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genotoul-bioinfo
ng6
Commits
489a7811
Commit
489a7811
authored
Jun 25, 2018
by
Maxime Manno
🍜
Browse files
Update archive name and fast5archive analysis visu
parent
64a64d88
Changes
3
Hide whitespace changes
Inline
Side-by-side
ui/nG6/pi1/analyzes/Fast5archive.tpl
View file @
489a7811
...
...
@@ -20,10 +20,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
assign
var
=
"params"
value
=
" "
|
explode
:
$analyse.params
}
{
foreach
from
=
$analyse_results
key
=
sample
item
=
sample_results
}
{
assign
var
=
"sample"
value
=
$sample
}
{/
foreach
}
<ul>
<li
class=
"parameter"
>
{
$analyse.params
}
: Reads that contain adapters in the middle will be removed.
</li>
</ul>
{/
foreach
}
>
{/
block
}
...
...
@@ -44,79 +41,18 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<legend>
Analyse results report - Sample name :
{
$descriptions.sample_1
}
</legend>
<br>
<table
id=
"ont_stats_datatable"
class=
"table table-striped table-bordered dataTable analysis-result-table"
>
<thead>
<tr>
{
assign
var
=
"nb_samples"
value
=
$ont_sample_count
}
<th
class=
"string-sort"
rowspan=
"2"
id=
"th_id_1"
><center>
Sample
{
if
$nb_samples
>
1
}
(
{
$nb_samples
}
)
{/
if
}
</center></th>
<th
colspan=
"
{
$ont_metrics_count
}
"
><center>
Trimmed ONT files results
</center></th>
</tr>
<tr>
{
assign
var
=
"th_id"
value
=
2
}
{
foreach
from
=
$ont_metrics_names
key
=
k
item
=
head
}
{
if
$head
==
'read_trim_start'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Read_trim_start
</th>
{
elseif
$head
==
'read_total_start'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Read_total_start
</th>
{
elseif
$head
==
'bp_removed_start'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Bp_removed_start
</th>
{
elseif
$head
==
'read_trim_end'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Read_trim_end
</th>
{
elseif
$head
==
'read_total_end'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Read_total_end
</th>
{
elseif
$head
==
'bp_removed_end'
}
<th
class =
"numeric-sort"
id=
"th_id_
{
$th_id
}
"
>
Bp_removed_end
</th>
{/
if
}
{
$th_id
=
$th_id
+
1
}
{/
foreach
}
</tr>
</thead>
<body>
{
foreach
from
=
$analyse_results_sorted
key
=
sample
item
=
sample_results
}
<tr>
<td
id=
'sample_
{
$i
}
_col_1'
class=
"sample_name"
>
{
$sample
}
</td>
{
$col_id
=
2
}
{
foreach
from
=
$ont_metrics_names
key
=
k
item
=
head
}
{
if
$head
==
'read_trim_start'
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:0:',':' '}
</th>
{
elseif
$head
==
'read_total_start'
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:0:',':' '}
</th>
{
elseif
$head
==
'bp_removed_start'
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:0:',':' '}
</th>
{
elseif
$head
==
'read_trim_end'
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:0:',':' '}
</th>
{
elseif
$head
==
'read_total_end'
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:0:',':' '}
</th>
{
elseif
$head
==
'bp_removed_end'
}
<th
id=
"sample_
{
$i
}
_col_
{
$col_id
}
"
>
{($sample_results.$head)|number_format:0:',':' '}
</th>
{/
if
}
{
$col_id
=
$col_id
+
1
}
{/
foreach
}
</tr>
{
$i
=
$i
+
1
}
{/
foreach
}
</body>
</table>
<div
class=
"tx-nG6-pi1-help"
>
<img
src=
""
alt=
""
class=
"img"
/>
<p>
Help for
Trimmed ONT
files results :
</p>
<p>
Help for
extract
files results :
</p>
<span
class=
"meta"
>
<ul>
<li><strong>
read_trim
</strong>
:
The number of reads trimmed for this sample.
<li><strong>
Download archive
</strong>
:
Use the Downloads view tab to download the archive.
The archive was compressed by tar + gzip.
</li>
<li><strong>
read_total
</strong>
:
The total number of reads for this sample.
<li><strong>
Decompress archive
</strong>
:
Use tar -xzf fast5archive.tar.gz
</li>
<li><strong>
bp_removed
</strong>
:
The number of bases removed for this sample.
</li>
<li><strong>
_start
</strong>
:
Previous metrics from the start of the read.
</li>
<li><strong>
_end
</strong>
:
Previous metrics to the end of the read.
</li>
</ul>
</span>
</div>
...
...
workflows/ont_qc/__init__.py
View file @
489a7811
...
...
@@ -54,5 +54,5 @@ class OntQualityCheck (NG6Workflow):
ontstat
=
self
.
add_component
(
"Run_stats"
,
[
self
.
summary_file
,
self
.
barcoded
])
trim_porechop
=
self
.
add_component
(
"Trim_porechop"
,
[
self
.
get_all_reads
(),
self
.
nb_threads
,
self
.
fileformat
,
"discard_middle"
])
if
self
.
fast5dir
!=
None
:
fast5archive
=
self
.
add_component
(
"Fast5archive"
,
[
self
.
fast5dir
,
"fast5archive"
])
fast5archive
=
self
.
add_component
(
"Fast5archive"
,
[
self
.
fast5dir
,
"fast5archive
.tar
"
])
workflows/ont_qc/components/fast5archive.py
View file @
489a7811
...
...
@@ -63,7 +63,7 @@ class Fast5archive (Analysis):
This module archive the fast5 files
"""
def
define_parameters
(
self
,
fast5dir
,
archivename
=
"fast5_archive"
):
def
define_parameters
(
self
,
fast5dir
,
archivename
=
"fast5_archive
.tar
"
):
self
.
add_parameter
(
"fast5dir"
,
"Path of the fast5 directory"
,
default
=
fast5dir
,
type
=
'str'
)
self
.
add_parameter
(
"archive_name"
,
"Name of the archive"
,
default
=
archivename
,
type
=
'str'
)
list_subdir
=
get_last_subdirectories
(
self
.
fast5dir
)
...
...
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