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GeT-nextflow-NGL-Bi
wf-Illumina-nf
Commits
564d1631
Commit
564d1631
authored
1 year ago
by
Jules Sabban
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Replace hyphen by NA in demuxStat
Ref:
#73
parent
41fd14b4
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1 merge request
!10
multipool
Pipeline
#120730
failed
1 year ago
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1 changed file
bin/demuxStatsFromXML.R
+2
-2
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bin/demuxStatsFromXML.R
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and
2 deletions
bin/demuxStatsFromXML.R
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2
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564d1631
...
@@ -84,7 +84,7 @@ for (pr in 1:length(projects)){
...
@@ -84,7 +84,7 @@ for (pr in 1:length(projects)){
if
(
length
(
PerfectBarcodeCount
)
==
0
)
{
PerfectBarcodeCount
<
-0
}
if
(
length
(
PerfectBarcodeCount
)
==
0
)
{
PerfectBarcodeCount
<
-0
}
OneMismatchBarcodeCount
<-
xml_text
(
xml_find_all
(
xml
,
paste0
(
lane_path
,
"/OneMismatchBarcodeCount"
)))
OneMismatchBarcodeCount
<-
xml_text
(
xml_find_all
(
xml
,
paste0
(
lane_path
,
"/OneMismatchBarcodeCount"
)))
if
(
length
(
OneMismatchBarcodeCount
)
==
0
)
{
OneMismatchBarcodeCount
<-
"-"
}
if
(
length
(
OneMismatchBarcodeCount
)
==
0
)
{
OneMismatchBarcodeCount
<-
NA
}
df_to_add
<-
data.frame
(
project
,
sample_name
,
barcode_names
[
bc
],
BarcodeCount
,
PerfectBarcodeCount
,
OneMismatchBarcodeCount
)
df_to_add
<-
data.frame
(
project
,
sample_name
,
barcode_names
[
bc
],
BarcodeCount
,
PerfectBarcodeCount
,
OneMismatchBarcodeCount
)
df
<-
concat_df
(
df
,
df_to_add
,
vec.names
)
df
<-
concat_df
(
df
,
df_to_add
,
vec.names
)
...
@@ -191,7 +191,7 @@ if(nrow(tabUndetermined) > 0) { head(tabUndetermined) }
...
@@ -191,7 +191,7 @@ if(nrow(tabUndetermined) > 0) { head(tabUndetermined) }
if
(
dim
(
tabUndetermined
)[
1
]
!=
0
)
{
if
(
dim
(
tabUndetermined
)[
1
]
!=
0
)
{
df.tabUndetermined
<-
data.frame
()
df.tabUndetermined
<-
data.frame
()
for
(
i
in
1
:
dim
(
tabUndetermined
)[
1
])
{
for
(
i
in
1
:
dim
(
tabUndetermined
)[
1
])
{
df.tabUndetermined.tmp
<-
data.frame
(
"default"
,
"Undetermined"
,
tabUndetermined
[
i
,
"Index"
],
tabUndetermined
[
i
,
"Count"
],
"-"
,
"-"
)
df.tabUndetermined.tmp
<-
data.frame
(
"default"
,
"Undetermined"
,
tabUndetermined
[
i
,
"Index"
],
tabUndetermined
[
i
,
"Count"
],
NA
,
NA
)
df.tabUndetermined
<-
concat_df
(
df.tabUndetermined
,
df.tabUndetermined.tmp
,
vec.names
)
df.tabUndetermined
<-
concat_df
(
df.tabUndetermined
,
df.tabUndetermined.tmp
,
vec.names
)
}
}
...
...
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