rule filterSampleAnnot:
input: config['SAMPLE_ANNOT']
output: temp("output/tmp/{subProject}_samples.tsv")
run:
if wildcards.subProject == 'ALL':
sampleAnnot.to_csv(output[0], sep="\t")
else:
sampleAnnotFiltered=sampleAnnot[sampleAnnot.subProject == wildcards.subProject]
sampleAnnotFiltered.to_csv(output[0], sep="\t")
rule makeHtmlSummaryDashboard:
input:
sampleAnnotationFile="output/tmp/{subProject}_samples.tsv",
allFastqTimeStamps="output/statsFiles/all.fastq.timestamps.tsv",
allReadLengths="output/statsFiles/all.readlength.summary.tsv",
allBasicMappingStats="output/statsFiles/all.basic.mapping.stats.tsv",
allHissStats="output/statsFiles/all.HiSS.stats.tsv",
allMergedStats="output/statsFiles/all.min{minReadSupport}reads.merged.stats.tsv",
allMatureRnaLengthStats="output/statsFiles/all.min{minReadSupport}reads.matureRNALengthSummary.stats.tsv",
allTmergeVsSirvStats="output/statsFiles/all.HiSS.tmerge.min{minReadSupport}reads.vs.SIRVs.stats.tsv",
allCagePolyASupportStats="output/statsFiles/all.min{minReadSupport}reads.splicing_status-all.cagePolyASupport.stats.tsv",
allNovelLociStats="output/statsFiles/all.tmerge.min{minReadSupport}reads.endSupport-all.novelLoci.stats.tsv",
allNovelFlLociStats="output/statsFiles/all.tmerge.min{minReadSupport}reads.endSupport-cagePolyASupported.novelLoci.stats.tsv",
allNovelLociQcStats="output/statsFiles/all.tmerge.min{minReadSupport}reads.endSupport-all.novelLoci.qc.stats.tsv",
allNovelFlLociQcStats="output/statsFiles/all.tmerge.min{minReadSupport}reads.endSupport-cagePolyASupported.novelLoci.qc.stats.tsv",
allNtCoverageStats="output/statsFiles/all.tmerge.min{minReadSupport}reads.endSupport-all.vs.ntCoverageByGenomePartition.stats.tsv",
conda: "envs/R_env.yml"
params: indexEntryPart= lambda wildcards: "(no filter, all samples)" if wildcards.subProject == 'ALL' else "sub-project"
output:
html="output/html/summary_table_min{minReadSupport}reads_{subProject}.html",
tsv="output/html/summary_table_min{minReadSupport}reads_{subProject}.tsv",
index=temp("output/html/summary_table_min{minReadSupport}reads_{subProject}.index.tmp.html")
shell:
'''
./LyRic/makeHtmlDashboard.r {output.html} {input.sampleAnnotationFile} {input.allFastqTimeStamps} {input.allReadLengths} {input.allBasicMappingStats} {input.allHissStats} {input.allMergedStats} {input.allMatureRnaLengthStats} {input.allTmergeVsSirvStats} {input.allCagePolyASupportStats} {input.allNovelLociStats} {input.allNovelFlLociStats} {input.allNovelLociQcStats} {input.allNovelFlLociQcStats} {input.allNtCoverageStats}
htmlBn=$(basename {output.html})
tsvBn=$(basename {output.tsv})
echo " {wildcards.subProject} {params.indexEntryPart}: HTML / TSV" > {output.index}
'''
rule makeHtmlSummaryDashboardIndex:
input: lambda wildcards: expand("output/html/summary_table_min{minReadSupport}reads_{subProject}.index.tmp.html", subProject=subProjects, minReadSupport='|'.join(MINIMUM_TMERGE_READ_SUPPORT))
output: "output/html/index.html"
shell:
'''
uuid=$(uuidgen)
# print start of html:
printf '
' > {TMPDIR}/$uuid.html
printf "
Summary statistics tables for {config[PROJECT_NAME]} project
Summary statistics tables for {config[PROJECT_NAME]} project
" >> {TMPDIR}/$uuid.html
# print list:
cat {input} | sort >> {TMPDIR}/$uuid.html
# print end of html:
printf '
' >> {TMPDIR}/$uuid.html
printf "
Produced with LyRic.
" >> {TMPDIR}/$uuid.html
date=$(date)
printf "
(Last updated $date)" >> {TMPDIR}/$uuid.html
printf '
' >> {TMPDIR}/$uuid.html
mv {TMPDIR}/$uuid.html {output}
'''