}
<td><label>
Length distribution
</label></td>
<td><a
class=
"imglink"
href=
"
{
$plots
.
$head
}
"
><i
class=
"glyphicon glyphicon-picture"
></i></a></td>
{
elseif
(
$head
==
'distriblength_bybases'
)
}
<td><label>
Length distribution by bases
</label></td>
<td><a
class=
"imglink"
href=
"
{
$plots
.
$head
}
"
><i
class=
"glyphicon glyphicon-picture"
></i></a></td>
{
elseif
(
$head
==
'distribquality'
)
}
<td><label>
Quality distribution
</label></td>
<td><a
class=
"imglink"
href=
"
{
$plots
.
$head
}
"
><i
class=
"glyphicon glyphicon-picture"
></i></a></td>
{/
if
}
{
if
$isCTD
==
true
}
{
if
(
$head
==
'seqrate'
)
}
<td><label>
Sequencing rate over time
</label></td>
<td><a
class=
"imglink"
href=
"
{
$plots
.
$head
}
"
><i
class=
"glyphicon glyphicon-picture"
></i></a></td>
{
elseif
(
$head
==
'channelbases'
)
}
<td><label>
FlowCell Channel overview for number of bases
</label></td>
<td><a
class=
"imglink"
href=
"
{
$plots
.
$head
}
"
><i
class=
"glyphicon glyphicon-picture"
></i></a></td>
{
elseif
(
$head
==
'channelreads'
)
}
<td><label>
FlowCell Channel overview for number of reads
</label></td>
<td><a
class=
"imglink"
href=
"
{
$plots
.
$head
}
"
><i
class=
"glyphicon glyphicon-picture"
></i></a></td>
{/
if
}
{/
if
}
</tr>
{
$data_col
=
$data_col
+
1
}
{/
foreach
}
{
if
$barcode_name_count
>
1
}
{
foreach
from
=
$plots_barcode_headers
key
=
k
item
=
head
}
<tr>
<td><label>
{
$head
|
replace
:
'_'
:
' '
}
</label></td>
<td><a
class=
"imglink"
href=
"
{
$plots_barcode
.
$head
}
"
><i
class=
"glyphicon glyphicon-picture"
></i></a></td>
</tr>
{
$data_col
=
$data_col
+
1
}
{/
foreach
}
{/
if
}
</tbody>
</table>
</div>
{/
if
}
</div>
{/
if
}
<br><br>
{*If there are barcodes file in the run*}
{
if
$barcode_name_count
>
1
}
<table
id=
"ont_stats_datatable"
class=
"table table-striped table-bordered dataTable analysis-result-table"
>
<table
id=
"ont_stats_datatable"
class=
"table table-striped table-bordered dataTable analysis-result-table"
style=
"white-space:nowrap;"
>
<thead>
<tr>
{
assign
var
=
"nb_samples"
value
=
$barcode_name_count
}
...
...
@@ -171,26 +319,50 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<tr>
{
assign
var
=
"th_id"
value
=
2
}
{
foreach
from
=
$barcode_headers
key
=
k
item
=
head
}
{
if
$head
==
'total_bases'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Total bases
</th>
{
elseif
$head
==
'nb_reads'
}
{
if
$head
==
'nb_reads'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Nb reads
</th>
{
elseif
$head
==
'median_read_length'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Median read length
</th>
{
elseif
$head
==
'median_read_quality'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Median read quality
</th>
{
elseif
$head
==
'total_bases'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Total bases
</th>
{
elseif
$head
==
'mean_read_length'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Mean read length
</th>
{
elseif
$head
==
'mean_read_quality'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Mean read quality
</th>
{
elseif
$head
==
'N50_read_length'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
N50 read length
</th>
{
elseif
$head
==
'barcode_score'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Barcode score
</th>
{
elseif
$head
==
'median_yield_per_sec'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Median yield per sec
</th>
{
elseif
(
$head
==
'nb_read_utils'
)
or
(
$head
==
'nb_read_useful_data'
)
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Nb reads useful data
</th>
{
elseif
(
$head
==
'total_bases_utils'
)
or
(
$head
==
'total_bases_useful_data'
)
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Total bases useful data
</th>
{
elseif
(
$head
==
'N50_read_length_useful_data'
)
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
N50 read length useful data
</th>
{
elseif
$head
==
'mean_yield_per_sec'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Mean yield per sec
</th>
{
elseif
$head
==
'nb_reads_Q7'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Nb reads Q7
</th>
{
elseif
$head
==
'total_bases_Q7'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Total bases Q7
</th>
{
elseif
$head
==
'mean_read_length_Q7'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Mean read length Q7
</th>
{
elseif
$head
==
'mean_read_quality_Q7'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Mean read quality Q7
</th>
{
elseif
$head
==
'N50_read_length_Q7'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
N50 read length Q7
</th>
{
elseif
$head
==
'barcode_score_Q7'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Barcode score Q7
</th>
{
elseif
$head
==
'mean_yield_per_sec_Q7'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Mean yield per sec Q7
</th>
{
elseif
$head
==
'nb_reads_Q9'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Nb reads Q9
</th>
{
elseif
$head
==
'total_bases_Q9'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Total bases Q9
</th>
{
elseif
$head
==
'mean_read_length_Q9'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Mean read length Q9
</th>
{
elseif
$head
==
'mean_read_quality_Q9'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Mean read quality Q9
</th>
{
elseif
$head
==
'N50_read_length_Q9'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
N50 read length Q9
</th>
{
elseif
$head
==
'barcode_score_Q9'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Barcode score Q9
</th>
{
elseif
$head
==
'mean_yield_per_sec_Q9'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Mean yield per sec Q9
</th>
{/
if
}
{
$th_id
=
$th_id
+
1
}
{/
foreach
}
...
...
@@ -207,26 +379,27 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<td
id=
'sample_
{
$i
}
_col_1'
class=
"sample_name"
>
{
$sample
}
</td>
{
$col_id
=
2
}
{
foreach
from
=
$barcode_headers
key
=
k
item
=
head
}
{
if
$head
==
'total_bases'
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:0:',':' '} ({($sample_results.$head / $basic.total_bases*100)|number_format:2:',':' '}%)
</th>
{
elseif
$head
==
'nb_reads'
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:0:',':' '} ({($sample_results.$head / $basic.nb_reads*100)|number_format:2:',':' '}%)
</th>
{
elseif
$head
==
'median_read_length'
}
{
if
$head
==
'nb_reads'
||
$head
==
'nb_reads_Q7'
||
$head
==
'nb_reads_Q9'
}
{
if
$template_status
==
"2.0"
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:0:',':' '} ({($sample_results.$head / $rawdata.nb_reads*100)|number_format:2:',':' '}%)
</th>
{
else
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:0:',':' '} ({($sample_results.$head / $basic.nb_reads*100)|number_format:2:',':' '}%)
</th>
{/
if
}
{
elseif
$head
==
'total_bases'
||
$head
==
'total_bases_Q7'
||
$head
==
'total_bases_Q9'
}
{
if
$template_status
==
"2.0"
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:0:',':' '} ({($sample_results.$head / $rawdata.total_bases*100)|number_format:2:',':' '}%)
</th>
{
else
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:0:',':' '} ({($sample_results.$head / $basic.total_bases*100)|number_format:2:',':' '}%)
</th>
{/
if
}
{
elseif
$head
==
'mean_read_length'
||
$head
==
'mean_read_length_Q7'
||
$head
==
'mean_read_length_Q9'
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:0:',':' '}
</th>
{
elseif
$head
==
'me
di
an_read_quality'
}
{
elseif
$head
==
'mean_read_quality
'
||
$head
==
'mean_read_quality_Q7'
||
$head
==
'mean_read_quality_Q9
'
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:1:',':' '}
</th>
{
elseif
$head
==
'N50_read_length'
}
{
elseif
$head
==
'N50_read_length'
||
$head
==
'N50_read_length_Q7'
||
$head
==
'N50_read_length_Q9'
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:0:',':' '}
</th>
{
elseif
$head
==
'barcode_score'
}
{
elseif
$head
==
'barcode_score'
||
$head
==
'barcode_score_Q7'
||
$head
==
'barcode_score_Q9'
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:1:',':' '}
</th>
{
elseif
$head
==
'median_yield_per_sec'
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:0:',':' '}
</th>
{
elseif
(
$head
==
'nb_read_utils'
)
or
(
$head
==
'nb_read_useful_data'
)
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:0:',':' '} ({($sample_results.$head / $basic.nb_reads*100)|number_format:2:',':' '}%)
</th>
{
elseif
(
$head
==
'total_bases_utils'
)
or
(
$head
==
'total_bases_useful_data'
)
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:0:',':' '} ({($sample_results.$head / $basic.total_bases*100)|number_format:2:',':' '}%)
</th>
{
elseif
(
$head
==
'N50_read_length_useful_data'
)
}
{
elseif
$head
==
'mean_yield_per_sec'
||
$head
==
'mean_yield_per_sec_Q7'
||
$head
==
'mean_yield_per_sec_Q9'
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:0:',':' '}
</th>
{/
if
}
...
...
@@ -303,8 +476,8 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<li><strong>
N50 read length
</strong>
:
50% of all bases come from reads longer than this value.
</li>
<li><strong>
Me
di
an yield per sec
</strong>
:
The me
di
an number of bases per second for the pores of this Flow Cell.
<li><strong>
Mean yield per sec
</strong>
:
The mean number of bases per second for the pores of this Flow Cell.
</li>
</ul>
</span>
...
...
@@ -314,15 +487,14 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<p>
Help for Quality report :
</p>
<span
class=
"meta"
>
<ul>
<li><strong>
Median read quality
</strong>
:
The median quality (qscore ONT) for this Flow Cell.
</li>
<li><strong>
Nb read/bases useful data
</strong>
:
The total number of reads/bases for the reads that have a quality > 7 and a length > 3000bp.
</li>
<li><strong>
N50 read length useful data
</strong>
:
50% of all bases come from reads longer than this value for the reads that have a quality > 7 and a length > 3000bp.
<li><strong>
Mean read quality
</strong>
:
The mean quality (qscore ONT) for this Flow Cell.
</li>
{
if
$template_status
!=
"2.0"
}
<li><strong>
Useful data
</strong>
:
Filtered data composed by reads with length > 3000 and quality > 7.
</li>
{/
if
}
</ul>
</span>
</div>
...
...
@@ -332,21 +504,15 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<p>
Help for Plots report :
</p>
<span
class=
"meta"
>
<ul>
<li><strong>
outrm
</strong>
:
For the length distribution plots and the density plot the outsiders have been removed.
</li>
<li><strong>
Cumulate yield per hour
</strong>
:
The cumulate number of bases per hour for this Flow Cell.
</li>
<li><strong>
Distribution length
</strong>
:
The length distribution of reads for this Flow Cell.
The length distribution of reads for this Flow Cell
with reads count or bases count
.
</li>
<li><strong>
Distribution qscore
</strong>
:
The quality (qscore ONT) distribution of reads for this Flow Cell.
</li>
<li><strong>
Length vs qscore density
</strong>
:
The length and qscore distribution of reads with density for this Flow Cell.
</li>
{
if
$barcode_name_count
>
1
}
<li><strong>
Qscore boxplot
</strong>
:
Boxplots for each barcode of the mean qscore of reads for this Flow Cell.
...
...
workflows/ont_qc/__init__.py
View file @
14d919ed
...
...
@@ -49,7 +49,7 @@ class OntQualityCheck (NG6Workflow):
addrawfiles
=
self
.
add_component
(
"AddRawFiles"
,
[
self
.
runobj
,
self
.
get_all_reads
(),
self
.
compression
])
#nanoplot = self.add_component("Nanoplot", [sample.name,self.get_all_reads(), self.nb_threads, True, "png", self.nanoplot_color,"nanoplot.tar.gz"])
ontstat
=
self
.
add_component
(
"Run_stats"
,
[
self
.
summary_file
,
self
.
barcoded
])
ontstat
=
self
.
add_component
(
"Run_stats"
,
[
self
.
summary_file
,
self
.
barcoded
,
sample_names
[
0
]
])
if
self
.
trimming
==
"yes"
:
trim_porechop
=
self
.
add_component
(
"Trim_porechop"
,
[
self
.
get_all_reads
()
,
"discard_middle"
])
if
self
.
fast5dir
!=
None
:
...
...
workflows/ont_qc/components/run_stats.py
View file @
14d919ed
This diff is collapsed.
Click to expand it.
workflows/ont_qc/data/ont_qc_barcoded.conf
View file @
14d919ed
...
...
@@ -16,7 +16,7 @@
#
--
date
25
/
0
6
/
201
8
08
/
0
4
/
201
9
--
data
-
nature
DNA
--
sequencer
...
...
@@ -33,16 +33,10 @@ arabido
test
-
dev
--
summary
-
file
workflows
/
ont_qc
/
data
/
sequencing_summary_barcoded_test
.
txt
/
save
/
ng6
-
test
/
src
/
ng6
-
git
-
mmanno
/
workflows
/
ont_qc
/
data
/
sequencing_summary_barcoded_test
.
txt
--
barcoded
yes
--
nb
-
threads
4
--
fileformat
fastq
--
fast5dir
workflows
/
ont_qc
/
data
/
fast5_dir
--
sample
sample
-
name
=
ONT_sample
read1
=
workflows
/
ont_qc
/
data
/
test
*.
fastq
read1
=
/
save
/
ng6
-
test
/
src
/
ng6
-
git
-
mmanno
/
workflows
/
ont_qc
/
data
/
test
*.
fastq
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