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Commit 8c2c17a2 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
Browse files

Add experiment and study rid's to multiqc report

parent 3bc88431
2 merge requests!37v0.0.1,!33Resolve "process_qc"
......@@ -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
......
......@@ -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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