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cellranger_mkfastq
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Astrocyte
cellranger_mkfastq
Commits
1fd6d350
Commit
1fd6d350
authored
5 years ago
by
Jeremy Mathews
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Fix countDesign
parent
6dda9f06
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2 merge requests
!45
Develop
,
!44
Resolve "Fix CountDesign"
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CHANGELOG.md
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CHANGELOG.md
workflow/scripts/countDesign.sh
+12
-12
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workflow/scripts/countDesign.sh
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13 additions
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12 deletions
CHANGELOG.md
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1
−
0
View file @
1fd6d350
# v1.3.0 (in development)
# v1.3.0 (in development)
**User Facing**
**User Facing**
*
Change Cellranger Version to 3.1.0
*
Change Cellranger Version to 3.1.0
*
Fix countDesign to take multiple samples
**Background**
**Background**
*
Add CI artifacts
*
Add CI artifacts
...
...
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workflow/scripts/countDesign.sh
+
12
−
12
View file @
1fd6d350
#!/bin/bash
#!/bin/bash
#countDesign.sh
#countDesign.sh
fastqs
=
$(
ls
*
.fastq.gz
)
fastqs
=
(
$(
ls
*
.fastq.gz
)
)
design
=
$(
ls
*
.csv
)
design
=
$(
ls
*
.csv
)
sample
=
$(
cat
${
design
}
|
tail
-n
+2 |
cut
-d
','
-f2
)
sample
=
$(
cat
${
design
}
|
tail
-n
+2 |
cut
-d
','
-f2
)
for
i
in
${
fastqs
}
;
echo
"Sample,fastq_R1,fastq_R2"
>
Cellranger_Count_Design.csv
;
for
i
in
${
sample
}
;
do
do
if
[[
${
i
}
==
*
_S0_
*
]]
;
then
for
j
in
$(
seq
1
${#
fastqs
[@]
}
)
;
continue
do
elif
[[
${
i
}
==
*
_I
*
]]
;
then
if
[[
${
fastqs
[
${
j
}
-1]
}
==
*
_I
*
]]
;
then
continue
continue
else
elif
[[
${
fastqs
[
${
j
}
-1]
}
==
*${
i
}*
&&
${
fastqs
[
${
j
}
]
}
==
*${
i
}*
]]
;
then
good
=(
${
good
[@]
}
${
i
}
)
echo
"
${
i
}
,
${
fastqs
[
${
j
}
-1]
}
,
${
fastqs
[
${
j
}
]
}
"
>>
Cellranger_Count_Design.csv
fi
fi
done
done
done
echo
"Sample,fastq_R1,fastq_R2"
>
Cellranger_Count_Design.csv
;
echo
"
${
sample
}
,
${
good
[0]
}
,
${
good
[1]
}
"
>>
Cellranger_Count_Design.csv
;
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