-
Notifications
You must be signed in to change notification settings - Fork 9
/
Copy pathparameters.homo_sapiens.hg19.solve-rd.csv
We can make this file beautiful and searchable if this error is corrected: It looks like row 2 should actually have 1 column, instead of 2 in line 1.
executable file
·188 lines (177 loc) · 9.94 KB
/
parameters.homo_sapiens.hg19.solve-rd.csv
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
##### BACKEND #####
stage,module load
checkStage,module list
jobname,jobname
##### Tools and versions #####
jdkVersion,Java/11-LTS
ngsUtilsVersion,ngs-utils/19.03.3-${GCCcoreVersion}
ngsRNAVersion,NGS_RNA/beta
fastqcVersion,FastQC/0.11.8-Java-11-LTS
samtoolsVersion,SAMtools/1.9-${GCCcoreVersion}
bedToolsVersion,BEDTools/2.28.0-${GCCcoreVersion}
sambambaVersion,sambamba/0.7.0
rVersion,R/3.6.1-${toolchain}-bare
rPlusVersion,RPlus/3.6.1-${toolchain}-v21.10.1
picardVersion,picard/2.20.5-Java-11-LTS
htseqVersion,HTSeq/0.11.0-${GCCcoreVersion}-Python-3.7.4
hisatVersion,hisat2/2.1.0-${toolchain}
htsLibVersion,HTSlib/1.11-${GCCcoreVersion}
pythonVersion,Python/3.7.4-${GCCcoreVersion}-bare
python2Version,Python/2.7.16-${GCCcoreVersion}-bare
python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
pythonPlusVersion,PythonPlus/3.7.4-${toolchain}-v20.02.1
gatkVersion,GATK/4.1.4.1-Java-8-LTS
multiqcVersion,multiqc_v1.12.sif
starVersion,STAR/2.7.3a-${toolchain}
picardJar,picard.jar
gatkJar,gatk-package-4.1.4.1-local.jar
mergeSamFilesJar,MergeSamFiles
trimGaloreVersion,TrimGalore/0.4.5-${GCCcoreVersion}-Python-3.7.4-bare
cutadaptVersion,cutadapt/2.6-${GCCcoreVersion}-Python-3.7.4-bare
rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.7.4
leafcutterVersion,leafcutter/aa12b1e-${toolchain}
vipVersion,vip/v3.3.1-${toolchain}
outriderVersion,outrider_latest.sif
rMATsVersion,rmats_v4.1.2.sif
sifDir,/apps/data/GAD/singularity/
rnaseqcVersion,${sifDir}/rnaseqc_2.4.2.sif
##### GENERAL DIRECTORIES #####
tmpDataDir,/groups/umcg-solve-rd/tmp01/rna/
tmpTmpDataDir,/groups/umcg-solve-rd/tmp01/rna/tmp/
##### RAW DATA FILES/DIRS #####
allRawNgsPrmDataDir,${permanentDir}/rawdata/ngs
allRawtmpDataDir,${tmpDataDir}/rawdata/
allRawNgstmpDataDir,${allRawtmpDataDir}/ngs/
rawtmpDataDir,${allRawNgstmpDataDir}/${runPrefix}
logsDir,${tmpDataDir}/logs
srInputFile,${rawtmpDataDir}/${filePrefix}.fq.gz
peEnd1FqGz,${rawtmpDataDir}/${filePrefix}_1.fq.gz
peEnd2FqGz,${rawtmpDataDir}/${filePrefix}_2.fq.gz
peEnd1BarcodeFqGz,${rawFile}_1.${rawFileExt}
peEnd2BarcodeFqGz,${rawFile}_2.${rawFileExt}
peEnd1BarcodeFq,${rawFile}_1.fq
srBarcodeFqGz,${rawFile}.${rawFileExt}
#srBarcodeFq,${intermediateDir}/${filePrefix}_${barcode}.fq
leftbarcode,${projectRawtmpDataDir}/${filePrefix}_${barcode}_1
rightbarcode,${projectRawtmpDataDir}/${filePrefix}_${barcode}_2
leftbarcodefq,${leftbarcode}.fq
rightbarcodefq,${rightbarcode}.fq
leftbarcodefqgz,${leftbarcodefq}.gz
rightbarcodefqgz,${rightbarcodefq}.gz
trimmedLeftBarcodeFqGz,${projectRawtmpDataDir}/${filePrefix}_${barcode}_1_val_1.fq.gz
trimmedRightBarcodeFqGz,${projectRawtmpDataDir}/${filePrefix}_${barcode}_2_val_2.fq.gz
trimmedSingleBarcodeFqGz,${projectRawtmpDataDir}/${filePrefix}_${barcode}_trimmed.fq.gz
mergedLeftBarcodeFqGz,${projectRawtmpDataDir}/${externalSampleID}_val_1.fq.gz
mergedRightBarcodeFqGz,${projectRawtmpDataDir}/${externalSampleID}_val_2.fq.gz
mergedSingleBarcodeFqGz,${projectRawtmpDataDir}/${externalSampleID}}_trimmed.fq.gz
workflowFile,$MC_HOME/NGS_RNA_seq_pipeline/workflow.csv
##### PREFIXES,POSTFIXES #####
rawFileExt,fq.gz
runPrefix,${sequencingStartDate}_${sequencer}_${run}_${flowcell}
rawFile,${projectRawtmpDataDir}/${filePrefix}_${barcode}
filePrefix,${runPrefix}_L${lane}
library,${filePrefix}
##### Projects #####
generalProjectDir,${tmpDataDir}/projects/
projectDir,${generalProjectDir}/${project}/${runid}
projectRawtmpDataDir,${projectDir}/rawdata/ngs/
projectRawArraytmpDataDir,${projectDir}/rawdata/array/
intermediateDir,${tempDir}/${project}/${runid}/
projectPrefix,${intermediateDir}/${project}
projectJobsDir,${projectDir}/jobs/
projectLogsDir,${projectDir}/logs/
projectResultsDir,${projectDir}/results/
projectQcDir,${projectDir}/qc/
rMATsOutputDir,${projectResultsDir}/rmats
tinDir,${intermediateDir}/TIN
##### Protocols 0,1a,1b, (FastQC,HisatAlignment,MergeBam) #####
peEnd1BarcodeFastQcZip,${intermediateDir}/${filePrefix}_${barcode}_1.fq_fastqc.zip
peEnd2BarcodeFastQcZip,${intermediateDir}/${filePrefix}_${barcode}_2.fq_fastqc.zip
srBarcodeFastQcZip,${intermediateDir}/${filePrefix}_${barcode}.fq_fastqc.zip
#barcodeFastQcFolder,${intermediateDir}/${filePrefix}_${barcode}.fq_fastqc
#barcodeFastQcFolderPE,${intermediateDir}/${filePrefix}_${barcode}_1.fq_fastqc
alignedSam,${intermediateDir}/${filePrefix}_${barcode}.sam
alignedBam,${intermediateDir}/${filePrefix}_${barcode}.bam
alignedFilteredBam,${intermediateDir}/${filePrefix}_${barcode}.bam
alignedFilteredBai,${intermediateDir}/${filePrefix}_${barcode}.bai
sortedBam,${intermediateDir}/${externalSampleID}.Aligned.sortedByCoord.out.bam
sortedBai,${intermediateDir}/${externalSampleID}.Aligned.sortedByCoord.out.bai
addOrReplaceGroupsBam,${intermediateDir}/${externalSampleID}.rg.sorted.bam
addOrReplaceGroupsBai,${intermediateDir}/${externalSampleID}.rg.sorted.bai
sampleMergedBam,${intermediateDir}/${externalSampleID}.sorted.merged.bam
sampleMergedBai,${intermediateDir}/${externalSampleID}.sorted.merged.bam.bai
sampleMergedBamExt,sorted.merged.bam
sampleMergedDedupBam,${intermediateDir}/${externalSampleID}.sorted.merged.dedup.bam
sampleMergedDedupBai,${intermediateDir}/${externalSampleID}.sorted.merged.dedup.bam.bai
starLogFile,${intermediateDir}/${externalSampleID}.hisat.final.log,
##### Protocols 4,5a,5b,5c (SplitAndTrim,GatkHaplotypeCallerGvcf,GatkMergeGvcf,GatkGenotypeGvcf) #####
splitAndTrimBam,${intermediateDir}${externalSampleID}.sorted.merged.dedup.splitAndTrim.bam
splitAndTrimBai,${intermediateDir}${externalSampleID}.sorted.merged.dedup.splitAndTrim.bai
splitAndTrimShortBam,${externalSampleID}.sorted.merged.dedup.splitAndTrim.bam
splitAndTrimShortBai,${externalSampleID}.sorted.merged.dedup.splitAndTrim.bai
indelRealignedBam,${intermediateDir}${externalSampleID}.sorted.merged.dedup.splitAndTrim.realigned.bam
indelRealignedBai,${intermediateDir}${externalSampleID}.sorted.merged.dedup.splitAndTrim.realigned.bai
bqsrBeforeGrp,${intermediateDir}${externalSampleID}.before.grp
bqsrBam,${intermediateDir}${externalSampleID}.sorted.merged.dedup.splitAndTrim.bqsr.bam
bqsrBai,${intermediateDir}${externalSampleID}.sorted.merged.dedup.splitAndTrim.bqsr.bai
gatkHaplotypeCallerGvcf,${intermediateDir}${externalSampleID}.GatkHaplotypeCallerGvcf.g.vcf.gz
gatkHaplotypeCallerGvcftbi,${intermediateDir}${externalSampleID}.GatkHaplotypeCallerGvcf.g.vcf.gz.tbi
gatkMergeGvcf,${intermediateDir}${externalSampleID}.MergeGvcf.g.vcf
gatkMergeGvcfidx,${intermediateDir}.MergeGvcf.g.vcf.idx
projectBatchGenotypedVariantCalls,${projectPrefix}.variant.calls.genotyped.vcf.gz
projectBatchCombinedVariantCalls,${projectPrefix}.variant.calls.combined.g.vcf.gz
projectBatchGenotypedVIPPrefix,${projectPrefix}.variant.calls.genotyped.vip
##### Protocols 2,7 (QCStats, QC_Report) #####
collectMultipleMetricsPrefix,${intermediateDir}${externalSampleID}
flagstatMetrics,${intermediateDir}${externalSampleID}.flagstat
idxstatsMetrics,${intermediateDir}${externalSampleID}.idxstats
dupStatMetrics,${intermediateDir}${externalSampleID}.mdupmetrics
rnaSeqMetrics,${intermediateDir}${externalSampleID}.collectrnaseqmetrics
strandedness,${intermediateDir}stranded.txt
alignmentMetrics,${intermediateDir}${externalSampleID}.alignment_summary_metrics
insertsizeMetrics,${intermediateDir}${externalSampleID}.insertsizemetrics
insertsizeMetricspdf,${intermediateDir}${externalSampleID}.insert_size_histogram.pdf
insertsizeMetricspng,${intermediateDir}${externalSampleID}.insert_size_histogram.png
qcMatricsList,${intermediateDir}/${project}_qcMatricsList.txt
gcPlotList,${intermediateDir}/${project}_gcPlotList.txt
recreateinsertsizepdfR,createInsertSizePlot.R
qcMatrics,${intermediateDir}/${externalSampleID}.total.qc.metrics.table
##### Protocols 3,6 (HTSeq count, MakeExpressionTable) #####
sampleHTseqExpressionText,${intermediateDir}/${externalSampleID}.counts.txt
projectHTseqExpressionTable,${intermediateDir}/${project}.expression.counts.table
rnaSeQCGTF,/groups/umcg-solve-rd/tmp01/rna/projects/ithaca/run01/results/RNA-SeQC/gencode.v19.annotation.patched_contigs.genes.gtf
rnaSeQCDir,${projectResultsDir}/RNA-SeQC
##### GENOME,INDEX,ANNOTATION FILES #####
geneAnnotationTxt,${ensembleDir}/${annotationFileName}.${ensembleReleaseVersion}.annotation.geneIds.txt.gz
annotationGtf,/groups/umcg-solve-rd/tmp01/resources/GAD/gtf/hg19.refseq.with_genes.gtf
houseKeepingGenesBed,/groups/umcg-solve-rd/tmp01/resources/GAD/gtf/hg19.HouseKeepingGenes.bed
annotationTxt,/groups/umcg-solve-rd/tmp01/resources/GAD/others/hg19.refseq.with_genes.txt
gencodeHg19AllExons,/groups/umcg-solve-rd/tmp01/resources/GAD/gtf/gencode_hg19_all_exons.txt.gz
annotationRefFlat,/groups/umcg-solve-rd/tmp01/resources/GAD/gtf/Homo_sapiens.hg19.refFlat
annotationIntervalList,/groups/umcg-solve-rd/tmp01/resources/GAD/gtf/hg19_rRNA.interval_list
gtexJunc,/groups/umcg-solve-rd/tmp01/resources/GAD/others/GTEx_v7_bflb_junctions.gct
omimList,/groups/umcg-solve-rd/tmp01/resources/GAD/others/OMIM2.list
indexFile,${indexSpecies}
dbsnpVcf,${dbSNPDir}/dbsnp_138.${genome}.vcf
starIndex,/groups/umcg-solve-rd/tmp01/resources/GAD/index/
#### GENOME VARIABLES ####
genome,hg19
ensembleReleaseVersion,75
##### GENOME,INDEX,ANNOTATION FILES #####
annotationFileName,Homo_sapiens.${genome}
speciesFileName,homo_sapiens
indexFileID,hg19_essential.fa
indexFolderName,human_g1k_v37
dbSNPFileID,dbsnp_138.${genome}
indicesDir,${dataDir}/ftp.broadinstitute.org/bundle/2.8/${genome}/
dbSNPDir,/groups/umcg-solve-rd/tmp01/resources/GAD/dbnsp/
indexFileFastaIndex,${indexSpecies}.fai
indexSpecies,/groups/umcg-solve-rd/tmp01/resources/GAD/index/${indexFileID}
indexChrIntervalList,${indicesDir}/${indexFileID}.chr${chr}.interval_list
indexFileDictionary,${indexSpecies}.dict
bed12,/groups/umcg-solve-rd/tmp01/resources/GAD/gtf/hg19.refGene.bed12
MillsAnd1000GGoldGtandard,/apps/data/1000G/phase1/Mills_and_1000G_gold_standard
annotationFile,${dataDir}Ensembl/GrCh37.75/pub/release-75/gtf/${speciesFileName}/${annotationFileName}.75_nodupes_genid.txt
ensembleDir,/groups/umcg-solve-rd/tmp01/resources/GAD/gtf/${speciesFileName}/
spliceaiSnv,/apps/data/SpliceAI/GRCh37/spliceai_scores.raw.snv.vcf.gz
spliceaiIndel,/apps/data/SpliceAI/GRCh37/spliceai_scores.raw.indel.vcf.gz