From 38bf0927edac492eab68b0952d3b77dc2e921318 Mon Sep 17 00:00:00 2001 From: julien lagarde Date: Mon, 13 Sep 2021 11:20:31 +0200 Subject: [PATCH] reformat json files. fix TOC in documentation.md --- cluster_config.json | 394 +++++++++++++++++++++---------------------- config_EXAMPLE.json | 98 +++++------ config_LRGASP.json | 49 +++--- config_cls3.json | 98 +++++------ config_cls3test.json | 98 +++++------ documentation.md | 4 +- 6 files changed, 370 insertions(+), 371 deletions(-) diff --git a/cluster_config.json b/cluster_config.json index 7be1978..0e0d613 100644 --- a/cluster_config.json +++ b/cluster_config.json @@ -1,198 +1,198 @@ { - "__default__": { - "queue": "rg-el7,short-sl7,long-sl7", - "virtual_free": "5G", - "h_rt": "03:00:00", - "email": "julien.lagarde@crg.eu", - "notify": "ae", - "err": "{workflow.basedir}/qsub_logs/", - "out": "{workflow.basedir}/qsub_logs/", - "project": "prj006070", - "threads": "", - "disk": "2G" - }, - "makeStarIndex": { - "virtual_free": "40G", - "h_rt": "06:00:00" - }, - "strandedGffToBed": { - "virtual_free": "15G" - }, - "makeReadsBlastDB": { - "h_rt": "00:20:00", - "virtual_free": "2G" - }, - "getHiSeqSupportedHCGMs": { - "virtual_free": "15G" - }, - "getReadLengthSummary": { - "virtual_free": "20G", - "h_rt": "01:30:00" - }, - "makeBigWigExonicRegions": { - "h_rt": "06:00:00" - }, - "mergedUnfilteredSirvReads": { - "h_rt": "05:30:00" - }, - "plotReadLength": { - "virtual_free": "25G", - "h_rt": "01:30:00" - }, - "aggTmStats": { - "h_rt": "04:00:00" - }, - "compareTargetsToTms": { - "disk": "30G", - "virtual_free": "15G" - }, - "removeIntraPriming": { - "virtual_free": "25G" - }, - "getGeneReadCoverageStats": { - "virtual_free": "25G", - "h_rt": "20:00:00" - }, - "longReadMapping": { - "virtual_free": "40G", - "h_rt": "20:00:00", - "threads": "-pe smp 12", - "queue": "rg-el7,long-sl7" - }, - "hiSeqReadMapping": { - "virtual_free": "70G", - "h_rt": "20:00:00", - "queue": "rg-el7,long-sl7", - "threads": "-pe smp 12" - }, - "highConfidenceReads": { - "h_rt": "6:00:00", - "virtual_free": "35G" - }, - "readBedToGff": { - "queue": "rg-el7,long-sl7", - "h_rt": "10:00:00", - "virtual_free": "5G" - }, - "polyAmapping": { - "h_rt": "3:00:00", - "virtual_free": "2G" - }, - "getPolyAreadsList": { - "virtual_free": "1G" - }, - "getPolyAreadsStats": { - "h_rt": "6:00:00" - }, - "makeIntrons": { - "h_rt": "10:00:00", - "queue": "rg-el7,long-sl7", - "virtual_free": "20G" - }, - "getIntronMotif": { - "virtual_free": "15G" - }, - "getReadsSpliceSites": { - "virtual_free": "10G" - }, - "getHiSSStats": { - "virtual_free": "65G", - "h_rt": "06:00:00" - }, - "mergeWithRef": { - "virtual_free": "20G", - "h_rt": "06:00:00" - }, - "mergedReads": { - "virtual_free": "60G", - "h_rt": "26:00:00" - }, - "mergedReadsToBed": { - "virtual_free": "10G" - }, - "collapseGencode": { - "virtual_free": "10G" - }, - "getHiSeqCanonicalIntronsList1": { - "h_rt": "6:00:00" - }, - "getHiSeqCanonicalIntronsList2": { - "virtual_free": "60G", - "h_rt": "16:00:00", - "threads": "-pe smp 6" - }, - "plotHistTmLengthStats": { - "virtual_free": "20G" - }, - "gffcompareToAnnotation": { - "virtual_free": "10G" - }, - "gffcompareToSirvAnnotation": { - "virtual_free": "1G" - }, - "getHCGMintrons": { - "virtual_free": "10G" - }, - "getClsSpliceJunctions": { - "h_rt": "04:30:00", - "virtual_free": "10G" - }, - "getTmSpliceSites": { - "h_rt": "04:30:00" - }, - "getCompareClsGencodeSJsStats": { - "h_rt": "04:30:00" - }, - "getGffCompareStats": { - "h_rt": "04:30:00" - }, - "cageSupportedfivepEnds": { - "virtual_free": "15G" - }, - "getReadBiotypeClassification": { - "disk": "30G", - "h_rt": "16:00:00" - }, - "aggGeneidScores": { - "threads": "-pe smp 8" - }, - "plotGeneidScores": { - "virtual_free": "35G", - "h_rt": "5:30:00" - }, - "getHiSeqMappingStats": { - "h_rt": "8:00:00", - "queue": "rg-el7,long-sl7" - }, - "mergeTmsWithGencode": { - "virtual_free": "10G", - "h_rt": "5:00:00" - }, - "polyASupportedthreepEnds": { - "virtual_free": "15G" - }, - "readBamToBed": { - "virtual_free": "1G" - }, - "tmergeAll": { - "disk": "60G", - "h_rt": "12:00:00", - "virtual_free": "20G", - "queue": "rg-el7,long-sl7" - }, - "getReadProfileMatrix": { - "h_rt": "12:00:00", - "threads": "-pe smp 6", - "queue": "rg-el7,long-sl7", - "virtual_free": "15G" - }, - "plotReadProfileMatrix": { - "virtual_free": "20G" - }, - "bamqc": { - "virtual_free": "25G" - }, - "mergedReadsGroupedSampleReps": { - "virtual_free": "15G" - } -} + "__default__": { + "queue": "rg-el7,short-sl7,long-sl7", + "virtual_free": "5G", + "h_rt": "03:00:00", + "email": "julien.lagarde@crg.eu", + "notify": "ae", + "err": "{workflow.basedir}/qsub_logs/", + "out": "{workflow.basedir}/qsub_logs/", + "project": "prj006070", + "threads": "", + "disk": "2G" + }, + "makeStarIndex": { + "virtual_free": "40G", + "h_rt": "06:00:00" + }, + "strandedGffToBed": { + "virtual_free": "15G" + }, + "makeReadsBlastDB": { + "h_rt": "00:20:00", + "virtual_free": "2G" + }, + "getHiSeqSupportedHCGMs": { + "virtual_free": "15G" + }, + "getReadLengthSummary": { + "virtual_free": "20G", + "h_rt": "01:30:00" + }, + "makeBigWigExonicRegions": { + "h_rt": "06:00:00" + }, + "mergedUnfilteredSirvReads": { + "h_rt": "05:30:00" + }, + "plotReadLength": { + "virtual_free": "25G", + "h_rt": "01:30:00" + }, + "aggTmStats": { + "h_rt": "04:00:00" + }, + "compareTargetsToTms": { + "disk": "30G", + "virtual_free": "15G" + }, + "removeIntraPriming": { + "virtual_free": "25G" + }, + "getGeneReadCoverageStats": { + "virtual_free": "25G", + "h_rt": "20:00:00" + }, + "longReadMapping": { + "virtual_free": "40G", + "h_rt": "20:00:00", + "threads": "-pe smp 12", + "queue": "rg-el7,long-sl7" + }, + "hiSeqReadMapping": { + "virtual_free": "70G", + "h_rt": "20:00:00", + "queue": "rg-el7,long-sl7", + "threads": "-pe smp 12" + }, + "highConfidenceReads": { + "h_rt": "6:00:00", + "virtual_free": "35G" + }, + "readBedToGff": { + "queue": "rg-el7,long-sl7", + "h_rt": "10:00:00", + "virtual_free": "5G" + }, + "polyAmapping": { + "h_rt": "3:00:00", + "virtual_free": "2G" + }, + "getPolyAreadsList": { + "virtual_free": "1G" + }, + "getPolyAreadsStats": { + "h_rt": "6:00:00" + }, + "makeIntrons": { + "h_rt": "10:00:00", + "queue": "rg-el7,long-sl7", + "virtual_free": "20G" + }, + "getIntronMotif": { + "virtual_free": "15G" + }, + "getReadsSpliceSites": { + "virtual_free": "10G" + }, + "getHiSSStats": { + "virtual_free": "65G", + "h_rt": "06:00:00" + }, + "mergeWithRef": { + "virtual_free": "20G", + "h_rt": "06:00:00" + }, + "mergedReads": { + "virtual_free": "60G", + "h_rt": "26:00:00" + }, + "mergedReadsToBed": { + "virtual_free": "10G" + }, + "collapseGencode": { + "virtual_free": "10G" + }, + "getHiSeqCanonicalIntronsList1": { + "h_rt": "6:00:00" + }, + "getHiSeqCanonicalIntronsList2": { + "virtual_free": "60G", + "h_rt": "16:00:00", + "threads": "-pe smp 6" + }, + "plotHistTmLengthStats": { + "virtual_free": "20G" + }, + "gffcompareToAnnotation": { + "virtual_free": "10G" + }, + "gffcompareToSirvAnnotation": { + "virtual_free": "1G" + }, + "getHCGMintrons": { + "virtual_free": "10G" + }, + "getClsSpliceJunctions": { + "h_rt": "04:30:00", + "virtual_free": "10G" + }, + "getTmSpliceSites": { + "h_rt": "04:30:00" + }, + "getCompareClsGencodeSJsStats": { + "h_rt": "04:30:00" + }, + "getGffCompareStats": { + "h_rt": "04:30:00" + }, + "cageSupportedfivepEnds": { + "virtual_free": "15G" + }, + "getReadBiotypeClassification": { + "disk": "30G", + "h_rt": "16:00:00" + }, + "aggGeneidScores": { + "threads": "-pe smp 8" + }, + "plotGeneidScores": { + "virtual_free": "35G", + "h_rt": "5:30:00" + }, + "getHiSeqMappingStats": { + "h_rt": "8:00:00", + "queue": "rg-el7,long-sl7" + }, + "mergeTmsWithGencode": { + "virtual_free": "10G", + "h_rt": "5:00:00" + }, + "polyASupportedthreepEnds": { + "virtual_free": "15G" + }, + "readBamToBed": { + "virtual_free": "1G" + }, + "tmergeAll": { + "disk": "60G", + "h_rt": "12:00:00", + "virtual_free": "20G", + "queue": "rg-el7,long-sl7" + }, + "getReadProfileMatrix": { + "h_rt": "12:00:00", + "threads": "-pe smp 6", + "queue": "rg-el7,long-sl7", + "virtual_free": "15G" + }, + "plotReadProfileMatrix": { + "virtual_free": "20G" + }, + "bamqc": { + "virtual_free": "25G" + }, + "mergedReadsGroupedSampleReps": { + "virtual_free": "15G" + } +} \ No newline at end of file diff --git a/config_EXAMPLE.json b/config_EXAMPLE.json index 9c9f3dc..0fb9712 100644 --- a/config_EXAMPLE.json +++ b/config_EXAMPLE.json @@ -1,53 +1,53 @@ { - "GENOMESDIR": "", - "produceStatPlots": true, - "produceTrackHub": true, - "produceHtmlStatsTable": true, - "capDesignToGenome": { - "HpreCap": "hg38", - "Hv3": "hg38", - "MpreCap": "mm10", - "Mv2": "mm10" - }, - "capDesignToTargetsGff": { - "Hv3": "", - "Mv2": "" - }, - "capDesignToCapDesign":{ - "HpreCap": "Hv3", - "MpreCap": "Mv2", - "Hv3": "Hv3", - "Mv2": "Mv2" - }, + "GENOMESDIR": "", + "produceStatPlots": true, + "produceTrackHub": true, + "produceHtmlStatsTable": true, + "capDesignToGenome": { + "HpreCap": "hg38", + "Hv3": "hg38", + "MpreCap": "mm10", + "Mv2": "mm10" + }, + "capDesignToTargetsGff": { + "Hv3": "", + "Mv2": "" + }, + "capDesignToCapDesign": { + "HpreCap": "Hv3", + "MpreCap": "Mv2", + "Hv3": "Hv3", + "Mv2": "Mv2" + }, "sampleRepGroupBy": [ - "seqPlatform", - "libraryPrep", - "species", - "captureDesign", - "sizeFrac", - "tissue", - "cellFrac", - "reverse_transcriptase" + "seqPlatform", + "libraryPrep", + "species", + "captureDesign", + "sizeFrac", + "tissue", + "cellFrac", + "reverse_transcriptase" ], - "CAPTURE": true, - "SAMPLE_ANNOT": "sample_annotations_EXAMPLE.tsv", - "genomeToAnnotGtf": { - "hg38": "", - "mm10": "" - }, - "USE_MATCHED_ILLUMINA": true, - "PROJECT_NAME": "short name for UCSC Track Hub", - "PROJECT_LONG_NAME": "long name for UCSC Track Hub", - "PROJECT_CONTACT_EMAIL": "contact email for UCSC Track Hub", - "TRACK_HUB_BASE_URL": "base http URL for UCSC Track Hub (i.e. the web-accessible directory where the genome browser will fetch the 'hub.txt' file). It has to point locally to './output/trackHub/, so you should configure your web server accordingly.", - "genomeToCAGEpeaks": { - "hg38": "path to BED file of CAGE clusters for hg38", - "mm10": "path to BED file of CAGE clusters for mm10" - }, - "REPEATMASKER_DIR": "annotations/repeatMasker/", - "genomeToDHSpeaks": { - "hg38": "path to BED file of DHS clusters for hg38", - "mm10": "path to BED file of DHS clusters for mm10" - }, - "SIRVinfo": "(optional) path to tab-separated file containing length and concentration information on each SIRV transcript" + "CAPTURE": true, + "SAMPLE_ANNOT": "sample_annotations_EXAMPLE.tsv", + "genomeToAnnotGtf": { + "hg38": "", + "mm10": "" + }, + "USE_MATCHED_ILLUMINA": true, + "PROJECT_NAME": "short name for UCSC Track Hub", + "PROJECT_LONG_NAME": "long name for UCSC Track Hub", + "PROJECT_CONTACT_EMAIL": "contact email for UCSC Track Hub", + "TRACK_HUB_BASE_URL": "base http URL for UCSC Track Hub (i.e. the web-accessible directory where the genome browser will fetch the 'hub.txt' file). It has to point locally to './output/trackHub/, so you should configure your web server accordingly.", + "genomeToCAGEpeaks": { + "hg38": "path to BED file of CAGE clusters for hg38", + "mm10": "path to BED file of CAGE clusters for mm10" + }, + "REPEATMASKER_DIR": "annotations/repeatMasker/", + "genomeToDHSpeaks": { + "hg38": "path to BED file of DHS clusters for hg38", + "mm10": "path to BED file of DHS clusters for mm10" + }, + "SIRVinfo": "(optional) path to tab-separated file containing length and concentration information on each SIRV transcript" } \ No newline at end of file diff --git a/config_LRGASP.json b/config_LRGASP.json index 9cca57e..6f1eeba 100644 --- a/config_LRGASP.json +++ b/config_LRGASP.json @@ -1,26 +1,25 @@ { - "GENOMESDIR": "genomes/", - "produceStatPlots": false, - "produceTrackHub": false, - "produceHtmlStatsTable": false, - "capDesignToGenome": { - "HpreCap": "hg38", - "MpreCap": "mm10" - }, - - "sampleRepGroupBy": [ - "seqPlatform", - "libraryPrep", - "species", - "captureDesign", - "sizeFrac", - "tissue", - "cellFrac", - "reverse_transcriptase" - ], - "CAPTURE": false, - "SAMPLE_ANNOT": "LyRic/sample_annotations_LRGASP.tsv", - "USE_MATCHED_ILLUMINA": false, - "PROJECT_NAME": "LRGASP-LyRic", - "PROJECT_LONG_NAME": "LRGASP LyRic entry" -} + "GENOMESDIR": "genomes/", + "produceStatPlots": false, + "produceTrackHub": false, + "produceHtmlStatsTable": false, + "capDesignToGenome": { + "HpreCap": "hg38", + "MpreCap": "mm10" + }, + "sampleRepGroupBy": [ + "seqPlatform", + "libraryPrep", + "species", + "captureDesign", + "sizeFrac", + "tissue", + "cellFrac", + "reverse_transcriptase" + ], + "CAPTURE": false, + "SAMPLE_ANNOT": "LyRic/sample_annotations_LRGASP.tsv", + "USE_MATCHED_ILLUMINA": false, + "PROJECT_NAME": "LRGASP-LyRic", + "PROJECT_LONG_NAME": "LRGASP LyRic entry" +} \ No newline at end of file diff --git a/config_cls3.json b/config_cls3.json index 173661d..d3706b3 100644 --- a/config_cls3.json +++ b/config_cls3.json @@ -1,53 +1,53 @@ { - "GENOMESDIR": "genomes/", - "produceStatPlots": true, - "produceTrackHub": true, - "produceHtmlStatsTable": true, - "capDesignToGenome": { - "HpreCap": "hg38", - "Hv3": "hg38", - "MpreCap": "mm10", - "Mv2": "mm10" - }, - "capDesignToTargetsGff": { - "Hv3": "targets/Hv3_primary_targets.exons.reduced.gene_type.segments.gtf", - "Mv2": "targets/Mv2_primary_targets.exons.reduced.gene_type.segments.gtf" - }, - "capDesignToCapDesign":{ - "HpreCap": "Hv3", - "MpreCap": "Mv2", - "Hv3": "Hv3", - "Mv2": "Mv2" - }, + "GENOMESDIR": "genomes/", + "produceStatPlots": true, + "produceTrackHub": true, + "produceHtmlStatsTable": true, + "capDesignToGenome": { + "HpreCap": "hg38", + "Hv3": "hg38", + "MpreCap": "mm10", + "Mv2": "mm10" + }, + "capDesignToTargetsGff": { + "Hv3": "targets/Hv3_primary_targets.exons.reduced.gene_type.segments.gtf", + "Mv2": "targets/Mv2_primary_targets.exons.reduced.gene_type.segments.gtf" + }, + "capDesignToCapDesign": { + "HpreCap": "Hv3", + "MpreCap": "Mv2", + "Hv3": "Hv3", + "Mv2": "Mv2" + }, "sampleRepGroupBy": [ - "seqPlatform", - "libraryPrep", - "species", - "captureDesign", - "sizeFrac", - "tissue", - "cellFrac", - "reverse_transcriptase" + "seqPlatform", + "libraryPrep", + "species", + "captureDesign", + "sizeFrac", + "tissue", + "cellFrac", + "reverse_transcriptase" ], - "CAPTURE": true, - "SAMPLE_ANNOT": "annotations/samples/sample_annotations.tsv", - "genomeToAnnotGtf": { - "hg38": "annotations/hs.gencode24+SIRVS.gff", - "mm10": "annotations/mm.gencodeM7+SIRVS.gff" - }, - "USE_MATCHED_ILLUMINA": true, - "PROJECT_NAME": "CLS3", - "PROJECT_LONG_NAME": "GENCODE CLS Phase 3", - "PROJECT_CONTACT_EMAIL": "julien.lagarde@crg.eu", - "TRACK_HUB_BASE_URL": "https://public-docs.crg.es/rguigo/Data/jlagarde/gencode/trackHubs/CLS3/", - "genomeToCAGEpeaks": { - "hg38": "annotations/cage/hg38_fair+new_CAGE_peaks_phase1and2.bed", - "mm10": "annotations/cage/mm10_fair+new_CAGE_peaks_phase1and2.bed" - }, - "REPEATMASKER_DIR": "annotations/repeatMasker/", - "genomeToDHSpeaks": { - "hg38": "annotations/dhs/ENCFF301VRH.hg38.sorted.bed", - "mm10": "annotations/dhs/ENCFF108APF.bed" - }, - "SIRVinfo": "annotations/SIRV_Set1_Lot00141_info-170612a.tsv" + "CAPTURE": true, + "SAMPLE_ANNOT": "annotations/samples/sample_annotations.tsv", + "genomeToAnnotGtf": { + "hg38": "annotations/hs.gencode24+SIRVS.gff", + "mm10": "annotations/mm.gencodeM7+SIRVS.gff" + }, + "USE_MATCHED_ILLUMINA": true, + "PROJECT_NAME": "CLS3", + "PROJECT_LONG_NAME": "GENCODE CLS Phase 3", + "PROJECT_CONTACT_EMAIL": "julien.lagarde@crg.eu", + "TRACK_HUB_BASE_URL": "https://public-docs.crg.es/rguigo/Data/jlagarde/gencode/trackHubs/CLS3/", + "genomeToCAGEpeaks": { + "hg38": "annotations/cage/hg38_fair+new_CAGE_peaks_phase1and2.bed", + "mm10": "annotations/cage/mm10_fair+new_CAGE_peaks_phase1and2.bed" + }, + "REPEATMASKER_DIR": "annotations/repeatMasker/", + "genomeToDHSpeaks": { + "hg38": "annotations/dhs/ENCFF301VRH.hg38.sorted.bed", + "mm10": "annotations/dhs/ENCFF108APF.bed" + }, + "SIRVinfo": "annotations/SIRV_Set1_Lot00141_info-170612a.tsv" } \ No newline at end of file diff --git a/config_cls3test.json b/config_cls3test.json index 75dbc03..9e21ebc 100644 --- a/config_cls3test.json +++ b/config_cls3test.json @@ -1,53 +1,53 @@ { - "GENOMESDIR": "genomes/", - "produceStatPlots": true, - "produceTrackHub": true, - "produceHtmlStatsTable": true, - "capDesignToGenome": { - "HpreCap": "hg38", - "Hv3": "hg38", - "MpreCap": "mm10", - "Mv2": "mm10" - }, - "capDesignToTargetsGff": { - "Hv3": "targets/Hv3_primary_targets.exons.reduced.gene_type.segments.gtf", - "Mv2": "targets/Mv2_primary_targets.exons.reduced.gene_type.segments.gtf" - }, - "capDesignToCapDesign":{ - "HpreCap": "Hv3", - "MpreCap": "Mv2", - "Hv3": "Hv3", - "Mv2": "Mv2" - }, + "GENOMESDIR": "genomes/", + "produceStatPlots": true, + "produceTrackHub": true, + "produceHtmlStatsTable": true, + "capDesignToGenome": { + "HpreCap": "hg38", + "Hv3": "hg38", + "MpreCap": "mm10", + "Mv2": "mm10" + }, + "capDesignToTargetsGff": { + "Hv3": "targets/Hv3_primary_targets.exons.reduced.gene_type.segments.gtf", + "Mv2": "targets/Mv2_primary_targets.exons.reduced.gene_type.segments.gtf" + }, + "capDesignToCapDesign": { + "HpreCap": "Hv3", + "MpreCap": "Mv2", + "Hv3": "Hv3", + "Mv2": "Mv2" + }, "sampleRepGroupBy": [ - "seqPlatform", - "libraryPrep", - "species", - "captureDesign", - "sizeFrac", - "tissue", - "cellFrac", - "reverse_transcriptase" + "seqPlatform", + "libraryPrep", + "species", + "captureDesign", + "sizeFrac", + "tissue", + "cellFrac", + "reverse_transcriptase" ], - "CAPTURE": true, - "SAMPLE_ANNOT": "annotations/samples/sample_annotations.tsv", - "genomeToAnnotGtf": { - "hg38": "annotations/hs.gencode24+SIRVS.gff", - "mm10": "annotations/mm.gencodeM7+SIRVS.gff" - }, - "USE_MATCHED_ILLUMINA": true, - "PROJECT_NAME": "CLS3test", - "PROJECT_LONG_NAME": "GENCODE CLS Phase 3 test", - "PROJECT_CONTACT_EMAIL": "julien.lagarde@crg.eu", - "TRACK_HUB_BASE_URL": "https://public-docs.crg.es/rguigo/Data/jlagarde/gencode/trackHubs/CLS3test/", - "genomeToCAGEpeaks": { - "hg38": "annotations/cage/hg38_fair+new_CAGE_peaks_phase1and2.bed", - "mm10": "annotations/cage/mm10_fair+new_CAGE_peaks_phase1and2.bed" - }, - "REPEATMASKER_DIR": "annotations/repeatMasker/", - "genomeToDHSpeaks": { - "hg38": "annotations/dhs/ENCFF301VRH.hg38.sorted.bed", - "mm10": "annotations/dhs/ENCFF108APF.bed" - }, - "SIRVinfo": "annotations/SIRV_Set1_Lot00141_info-170612a.tsv" + "CAPTURE": true, + "SAMPLE_ANNOT": "annotations/samples/sample_annotations.tsv", + "genomeToAnnotGtf": { + "hg38": "annotations/hs.gencode24+SIRVS.gff", + "mm10": "annotations/mm.gencodeM7+SIRVS.gff" + }, + "USE_MATCHED_ILLUMINA": true, + "PROJECT_NAME": "CLS3test", + "PROJECT_LONG_NAME": "GENCODE CLS Phase 3 test", + "PROJECT_CONTACT_EMAIL": "julien.lagarde@crg.eu", + "TRACK_HUB_BASE_URL": "https://public-docs.crg.es/rguigo/Data/jlagarde/gencode/trackHubs/CLS3test/", + "genomeToCAGEpeaks": { + "hg38": "annotations/cage/hg38_fair+new_CAGE_peaks_phase1and2.bed", + "mm10": "annotations/cage/mm10_fair+new_CAGE_peaks_phase1and2.bed" + }, + "REPEATMASKER_DIR": "annotations/repeatMasker/", + "genomeToDHSpeaks": { + "hg38": "annotations/dhs/ENCFF301VRH.hg38.sorted.bed", + "mm10": "annotations/dhs/ENCFF108APF.bed" + }, + "SIRVinfo": "annotations/SIRV_Set1_Lot00141_info-170612a.tsv" } \ No newline at end of file diff --git a/documentation.md b/documentation.md index 18de044..0047877 100644 --- a/documentation.md +++ b/documentation.md @@ -11,8 +11,8 @@ LyRic is platform-agnostic, _i.e._ it can deal with FASTQ data coming from both # Table of Contents -- TOC - {:toc} +* TOC +{:toc} # Installation & Dependencies