0c43ed269b3d58f6f3c47bc1f1c9f40d *CITATION
a8ac90199d663abb0101a60bb5386381 *DESCRIPTION
5b655613a419a5f62868cf61996033f7 *INDEX
d2151b1567439b3b9e636e3404d2038d *Meta/Rd.rds
e00065855163c282e8adab2a116bf019 *Meta/features.rds
1ab04926d049307e5338fa893bb36a61 *Meta/hsearch.rds
6cc5d10448f05056521bf1cd882c5f6f *Meta/links.rds
8dd2c65310f7b815e3cac1058cf8d897 *Meta/nsInfo.rds
25557b02cacb464718f068bf966ebf9c *Meta/package.rds
f7652ce25f6cd7e9e6e79723a2c2d895 *Meta/vignette.rds
3ece638c3f3f16caee251f39538afc9f *NAMESPACE
2efec1ffbbbc958099ef4809aeba8c9f *NEWS
ebf0fc819595d631b8bf280c4b049940 *R/systemPipeR
1e82a4e334a0087236dcb0783399bd4d *R/systemPipeR.rdb
0d057c523763ab66e8105887fbe63845 *R/systemPipeR.rdx
6c1ebb8eb8f4e54cb3f93d7cac14454c *doc/index.html
c1ae1956fd9539dfec06aba0ec058677 *doc/systemPipeR.R
a228a234ab897052c80054b9e1e63d17 *doc/systemPipeR.Rmd
42127cea01c4cde032e42c24d982d39a *doc/systemPipeR.html
8da01a65a12cc7e36c98e800da6116e7 *doc/systemPipeR_workflows.R
4c87f80625a8f8fab1fdaffac8f65fae *doc/systemPipeR_workflows.Rmd
926e13ad5fec4063c68c56133b1e10a9 *doc/systemPipeR_workflows.html
2dfc76227438c9764f47c48e2bec4f74 *extdata/Makefile
78dda8645d323b468922f7e483be4c9c *extdata/alignStats.xls
f11c8bb8f32228337b590ea3f00b3ea1 *extdata/annotate_peaks.param
2930ca439a416d3be1692445c4570ae2 *extdata/annotate_vars.param
b56ac54dfe8a00a3c0cf69b9f8bb5412 *extdata/batchtools.sge.tmpl
d6101b3d20dd941fe80804bb501e37f3 *extdata/batchtools.slurm.tmpl
92f0f8ab7128a46c373df4c9bcf4a64f *extdata/batchtools.torque.tmpl
3dd1314bc7adebaf6a5e5c6baf32422a *extdata/bowtiePE.param
5ab954737e604f7db27511ad75bcd8d9 *extdata/bowtieSE.param
aae4033870a0ef00a873be0b1b057f76 *extdata/bwa.param
784a3074752b394df008f0fb9e6ab9fc *extdata/countDFeByg.xls
c6911d9f8ebc54a6775821f1dc44286a *extdata/count_rangesets.param
b430bc8fb548a51d84917a8c587280e6 *extdata/custom_Fct.R
ad2d494b8a42a669bbecf717367309f6 *extdata/cwl/MACS2/MACS2-input/macs2-input.cwl
138154e1300b79299d701afdecc7ef98 *extdata/cwl/MACS2/MACS2-input/macs2.yml
eabccde8c21d7d9f6149e5e808e85266 *extdata/cwl/MACS2/MACS2-noinput/macs2.cwl
9325331c837319f7e159c8cba7ae50e4 *extdata/cwl/MACS2/MACS2-noinput/macs2.yml
b8a7271f18209dbcc61531e4caf18d6c *extdata/cwl/annotate_peaks/annotate-peaks.cwl
f8ad9796ec75f3dec67e7c72c5198c78 *extdata/cwl/annotate_peaks/annotate-peaks.yml
c46659e93c06113fdba278ed3d058339 *extdata/cwl/bowtie2/bowtie2-idx/bowtie2-index.cwl
074c68ef3a8688a2c68efd0aab5066d8 *extdata/cwl/bowtie2/bowtie2-idx/bowtie2-index.yml
93d2a8f482ed0b9255147613c7efd6d0 *extdata/cwl/bowtie2/bowtie2-pe/bowtie2-mapping-pe.cwl
860d6e45cfd99eabc2df1f609d883696 *extdata/cwl/bowtie2/bowtie2-pe/bowtie2-mapping-pe.yml
c13224f961042c180c4d0a3e88e86e95 *extdata/cwl/bowtie2/bowtie2-se/bowtie2-mapping-se.cwl
4c6fe7be83e5c038a1e9ba7dab14862b *extdata/cwl/bowtie2/bowtie2-se/bowtie2-mapping-se.yml
5e4846fe2ede5d84e4c8d712046e8786 *extdata/cwl/bwa/bwa-idx/bwa-index.cwl
dbd2f9296d4cfb487f6c2055722ef793 *extdata/cwl/bwa/bwa-idx/bwa-index.yml
571d37b728d9543cfdbdd30cc7336f33 *extdata/cwl/bwa/bwa-pe/bwa-pe.cwl
19f4aa64fb8206751c229a01ccdb14b6 *extdata/cwl/bwa/bwa-pe/bwa-pe.yml
a99bbeac41f843ae70615b879538cd6e *extdata/cwl/bwa/bwa-se/bwa-se.cwl
0ef2cacf62fc0991f4406d7589d65ea6 *extdata/cwl/bwa/bwa-se/bwa-se.yml
542a6f92bcec946ce28492ffd44f9b4b *extdata/cwl/count_rangesets/count_rangesets.cwl
87fff4c7241c85412837bd1e1951847d *extdata/cwl/count_rangesets/count_rangesets.yml
0264eec98b631e515e0c1cf6fd0144dd *extdata/cwl/gatk/bwa-index.cwl
5460201a1aa290de2884c1f9ed0066a2 *extdata/cwl/gatk/bwa-pe.cwl
eec0150fcbec4407df535b615f51d873 *extdata/cwl/gatk/fasta_dict.cwl
8f72c86dfeaf1bf4d5a72381998e71d6 *extdata/cwl/gatk/fasta_faidx.cwl
b71356111ae5b4432915b3c0b26d8293 *extdata/cwl/gatk/gatk.yaml
2ec7db6323d0d8a31cc9be37ca10dc6b *extdata/cwl/gatk/gatk_fastq2ubam.cwl
92761ca77b29c9851af519a8360df3aa *extdata/cwl/gatk/gatk_fixtag.cwl
e59adecfbe59a3b26888c7fc32e50e3c *extdata/cwl/gatk/gatk_genomicsDBImport.cwl
b159f2bf3d9b8249d89dcb0269ea4351 *extdata/cwl/gatk/gatk_genomicsDBImport.sh
c96504ede752cae32e7a2de2c8850ada *extdata/cwl/gatk/gatk_genotypeGVCFs.cwl
9c9178e982a3f6ebdf9a0adaf830cff2 *extdata/cwl/gatk/gatk_haplotypecaller.cwl
c00b9c20baf6adc90c92873a4ca5a52e *extdata/cwl/gatk/gatk_markduplicates.cwl
f6328528317795de046e1ed278df26f3 *extdata/cwl/gatk/gatk_mergebams.cwl
d8b02e18e3967bb73633a689f3d3a0cf *extdata/cwl/gatk/gatk_select_variant.cwl
ab1d5764848e0a7334eec76e7b2ef5c8 *extdata/cwl/gatk/gatk_sort.cwl
c479c3e866bbdc2efcf9914334a4aaf7 *extdata/cwl/gatk/gatk_variantFiltration.cwl
f2e9533282a015dba0be1cab2dca1cb7 *extdata/cwl/gatk/gatk_variantFiltration.sh
f9ff79b0096a19afa68a880cdf8c3e9a *extdata/cwl/gsnap/gsnap-idx/gsnap-index.cwl
15ca93f47e038af192f65449c398af46 *extdata/cwl/gsnap/gsnap-idx/gsnap-index.yml
ecbc477a42d13370b3957f90cf1807e4 *extdata/cwl/gsnap/gsnap-pe/gsnap-mapping-pe.cwl
e180fe69b680a9b721ca9e11703a1c5e *extdata/cwl/gsnap/gsnap-pe/gsnap-mapping-pe.yml
5b946d38a49b7253fa77b605da8ca29d *extdata/cwl/hisat2/hisat2-idx/hisat2-index.cwl
e053c7f8e6878c685b1b48df74b95734 *extdata/cwl/hisat2/hisat2-idx/hisat2-index.yml
1433c7bad84c86f21f055daccc799232 *extdata/cwl/hisat2/hisat2-pe/hisat2-mapping-pe.cwl
bb0c848659a9860b00cab1c6c7138ff7 *extdata/cwl/hisat2/hisat2-pe/hisat2-mapping-pe.yml
bece5fff5abbbfb37c821f3a7b7612a4 *extdata/cwl/hisat2/hisat2-se/hisat2-mapping-se.cwl
5d21252ade2596c7f685e167539b64ce *extdata/cwl/hisat2/hisat2-se/hisat2-mapping-se.yml
b45e995b9d19171536d301adc2f13a62 *extdata/cwl/mergeBamByFactor/merge-bam.cwl
3b77796ba8545f7f54cc3473c03850a2 *extdata/cwl/mergeBamByFactor/merge-bam.yml
8418a0d62a03e41843f478e71fbf01f7 *extdata/cwl/preprocessReads/trim-pe/trim-pe.cwl
f3ad0e3059effd3cfb2723b224313dc7 *extdata/cwl/preprocessReads/trim-pe/trim-pe.yml
816d9e802151975c4c951b357d6d971e *extdata/cwl/preprocessReads/trim-se/trim-se.cwl
591ec4f02d59f137f7c0e77ebbda9837 *extdata/cwl/preprocessReads/trim-se/trim-se.yml
f266993b828d16d182cb5ae9acb8a1bc *extdata/cwl/rsubread/rsubread-idx/rsubread-index.cwl
a202c6f0ae327084e9ebdd7015bb16ff *extdata/cwl/rsubread/rsubread-idx/rsubread-index.yml
402eece40e1b5e30da72262ef73c90c9 *extdata/cwl/rsubread/rsubread-se/rsubread-mapping-se.cwl
41b84d7f1b22e68914a7e6c026abda95 *extdata/cwl/rsubread/rsubread-se/rsubread-mapping-se.yml
12b543f2caaa637869ae25d8c7a400ea *extdata/cwl/rundiff/rundiff.cwl
b97ca177a782e76f50f080515f073f97 *extdata/cwl/rundiff/rundiff.yml
d9efe31a8181665e53cb5d0e54dc601b *extdata/cwl/samtools/samtools-index.cwl
c36e837ac995448232323e4710ed5015 *extdata/cwl/samtools/samtools-index.yml
72534747d6f071e492817da30e8c88f7 *extdata/cwl/samtools/samtools-sort.cwl
220ace1269ea979e079c0d3f271d7812 *extdata/cwl/samtools/samtools-sort.yml
299399dfd6706ed4eaf6de44f9606a73 *extdata/cwl/samtools/samtools-view.cwl
aaacae9ba755d21358115f6156025a5c *extdata/cwl/samtools/samtools-view.yml
4f6455082e226f8178f1b9b264098adb *extdata/cwl/tophat2/tophat2-pe/tophat2-mapping-pe.cwl
a236733cbceb98f71bb7b67586743538 *extdata/cwl/tophat2/tophat2-pe/tophat2-mapping-pe.yml
b5f69ba05cb5c33c569a589746316342 *extdata/cwl/tophat2/tophat2-se/tophat2-mapping-se.cwl
d77a1a65e88e9581ff365c346608a032 *extdata/cwl/tophat2/tophat2-se/tophat2-mapping-se.yml
4332c7313f61f054258ef3183ad2b370 *extdata/cwl/trim_galore/trim_galore-pe/trim_galore-pe.cwl
0cf3af2c43f8c687ae8c0624da69da24 *extdata/cwl/trim_galore/trim_galore-pe/trim_galore-pe.yml
ef9f218ebde44c1068443eb85ed4599c *extdata/cwl/trim_galore/trim_galore-se/trim_galore-se.cwl
81f30b192f792647b8368f90dd4daa9c *extdata/cwl/trim_galore/trim_galore-se/trim_galore-se.yml
f770eef02f17989f8c62069900a9fafe *extdata/cwl/trimmomatic/trimmomatic-pe/trimmomatic-pe.cwl
6ce905e9226c0a161aecd50d8db0ca92 *extdata/cwl/trimmomatic/trimmomatic-pe/trimmomatic-pe.yml
5a00ddd355642e84938301850ebe79f0 *extdata/cwl/trimmomatic/trimmomatic-se/trimmomatic-se.cwl
078c239a55434136335ef053affbeb45 *extdata/cwl/trimmomatic/trimmomatic-se/trimmomatic-se.yml
1056c6328f74e6b0f57f83ef92a781e6 *extdata/cwl/varseq/annotate.cwl
1f851380858e6e67470ed1754754aadc *extdata/cwl/varseq/combine.cwl
51cd86db31f5c5f71bde57e1a79eb44e *extdata/cwl/varseq/filter.cwl
d06cbf7091c24cf9bd39c5afa5873b6a *extdata/cwl/varseq/varseq.yml
b24da5219c28140ba5463f235180e12c *extdata/cwl/workflow-bcftools/bcftools-call.cwl
808d94b0df0022bdf6dcf849ea71b350 *extdata/cwl/workflow-bcftools/bcftools.cwl
3d23f205be4bb97e3132cdd36080b63a *extdata/cwl/workflow-bcftools/bcftools.yml
d55562228ef70b139adb64427de66278 *extdata/cwl/workflow-bcftools/samtools-index.cwl
1de676e598818d5b16f5fb2714bf7a60 *extdata/cwl/workflow-bcftools/samtools-sort.cwl
304d725d22ea3f8c8cbc67882d8158a6 *extdata/cwl/workflow-bcftools/samtools_markduplicates.cwl
26b49975cea219e90b860b19bfeef6f6 *extdata/cwl/workflow-bcftools/workflow_bcftools.cwl
ef0b0b7e72d840570eeaed4b7add1976 *extdata/cwl/workflow-hisat2/workflow-hisat2-pe/workflow_hisat2-pe.cwl
0c7bb5d35129b2f55c34d3f478f1bfb1 *extdata/cwl/workflow-hisat2/workflow-hisat2-pe/workflow_hisat2-pe.yml
87c865621678cfd6c850bf980eff478f *extdata/cwl/workflow-hisat2/workflow-hisat2-se/workflow_hisat2-se.cwl
510bb691438fece4116cb413b5a5307d *extdata/cwl/workflow-hisat2/workflow-hisat2-se/workflow_hisat2-se.yml
a80b83abfb0c20e49ae8a20e02bd8210 *extdata/docopt.R/gsnap/gsnap.doc.R
0ec60142b201f97921e6a87f120db4c4 *extdata/docopt.R/gsnap/gsnap_idx.doc.R
dd6d76edff3a0fdb745d262986eee40b *extdata/docopt.R/rsubread/rsubread.doc.R
a11980ef04b43cd7e88c186db7cbd165 *extdata/docopt.R/rsubread/rsubread_idx.doc.R
54e3d6c10356c74053ca1924b8576e21 *extdata/filter_gatk.param
7dcf24ed0132ec529de84fd04c14b202 *extdata/filter_sambcf.param
7cccff803c025141d49159ebe402aece *extdata/filter_vartools.param
78703d16e099b08f184a7b0cae1f08a0 *extdata/gatk.param
b394006139d9d91099117f3916fc4c31 *extdata/gatk_run.sh
ee61c831d0762f41d6182fb4e2d36c8a *extdata/gsnap.param
fc13720d3fe63fcdc3d7a5cfede7a9ed *extdata/hisat2.param
be7fc12857ebb0c00499a5c4e55bd487 *extdata/hisat2PE.param
f95f0134cbad66a16c8307056a8ab4cc *extdata/macs2.param
dca9b2f81e39bad7b57af01f094bc56e *extdata/macs2_noinput.param
9cca89e6cd2ea6e3b8a4e3037d2891e3 *extdata/rpkmDFeByg.xls
3d30cad15d64aebc718192ef099fecd5 *extdata/rsubread.param
7004f0a88e037520b4a65ddd9a85999e *extdata/rundiff.param
205f33a7c2dfc67418ec0303621a141c *extdata/sambcf.param
939b5de645b9bb23b26564c42cc90b10 *extdata/sambcf_run.sh
9cf4caaa9a2dfb19eb995fd70d97e06d *extdata/targets.txt
a258ef22ea89fd10cb48316d8a492ee1 *extdata/targetsPE.txt
d28177ccf41e00d7375d7db800f159c6 *extdata/targetsPE_chip.txt
ecd47d62b4b4f37d60f51b8a58e961b0 *extdata/targets_chip.txt
c67415d483577a02b783755824ba886f *extdata/tophat.param
5b96dca6a17c61b43b5db71e20b54c30 *extdata/trim.param
a3f4e242449c101af6f2c9056696d3a1 *extdata/trimPE.param
5904e0c94dbae1e112a42b42ab9f574b *extdata/trim_galore.param
d4388913521da15431b7c94c17212f5a *extdata/trim_galore_run.sh
f57aa9edff5506cc819e15368b8ab9ad *extdata/vartools.param
1bbd18a89e38974f0d4397078edc597a *help/AnIndex
79fc550bb7750fbb2df4492000a0b987 *help/aliases.rds
77ad469b8d84f21ad72be297c6a5ec8b *help/paths.rds
99b2aa015e5774d1abfe92c3a235d968 *help/systemPipeR.rdb
c5fc81c7910b01328f331673b3ee67ef *help/systemPipeR.rdx
20de46cfba4589b44c0ee617372ad21d *html/00Index.html
354d6ea1a7d67797b7974262f3e9e3a2 *html/GOHyperGAll.html
07c229a11825f6fb5976c650350e69bd *html/INTERSECTset-class.html
b6763e6916890c631fdc3f2643803b1a *html/R.css
b6c47cec2f3481c73bd0f9c55d4db11b *html/SYSargs-class.html
0bbdbeec5fd84e96df7f438375fdfd1a *html/SYSargs2-class.html
aeef06be9ddbb7df233dbfc7bd4e3343 *html/SYSargs2Pipe-class.html
4794b59a05806609fac97ed6ee786148 *html/SYSargs2Pipe-methods.html
cab9a8ce1f0fa61b78dc36b1d75a01c0 *html/SYSargsList-class.html
b2b0480ae01927d171e7af21fe7d5cc5 *html/VENNset-class.html
a9b9fd619f3d6f05da601e7625c4c05b *html/alignStats.html
dd62e6b412f33ed5c851344162c4f3d0 *html/catDB-class.html
e40c35c37fe027c60611b2dd8028c8aa *html/catmap.html
d7bcf6b28ab9e8da2e0a141570bfbafe *html/clusterRun.html
5081fa5d89bf4a72e3bbf9a09d8a0a2a *html/config.param.html
daa5cfd9bbfe9973cbc380f4520655bf *html/configWF.html
ba48e48e20f43d93245b4091d9b4f047 *html/countRangeset.html
3a47b9b46fba1dff5507845ba479092d *html/createWF.html
d74f7005454d26579e9e69c70828a413 *html/evalCode.html
08a9ad378d9c2b13cf0a526c163c80db *html/featureCoverage.html
006d9a263e62fd90e20b7222620f452b *html/featuretypeCounts.html
cb11ac1de0fec06236e96f79f091cf18 *html/filterDEGs.html
e9f83845186a2a7749ed653633721669 *html/filterVars.html
34c805ad9e343f654f736f1509496b73 *html/genFeatures.html
533d6f36f2a2d94ff7b62b187763ff5e *html/getQsubargs.html
8b0db4420a9985c3667e8bc096a9fa3a *html/initWF.html
d3b354020c8baa6dc2612ceb88430e3b *html/loadWorkflow.html
304f1c1dbeeeb639b7c196aa70fa03d4 *html/mergeBamByFactor.html
5f59ddc31f68e72976dc86d33993c28e *html/module.html
157c65c7ec77c1f9e8d485707968ca9e *html/moduleload.html
18620f2dc4acc81b47503dff5409e14a *html/olBarplot.html
d9a3007b7a7df1134fcfdbc80c8d81f1 *html/olRanges.html
f835a3c81d29c09490ff5da342759696 *html/output_update.html
683e68ad1dbd79609d6dc53287280959 *html/overLapper.html
0177b336682ac536f3cdb8054717a582 *html/plotWF.html
6a142a6d550800bc77ea7842774e6b0b *html/plotfeatureCoverage.html
e79f4283bb19fe31c069b3e5e03f7237 *html/plotfeaturetypeCounts.html
c4057729af5f2b53c70a4b6747d70570 *html/predORF.html
2204f2be4bfb02d9a73e3b5bb6e4614e *html/preprocessReads.html
88a94854e75a912f547468996ccca8d0 *html/qsubRun.html
fd382f6978415169368806b5bf92048a *html/readComp.html
03316f406ae24b25b0586ff2acba178a *html/renderReport.html
228da66c57954cb5ec3c29ab324f421a *html/renderWF.html
144131816c08d165870c82a8fdbf5eb6 *html/returnRPKM.html
71498e3ec200c543034f0e9fa49eb89d *html/runCommandline.html
fd109755bb7de701dff27986d76266df *html/runDiff.html
c51bbf2f3744c34a720e09eab34a767e *html/runWF.html
32a156fd1baf3ffa5c9b72127e77d2fc *html/run_DESeq2.html
cbf2b7f3f2919fa37c4d9d720da4d258 *html/run_edgeR.html
d1dc8393ebccae599228cf45ba713dfc *html/run_track.html
7c0df7fc7ea7749cbc7984eb67c41426 *html/scaleRanges.html
8c79039056f6288192958976dbdf7c9c *html/seeFastq.html
17f2aebbf79abf07c83d9d7a43d03ad1 *html/subsetWF.html
9a1a64811fc34069c918a0a060910c35 *html/symLink2bam.html
1b34149b0ddcf29e9db9f0bd23b8ed8f *html/sysargs.html
991ce15aaaf4db549fcbd6e600a25134 *html/sysargs2-methods.html
d661ab4b1f7e4aebd84d2b935eb12d40 *html/sysargslist-methods.html
8471808084c912c357bf7906aeef4e2f *html/systemArgs.html
63f07e2e194ff9036e3dcf5c9bd2d5cd *html/targets.as.df.html
07c351bc59427f5f6b435a24c5dbf916 *html/tryCL.html
d83f7bcb072f78edbad4d8c893d2a84d *html/tryPath.html
773eb00d20964e70008a8dc8851c5e82 *html/variantReport.html
dcb76e8cda3819b08160d334d3d12808 *html/vennPlot.html
1352bc58892b5fd0f2a4bbb73392445e *html/writeTargetsRef.html
5a83007049c1c5033731ada2813eee04 *html/writeTargetsout.html
f02e326f800ee26f04df7961adbf7c0a *unitTests/SRR446027_1.fastq
f02e326f800ee26f04df7961adbf7c0a *unitTests/SRR446028_1.fastq
f02e326f800ee26f04df7961adbf7c0a *unitTests/SRR446029_1.fastq
f02e326f800ee26f04df7961adbf7c0a *unitTests/SRR446030_1.fastq
d3a1df6db3d820a1887c92b6385f113f *unitTests/targets.txt
48bb7620b0ea30ecde2cacf14e388025 *unitTests/test_classes.R
271e9a808cf0872c3a4012f003658498 *unitTests/tophat.param
