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GUDMAP_RBK
RNA-seq
Commits
8c2c17a2
Commit
8c2c17a2
authored
5 years ago
by
Gervaise Henry
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Add experiment and study rid's to multiqc report
parent
3bc88431
2 merge requests
!37
v0.0.1
,
!33
Resolve "process_qc"
Changes
2
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2 changed files
workflow/rna-seq.nf
+17
-3
17 additions, 3 deletions
workflow/rna-seq.nf
workflow/scripts/parseMeta.py
+18
-1
18 additions, 1 deletion
workflow/scripts/parseMeta.py
with
35 additions
and
4 deletions
workflow/rna-seq.nf
+
17
−
3
View file @
8c2c17a2
...
...
@@ -179,7 +179,15 @@ process parseMetadata {
# Check replicate RID metadata
rep=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p repRID)
echo "LOG: replicate RID metadata parsed: \${rep}" >> ${repRID}.parseMetadata.err
# Get experiment RID metadata
exp=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p expRID)
echo "LOG: experiment RID metadata parsed: \${exp}" >> ${repRID}.parseMetadata.err
# Get study RID metadata
study=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p studyRID)
echo "LOG: study RID metadata parsed: \${study}" >> ${repRID}.parseMetadata.err
# Get endedness metadata
endsMeta=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p endsMeta)
echo "LOG: endedness metadata parsed: \${endsMeta}" >> ${repRID}.parseMetadata.err
...
...
@@ -201,7 +209,7 @@ process parseMetadata {
echo "LOG: species metadata parsed: \${species}" >> ${repRID}.parseMetadata.err
# Save design file
echo "\${endsMeta},\${endsManual},\${stranded},\${spike},\${species}" > design.csv
echo "\${endsMeta},\${endsManual},\${stranded},\${spike},\${species}
,\${exp},\${study}
" > design.csv
"""
}
...
...
@@ -211,12 +219,16 @@ endsManual = Channel.create()
strandedMeta = Channel.create()
spikeMeta = Channel.create()
speciesMeta = Channel.create()
expRID = Channel.create()
studyRID = Channel.create()
metadata.splitCsv(sep: ",", header: false).separate(
endsMeta,
endsManual,
strandedMeta,
spikeMeta,
speciesMeta
speciesMeta,
expRID,
studyRID
)
// Replicate metadata for multiple process inputs
endsManual.into {
...
...
@@ -914,6 +926,8 @@ process aggrQC {
val strandedI from strandedInfer_aggrQC
val spikeI from spikeInfer_aggrQC
val speciesI from speciesInfer_aggrQC
val expRID
val studyRID
output:
path "${repRID}.aggrQC.{out,err}" optional true
...
...
@@ -924,7 +938,7 @@ process aggrQC {
ulimit -a >> ${repRID}.aggrQC.err
echo -e "Replicate RID\tExperiment RID\tStudy RID" > rid.tsv
echo -e "${repRID}\t
-\t-
" >> rid.tsv
echo -e "${repRID}\t
${expRID}\t${studyRID}
" >> rid.tsv
echo -e "Source\tSpecies\tEnds\tStranded\tSpike-in" > metadata.tsv
echo -e "Infered\t${speciesI}\t${endsI}\t${strandedI}\t${spikeI}" >> metadata.tsv
...
...
This diff is collapsed.
Click to expand it.
workflow/scripts/parseMeta.py
+
18
−
1
View file @
8c2c17a2
...
...
@@ -17,7 +17,6 @@ def get_args():
def
main
():
args
=
get_args
()
metaFile
=
pd
.
read_csv
(
args
.
metaFile
,
sep
=
"
,
"
,
header
=
0
)
endsManual
=
""
# Check replicate RID metadata from 'File.csv'
if
(
args
.
parameter
==
"
repRID
"
):
...
...
@@ -33,6 +32,24 @@ def main():
if
(
len
(
metaFile
[
metaFile
[
"
File_Type
"
]
==
"
FastQ
"
])
>
2
):
print
(
"
There are more then 2 fastq
'
s in the metadata:
"
+
"
"
.
join
(
metaFile
[
metaFile
[
"
File_Type
"
]
==
"
FastQ
"
].
RID
))
exit
(
1
)
# Check experiment RID metadata from 'Experiment.csv'
if
(
args
.
parameter
==
"
expRID
"
):
if
(
len
(
metaFile
.
Experiment_RID
.
unique
())
>
1
):
print
(
"
There are multiple experoment RID
'
s in the metadata:
"
+
"
"
.
join
(
metaFile
.
Experiment_RID
.
unique
()))
exit
(
1
)
else
:
exp
=
metaFile
[
"
Experiment_RID
"
].
unique
()[
0
]
print
(
exp
)
# Check study RID metadata from 'Experiment.csv'
if
(
args
.
parameter
==
"
studyRID
"
):
if
(
len
(
metaFile
.
Study_RID
.
unique
())
>
1
):
print
(
"
There are multiple study RID
'
s in the metadata:
"
+
"
"
.
join
(
metaFile
.
Study_RID
.
unique
()))
exit
(
1
)
else
:
study
=
metaFile
[
"
Study_RID
"
].
unique
()[
0
]
print
(
study
)
# Get endedness metadata from 'Experiment Settings.csv'
if
(
args
.
parameter
==
"
endsMeta
"
):
...
...
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