0c43ed269b3d58f6f3c47bc1f1c9f40d *CITATION
ba7c7f33f7c7d00f2d51fffead93b1e5 *DESCRIPTION
343121bf2887732c40246d5dc2d05f07 *INDEX
6f3cad6d275d03ea2fb0f05694fe3bf3 *Meta/Rd.rds
41622305d1b139d0fa70aaba76dca134 *Meta/features.rds
2b4871b511ee77d86dfd4bb8e8675636 *Meta/hsearch.rds
b9935ac22fa1f4f491c67b17b86150d8 *Meta/links.rds
c57fd2b3051ef5dc5a422a903c0dd970 *Meta/nsInfo.rds
35676e7f17829d7c133a4ff591881660 *Meta/package.rds
2528cfa87fbcba208f70542f764f53a6 *Meta/vignette.rds
5039ed970554e5064781652457b75d3c *NAMESPACE
2efec1ffbbbc958099ef4809aeba8c9f *NEWS
d6c68f1fe41ced6e98a766a3757313da *R/systemPipeR
873745d3a72f6fcf8a68495a9910363f *R/systemPipeR.rdb
4b7ec8abfdbeb0f32cf966576fb8d07d *R/systemPipeR.rdx
8db74218c652f5c486cdc6ecf2ee2a84 *doc/index.html
1f00e2c97bf6ecc9b2ccac9440d1eed1 *doc/systemPipeR.R
42b6e579a85e7736f0012035036ac696 *doc/systemPipeR.Rmd
cade23f534452c49ac4211930888f1c0 *doc/systemPipeR.html
942fb7cc756b8e93bd2826ba2b7e6735 *doc/systemPipeR_workflows.R
8ce2ddfe48139201765d5cb4cdca5162 *doc/systemPipeR_workflows.Rmd
f2ce27ac1160799d7adff67b8a972555 *doc/systemPipeR_workflows.html
2dfc76227438c9764f47c48e2bec4f74 *extdata/Makefile
a69a77c9f9594a49ccd98aca578aa083 *extdata/SPR_software.csv
0135dc75ac8eb4048acd3d0b94ee5b30 *extdata/SPRtest.Rmd
78dda8645d323b468922f7e483be4c9c *extdata/alignStats.xls
f11c8bb8f32228337b590ea3f00b3ea1 *extdata/annotate_peaks.param
2930ca439a416d3be1692445c4570ae2 *extdata/annotate_vars.param
b56ac54dfe8a00a3c0cf69b9f8bb5412 *extdata/batchtools.sge.tmpl
bf776f7e37868b525fcac63222ddb851 *extdata/batchtools.slurm.tmpl
019e928f86c0f129cd54810ba3997599 *extdata/batchtools.torque.tmpl
3dd1314bc7adebaf6a5e5c6baf32422a *extdata/bowtiePE.param
5ab954737e604f7db27511ad75bcd8d9 *extdata/bowtieSE.param
08d4b5aa439c40e5579c62040e084e0f *extdata/bwa.param
784a3074752b394df008f0fb9e6ab9fc *extdata/countDFeByg.xls
c6911d9f8ebc54a6775821f1dc44286a *extdata/count_rangesets.param
b430bc8fb548a51d84917a8c587280e6 *extdata/custom_Fct.R
f9b49d465d2fd5170140d4b9b128ee57 *extdata/cwl/BUSCO/BUSCO.cwl
fad6d24691ba15c121b2f570d6b34b89 *extdata/cwl/BUSCO/BUSCO.yml
3ba4f8e7bdae88c8bdfdc1b494ffc519 *extdata/cwl/BUSCO/runME
eec429570256ec35390f884c5600d22e *extdata/cwl/BUSCO/workflow_BUSCO.cwl
ad2d494b8a42a669bbecf717367309f6 *extdata/cwl/MACS2/MACS2-input/macs2-input.cwl
5f6ceb2af55a96e664879cc68c9db2e1 *extdata/cwl/MACS2/MACS2-input/macs2.yml
eabccde8c21d7d9f6149e5e808e85266 *extdata/cwl/MACS2/MACS2-noinput/macs2.cwl
0e9d5221a833e64afdc7e58f7e01d998 *extdata/cwl/MACS2/MACS2-noinput/macs2.yml
3cf1d208a19ba6346a1739a004f96b7c *extdata/cwl/MACS2/macs2-input.cwl
57fd101de41380bea29a747dce3aef48 *extdata/cwl/MACS2/macs2-input.yml
5b8e0b431e5f32e1daf7290743effaba *extdata/cwl/MACS2/macs2-noinput.cwl
8616b76b1a747224a7a528f19b2d6f90 *extdata/cwl/MACS2/macs2-noinput.yml
ddfef8e40cc231287c62f5fc46a40dc9 *extdata/cwl/MACS2/workflow_macs2-input.cwl
2de066310d4970d53b3cfd54a7c194eb *extdata/cwl/MACS2/workflow_macs2-noinput.cwl
b8a7271f18209dbcc61531e4caf18d6c *extdata/cwl/annotate_peaks/annotate_peaks.cwl
f8ad9796ec75f3dec67e7c72c5198c78 *extdata/cwl/annotate_peaks/annotate_peaks.yml
3dc1b8275f57251d29959d714cc90816 *extdata/cwl/annotate_peaks/workflow_annotate_peaks.cwl
f703989056352d66f929efad8fac2365 *extdata/cwl/blast/blastdbcmd.cwl
eb2c79a34dded3039cdbf85bf140911e *extdata/cwl/blast/blastdbcmd.yml
69e8016744a2e0302f25557da06f3603 *extdata/cwl/blast/blastp.cwl
40369e1b9c5182ceedb1205fb1d9c91c *extdata/cwl/blast/blastp.yml
95fbf1f05d45d5971add59ed3375824a *extdata/cwl/blast/cat.cwl
00f0be007c4c1e6af034d6006eed85e8 *extdata/cwl/blast/cat.yml
ce3ddb8e6138979d6c33d8bfb8f8a50d *extdata/cwl/blast/makeblastdb.cwl
243a21980163409702dcfb3cfb233f9e *extdata/cwl/blast/makeblastdb.yml
992399e405f3a44ec6ccba733650d519 *extdata/cwl/blast/workflow_blastp.cwl
a1869dfed9241038c81579f88c0d2e0a *extdata/cwl/blast/workflow_makeblastdb.cwl
0559abd1991308d95aa2c2b2cd18eb99 *extdata/cwl/bowtie2/bowtie2-idx/bowtie2-index.cwl
cb02d1fe51abf551dfca61866e8da309 *extdata/cwl/bowtie2/bowtie2-idx/bowtie2-index.yml
0559abd1991308d95aa2c2b2cd18eb99 *extdata/cwl/bowtie2/bowtie2-index.cwl
cb02d1fe51abf551dfca61866e8da309 *extdata/cwl/bowtie2/bowtie2-index.yml
64fd352bd26d049ef9c7e5bde260f455 *extdata/cwl/bowtie2/bowtie2-mapping-mi.cwl
c9dab4031967f7339455231e8ade2539 *extdata/cwl/bowtie2/bowtie2-mapping-mi.yml
38014814db0cac22544cf17d42bf3113 *extdata/cwl/bowtie2/bowtie2-mapping-pe.cwl
f21c94ce1f2e7ac11392075657c35d12 *extdata/cwl/bowtie2/bowtie2-mapping-pe.yml
5089992573a7e5705f02ec23781d2b27 *extdata/cwl/bowtie2/bowtie2-mapping-se.cwl
2213f42b9e75b63f6b79b0d7554d02fe *extdata/cwl/bowtie2/bowtie2-mapping-se.yml
38014814db0cac22544cf17d42bf3113 *extdata/cwl/bowtie2/bowtie2-pe/bowtie2-mapping-pe.cwl
f21c94ce1f2e7ac11392075657c35d12 *extdata/cwl/bowtie2/bowtie2-pe/bowtie2-mapping-pe.yml
712eab71f0d881c20250722957a100d8 *extdata/cwl/bowtie2/workflow_bowtie2-index.cwl
4346542b160830475944ba2f1bd56f0e *extdata/cwl/bowtie2/workflow_bowtie2-mapping-mi.cwl
c53785dc019fdfe6afd90d4d0b5b140a *extdata/cwl/bowtie2/workflow_bowtie2-mapping-pe.cwl
96387891b25d8d746e2238eff6805e74 *extdata/cwl/bowtie2/workflow_bowtie2-mapping-se.cwl
f171daecf24a9d97d4f4ff75c5fb3469 *extdata/cwl/bwa/bwa-aln.cwl
ea6c2642e0edc6f0b42dda097a01dc9b *extdata/cwl/bwa/bwa-aln.yml
5e4846fe2ede5d84e4c8d712046e8786 *extdata/cwl/bwa/bwa-index.cwl
dbd2f9296d4cfb487f6c2055722ef793 *extdata/cwl/bwa/bwa-index.yml
5e09ec0d877b15d4cc2e9cfa4dc4d75a *extdata/cwl/bwa/bwa-mem-pe.cwl
19f4aa64fb8206751c229a01ccdb14b6 *extdata/cwl/bwa/bwa-mem-pe.yml
a99bbeac41f843ae70615b879538cd6e *extdata/cwl/bwa/bwa-mem-se.cwl
0ef2cacf62fc0991f4406d7589d65ea6 *extdata/cwl/bwa/bwa-mem-se.yml
571d37b728d9543cfdbdd30cc7336f33 *extdata/cwl/bwa/bwa-pe.cwl
19f4aa64fb8206751c229a01ccdb14b6 *extdata/cwl/bwa/bwa-pe.yml
f82c58819859ecfa0eb24ec265cac451 *extdata/cwl/bwa/bwa-samse.cwl
7727f73b28c6a0e9f3f7e2951f7228c9 *extdata/cwl/bwa/bwa-samse.yml
a99bbeac41f843ae70615b879538cd6e *extdata/cwl/bwa/bwa-se.cwl
0ef2cacf62fc0991f4406d7589d65ea6 *extdata/cwl/bwa/bwa-se.yml
404e4e8f61d136f26f1e36a78e2168cf *extdata/cwl/bwa/workflow_bwa-aln.cwl
01bfa8c0be0586ad4cd7b06c96661403 *extdata/cwl/bwa/workflow_bwa-index.cwl
0dbcdcbb9cfe555146fc20c16ed03a27 *extdata/cwl/bwa/workflow_bwa-mem-pe.cwl
7df8f9f9c46cfe57c22e1c0d30ec02d3 *extdata/cwl/bwa/workflow_bwa-mem-se.cwl
999468ac4b9731b443259a88dedfa4d4 *extdata/cwl/bwa/workflow_bwa-pe.cwl
03a81f144c76b799cdc44f50eece1771 *extdata/cwl/bwa/workflow_bwa-samse.cwl
1b27acaf63b50b20e3af2c5ab3a24b45 *extdata/cwl/bwa/workflow_bwa-se.cwl
542a6f92bcec946ce28492ffd44f9b4b *extdata/cwl/count_rangesets/count_rangesets.cwl
87fff4c7241c85412837bd1e1951847d *extdata/cwl/count_rangesets/count_rangesets.yml
f3618024c8aed6e4904b67a035159e4a *extdata/cwl/count_rangesets/workflow_count_rangesets.cwl
47b20dd410fd56413aabf5d71ca19270 *extdata/cwl/cutadapt/cutadapt.cwl
34f424d1b167136ff2bc3d3300191c3d *extdata/cwl/cutadapt/cutadapt.yml
bb2d6a45bb754c57750e27148a5deca7 *extdata/cwl/cutadapt/workflow_cutadapt.cwl
a749f49000c8139c7b846253b0a2f9b4 *extdata/cwl/example/example.cwl
da84395c5687286a117e1ab771947b03 *extdata/cwl/example/example.yml
8a9362e70c8b5c591e7e98bcdb25f096 *extdata/cwl/example/example_single.yml
1adcaac00169b440d26278c9252cdd2c *extdata/cwl/example/targets_example.txt
b62a9160a5fa3da0e704d541578e19b2 *extdata/cwl/example/workflow_example.cwl
bdd2edbc16f9a2c5381faea96cdd7f5e *extdata/cwl/fastq-dump/fastq-dump.cwl
d81e0f33a0f2b65d53e0a9ed99c63e1d *extdata/cwl/fastq-dump/fastq-dump.yml
0df0eeb0ef61c2e1121feee411eef244 *extdata/cwl/fastq-dump/workflow_fastq-dump.cwl
cbe815ffa17d130d00fbd1f9df212e72 *extdata/cwl/fastqc/fastqc-se.cwl
94cdec3b692a4569133bd21884801cd8 *extdata/cwl/fastqc/fastqc-se.yml
c09d50fcbaaf24312526d79c3780a350 *extdata/cwl/fastqc/fastqc.cwl
07cbac60b9b0e621eef7248386484f98 *extdata/cwl/fastqc/fastqc.yml
f7b545f3253d668e83a195cb4a959c68 *extdata/cwl/fastqc/workflow_fastqc.cwl
8b7d9b5b56e646790d76580089926420 *extdata/cwl/fastx_toolkit/fastx_clipper.cwl
ab515ca5b267b71f815c26b79886df51 *extdata/cwl/fastx_toolkit/fastx_clipper.yml
defef2a3f400fc637004c3e851edd89e *extdata/cwl/fastx_toolkit/workflow_fastx_clipper.cwl
0264eec98b631e515e0c1cf6fd0144dd *extdata/cwl/gatk/bwa-index.cwl
5abcfe9245ee335af19ea252f9ee6603 *extdata/cwl/gatk/bwa-pe.cwl
eec0150fcbec4407df535b615f51d873 *extdata/cwl/gatk/fasta_dict.cwl
c91e3abb1f4a8e038d5bb9db10ef96a6 *extdata/cwl/gatk/fasta_faidx.cwl
dc01f629dc157555e0a48b1fe52db4bc *extdata/cwl/gatk/gatk.yaml
2ec7db6323d0d8a31cc9be37ca10dc6b *extdata/cwl/gatk/gatk_fastq2ubam.cwl
92761ca77b29c9851af519a8360df3aa *extdata/cwl/gatk/gatk_fixtag.cwl
da8deea0a0fd319f85bba3c1ea123227 *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
b2ccce4e160f0f01ef84a4dcf88d3839 *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
507a3ad9b622b8438312a4146be8de27 *extdata/cwl/gatk/workflow_bwa-index.cwl
d508e53e58bfcb8994347442ba8fcf87 *extdata/cwl/gatk/workflow_bwa-pe.cwl
c2a81e426f234f729debece64c65c821 *extdata/cwl/gatk/workflow_fasta_dict.cwl
773490e5bfe106b6b71ab7ee12c5cb9f *extdata/cwl/gatk/workflow_fasta_faidx.cwl
7352adecc6b2bc8774068d3a7b55e7a6 *extdata/cwl/gatk/workflow_gatk_fastq2ubam.cwl
3afb2ab6e3ef928cb4ff54aed0ba504f *extdata/cwl/gatk/workflow_gatk_fixtag.cwl
b5f8c9a81290851682e1978abe8a51ec *extdata/cwl/gatk/workflow_gatk_genomicsDBImport.cwl
56617b7f1065c1af012ea6a1b7d09cdb *extdata/cwl/gatk/workflow_gatk_genotypeGVCFs.cwl
b79e6a8cc3f55cd446e48208661f9616 *extdata/cwl/gatk/workflow_gatk_haplotypecaller.cwl
ae892c4512b70a472f65fdbd01b6acb8 *extdata/cwl/gatk/workflow_gatk_markduplicates.cwl
a537942dc80cc07f5e3f2eb284c45d27 *extdata/cwl/gatk/workflow_gatk_mergebams.cwl
87ebaf7bb8c302beda092463b90d256f *extdata/cwl/gatk/workflow_gatk_select_variant.cwl
934adcf8a690175c898d7e15fa1f87c6 *extdata/cwl/gatk/workflow_gatk_sort.cwl
2a53eb309a895dbe03eb928f9f9ed925 *extdata/cwl/gatk/workflow_gatk_variantFiltration.cwl
f9ff79b0096a19afa68a880cdf8c3e9a *extdata/cwl/gsnap/gsnap-index.cwl
15ca93f47e038af192f65449c398af46 *extdata/cwl/gsnap/gsnap-index.yml
ecbc477a42d13370b3957f90cf1807e4 *extdata/cwl/gsnap/gsnap-mapping-pe.cwl
e180fe69b680a9b721ca9e11703a1c5e *extdata/cwl/gsnap/gsnap-mapping-pe.yml
b6262a1e45fc3900895607b92e305833 *extdata/cwl/gsnap/workflow_gsnap-index.cwl
89eca7334cfb243f6e5a189086fc94d2 *extdata/cwl/gsnap/workflow_gsnap-mapping-pe.cwl
093220ab7cef93c0061cff16e42acca9 *extdata/cwl/gunzip/gunzip.cwl
7c5ffec1844681de59b157c917147e9d *extdata/cwl/gunzip/gunzip.yml
82777f870c58cae71247a2169d7a598c *extdata/cwl/gunzip/gzip.cwl
3e5262accb0ab5564e13ea2a80afd2b2 *extdata/cwl/gunzip/gzip.yml
6902696a27c057ef31be727ca5b96d57 *extdata/cwl/gunzip/targets_gunzip.txt
1df3b4470694d4ee884601542970c191 *extdata/cwl/gunzip/workflow_gunzip.cwl
a6596876e361ad3c2506b4ff858cdffe *extdata/cwl/gunzip/workflow_gzip.cwl
ddc99bb5bc3aea62bf0485fbfb7820d8 *extdata/cwl/hisat2/hisat2-index.cwl
e053c7f8e6878c685b1b48df74b95734 *extdata/cwl/hisat2/hisat2-index.yml
ae728ab7f04f42fea16684f16e41edc3 *extdata/cwl/hisat2/hisat2-mapping-pe.cwl
bb0c848659a9860b00cab1c6c7138ff7 *extdata/cwl/hisat2/hisat2-mapping-pe.yml
ab26a15b239b45170d9a62219756c742 *extdata/cwl/hisat2/hisat2-mapping-se.cwl
5d21252ade2596c7f685e167539b64ce *extdata/cwl/hisat2/hisat2-mapping-se.yml
9b040df419a4e140fc0ee9bcaf455c86 *extdata/cwl/hisat2/workflow_hisat2-index.cwl
16171cfef8c56aa857de32cb5ef80470 *extdata/cwl/hisat2/workflow_hisat2-mapping-pe.cwl
c100296066859fa9c9d0984ca58f051f *extdata/cwl/hisat2/workflow_hisat2-mapping-se.cwl
86623ba7cd4ae63fac723921333eabac *extdata/cwl/kallisto/kallisto-index.cwl
aad18d7d92048a316094c1292706eeab *extdata/cwl/kallisto/kallisto.cwl
71b87df5275f4795e6839b3836a22c74 *extdata/cwl/kallisto/kallisto.yml
37ac2de807e23ea176edbe4917dd5a18 *extdata/cwl/kallisto/runME
9b7f6dff56d2819adbf496fde8ebe624 *extdata/cwl/kallisto/workflow_kallisto-index.cwl
0b5290fa34a73dcddeca28fdb869cca6 *extdata/cwl/kallisto/workflow_kallisto.cwl
b45e995b9d19171536d301adc2f13a62 *extdata/cwl/mergeBamByFactor/merge-bam.cwl
3b77796ba8545f7f54cc3473c03850a2 *extdata/cwl/mergeBamByFactor/merge-bam.yml
dd8d60eb988011e15725b56c57efe32a *extdata/cwl/mergeBamByFactor/workflow_merge-bam.cwl
201a31598ec2ada345d50f56d257058f *extdata/cwl/picard/picard_markduplicates.cwl
8fcb2fe0367d53738d12b6ac6a856364 *extdata/cwl/picard/picard_markduplicates.yml
8d71dfe2c3ade0557fb0b611a5d6076e *extdata/cwl/picard/workflow_picard_markduplicates.cwl
f20196e33fa257ede62348648d508ae5 *extdata/cwl/preprocessReads/preprocessReads-pe.cwl
6d15de4e866784d207938d6548994e84 *extdata/cwl/preprocessReads/preprocessReads-pe.yml
c13c0f31fd8740e38e94504f6016755d *extdata/cwl/preprocessReads/preprocessReads-pe_riboseq.yml
f7c04de1daeea9a1ed1132f72964b43e *extdata/cwl/preprocessReads/preprocessReads-se.cwl
a7f47b8b498c2d137a8bd1f191c34f39 *extdata/cwl/preprocessReads/preprocessReads-se.yml
8418a0d62a03e41843f478e71fbf01f7 *extdata/cwl/preprocessReads/trim-pe.cwl
f3ad0e3059effd3cfb2723b224313dc7 *extdata/cwl/preprocessReads/trim-pe.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.cwl
591ec4f02d59f137f7c0e77ebbda9837 *extdata/cwl/preprocessReads/trim-se.yml
816d9e802151975c4c951b357d6d971e *extdata/cwl/preprocessReads/trim-se/trim-se.cwl
591ec4f02d59f137f7c0e77ebbda9837 *extdata/cwl/preprocessReads/trim-se/trim-se.yml
07cf9d446bddea795b0ba251460250be *extdata/cwl/preprocessReads/workflow_trim-pe.cwl
58cacdbf2c9014d5263fa9ccc228d027 *extdata/cwl/preprocessReads/workflow_trim-se.cwl
43f35e656ef2c0cc1832e041ee5596e1 *extdata/cwl/repo_version.txt
f266993b828d16d182cb5ae9acb8a1bc *extdata/cwl/rsubread/rsubread-index.cwl
a202c6f0ae327084e9ebdd7015bb16ff *extdata/cwl/rsubread/rsubread-index.yml
402eece40e1b5e30da72262ef73c90c9 *extdata/cwl/rsubread/rsubread-mapping-se.cwl
41b84d7f1b22e68914a7e6c026abda95 *extdata/cwl/rsubread/rsubread-mapping-se.yml
a5fa9ece57edfec449306747948c53f2 *extdata/cwl/rsubread/workflow_rsubread-index.cwl
a7aa8e1906f5d693d92b8dee323973d0 *extdata/cwl/rsubread/workflow_rsubread-mapping-se.cwl
12b543f2caaa637869ae25d8c7a400ea *extdata/cwl/rundiff/rundiff.cwl
b97ca177a782e76f50f080515f073f97 *extdata/cwl/rundiff/rundiff.yml
8d25161fcf8b483399412ca2d8e8773c *extdata/cwl/rundiff/workflow_rundiff.cwl
70a026c47c7512c757fc1b782926d8d9 *extdata/cwl/samtools/samtools-index.cwl
03916cd4d0a22c4772f0ad4a43892dd5 *extdata/cwl/samtools/samtools-index.yml
581c9a29c7efed382fb7eecc6f4b79f8 *extdata/cwl/samtools/samtools-sort.cwl
909b43097faecfd44686b7fcc1e72855 *extdata/cwl/samtools/samtools-sort.yml
589d97374e1f58f040694c04a7caeebe *extdata/cwl/samtools/samtools-view.cwl
b257f5e6d79e5f239f2e952feddeb0bc *extdata/cwl/samtools/samtools-view.yml
6db64b29887e588a41d9a199f698f1b5 *extdata/cwl/samtools/workflow_samtools-index.cwl
463807d3c95930eecc374bbf163efff8 *extdata/cwl/samtools/workflow_samtools-sort.cwl
3b2980462c4a510b3e043958b5bf65b8 *extdata/cwl/samtools/workflow_samtools-view.cwl
4b5dc6a1b54df2f01d9f48021020dbbe *extdata/cwl/star/runMe
d77068cb2a657032baf6f12a73cda630 *extdata/cwl/star/star-index.cwl
0689d1e528d7aac540ed223ae59501f0 *extdata/cwl/star/star-index.yml
244e1894da0dd919208f2bbef4f15f17 *extdata/cwl/star/star-mapping-pe.cwl
337ae4ff76431f70a07e3740210a4a1c *extdata/cwl/star/star-mapping-pe.yml
2a04a905afa7f2fc472c14bc9e0ba4cb *extdata/cwl/star/star-mapping-se.cwl
cab12ccb0a7785d3eb29ed1f10d37260 *extdata/cwl/star/star-mapping-se.yml
2ac1ee78b2389752ccbbb85cf086c78c *extdata/cwl/star/workflow_star-index.cwl
5f700f69541d16043d326e8b38b8328e *extdata/cwl/star/workflow_star-mapping-pe.cwl
2fe5e6f8fe3e18f7cbd403231f52d9a4 *extdata/cwl/star/workflow_star-mapping-se.cwl
df708071a185bd10a6a35ca7979ff7e2 *extdata/cwl/star/workflow_star-pe-sam_samtools.cwl
6aa01542cc2280d1188935e715da0d70 *extdata/cwl/test/test.cwl
259c043e12754d7b64d3bea8e91ee024 *extdata/cwl/test/test.yml
bb5e80893a2c7dc364d9a5112649181e *extdata/cwl/test/workflow_test.cwl
4f6455082e226f8178f1b9b264098adb *extdata/cwl/tophat2/tophat2-mapping-pe.cwl
a236733cbceb98f71bb7b67586743538 *extdata/cwl/tophat2/tophat2-mapping-pe.yml
b5f69ba05cb5c33c569a589746316342 *extdata/cwl/tophat2/tophat2-mapping-se.cwl
d77a1a65e88e9581ff365c346608a032 *extdata/cwl/tophat2/tophat2-mapping-se.yml
a0d46fd4d2e44c73178e41d9c3f28dd7 *extdata/cwl/tophat2/workflow_tophat2-mapping-pe.cwl
4d3d90a4e7125086ca2bdfdd8bcd5a38 *extdata/cwl/tophat2/workflow_tophat2-mapping-se.cwl
7068ca1126e7d9e6a28cf5647bb8b758 *extdata/cwl/trim_galore/trim_galore-pe.cwl
0bd641dd9fd004126d55313fe390470e *extdata/cwl/trim_galore/trim_galore-pe.yml
633211d9bb774910001308b1e6f49632 *extdata/cwl/trim_galore/trim_galore-se.cwl
8f103ae9e0cb04d8b5a91537f9d4d1b4 *extdata/cwl/trim_galore/trim_galore-se.yml
f8cdf27991c6877921cae2c6aa058676 *extdata/cwl/trim_galore/workflow_trim_galore-pe.cwl
6fbac55ba8f0624118de11feaba98f42 *extdata/cwl/trim_galore/workflow_trim_galore-se.cwl
f0d85d91dfe27b7da02ff24fc0dafb41 *extdata/cwl/trimmomatic/trimmomatic-pe.cwl
57747ea5ecb0479cb8499bf9e98145d8 *extdata/cwl/trimmomatic/trimmomatic-pe.yml
094eee74f5b3259615a98211029c8aac *extdata/cwl/trimmomatic/trimmomatic-se.cwl
0b27dc1eb96e8372d448c84147398c72 *extdata/cwl/trimmomatic/trimmomatic-se.yml
bb1023b004b5668f72a5c0298dae3590 *extdata/cwl/trimmomatic/workflow_trimmomatic-pe.cwl
c4ec8d98d93141009275aea0c8e5a0c6 *extdata/cwl/trimmomatic/workflow_trimmomatic-se.cwl
29196036cf1340e1df9853a05b647794 *extdata/cwl/trinity/runME
0f8cc7f801c97e31df661cf1ed88545e *extdata/cwl/trinity/trinity.cwl
7ba68fc15efacc51b5ab13cc989751e2 *extdata/cwl/trinity/trinity.yml
af117eeceb50063bfba315880205c749 *extdata/cwl/trinity/trinity_stats.cwl
c2e74785a2547458fdc3bbbf80bf94f5 *extdata/cwl/trinity/trinity_stats.yml
1056c6328f74e6b0f57f83ef92a781e6 *extdata/cwl/varseq/annotate.cwl
1f851380858e6e67470ed1754754aadc *extdata/cwl/varseq/combine.cwl
51cd86db31f5c5f71bde57e1a79eb44e *extdata/cwl/varseq/filter.cwl
7d03fe8d8ccf49ec879cfda9faa3a9a4 *extdata/cwl/varseq/varseq.yml
b6130716e1f5846351412cdec81ab11c *extdata/cwl/varseq/workflow_annotate.cwl
06980e5b742557caf50ba626cc526296 *extdata/cwl/varseq/workflow_combine.cwl
eaec76c0028e4afb80e27f566219294c *extdata/cwl/varseq/workflow_filter.cwl
e9762d782d8ba94311b4aeb9ed57a92d *extdata/cwl/workflow-bcftools/bcftools-call.cwl
3a6fbad8f0cad164c83ce2f3cfbdbf81 *extdata/cwl/workflow-bcftools/bcftools.cwl
7d826731c95ee2f449998971f881d643 *extdata/cwl/workflow-bcftools/bcftools.yml
d442f2068e41fc970609526f647b516f *extdata/cwl/workflow-bcftools/samtools-index.cwl
bab3ee831b087ee2eac29bf94890641d *extdata/cwl/workflow-bcftools/samtools-sort.cwl
b9c283f549397a9c611af9240bcccade *extdata/cwl/workflow-bcftools/samtools_markduplicates.cwl
ab95620e8bac0f969c789e3240bbe1ff *extdata/cwl/workflow-bcftools/workflow_bcftools.cwl
faeb82f25292d62ff5e4ee6ebd865716 *extdata/cwl/workflow-bowtie2/workflow_bowtie2-pe.cwl
1f314b5437feb27f504080b5ed9000ad *extdata/cwl/workflow-bowtie2/workflow_bowtie2-pe.yml
76eabc1b2a8493206de579998b5e5e6f *extdata/cwl/workflow-bowtie2/workflow_bowtie2-se.cwl
0219f28fd84da76437406d41268726a7 *extdata/cwl/workflow-bowtie2/workflow_bowtie2-se.yml
ffcd5d14b5d22ba4de3d87d5297fa01d *extdata/cwl/workflow-bwa-aln/workflow_bwa-aln-se.cwl
96e719886528320a82308ebebe6cf384 *extdata/cwl/workflow-bwa-aln/workflow_bwa-aln-se.yml
ef0b0b7e72d840570eeaed4b7add1976 *extdata/cwl/workflow-hisat2/workflow-hisat2-pe/workflow_hisat2-pe.cwl
c66376841a9c1b21ad06f6d902d3419b *extdata/cwl/workflow-hisat2/workflow-hisat2-pe/workflow_hisat2-pe.yml
87c865621678cfd6c850bf980eff478f *extdata/cwl/workflow-hisat2/workflow-hisat2-se/workflow_hisat2-se.cwl
f1dd6219717e70ab0467cde24dea3b61 *extdata/cwl/workflow-hisat2/workflow-hisat2-se/workflow_hisat2-se.yml
28e5feceff8dd05f4296e26883741138 *extdata/cwl/workflow-hisat2/workflow_hisat2-pe.cwl
724cad3757ce67dd82a688639c255f53 *extdata/cwl/workflow-hisat2/workflow_hisat2-pe.yml
5cef7d1b38dac27458199b2de1543c3e *extdata/cwl/workflow-hisat2/workflow_hisat2-se.cwl
f1dd6219717e70ab0467cde24dea3b61 *extdata/cwl/workflow-hisat2/workflow_hisat2-se.yml
a80b83abfb0c20e49ae8a20e02bd8210 *extdata/docopt.R/gsnap/gsnap.doc.R
0ec60142b201f97921e6a87f120db4c4 *extdata/docopt.R/gsnap/gsnap_idx.doc.R
c3cbfad1bfc07acf3d09c517b0b5cbb9 *extdata/docopt.R/preprocessReads/preprocessReads.doc.R
dd6d76edff3a0fdb745d262986eee40b *extdata/docopt.R/rsubread/rsubread.doc.R
a11980ef04b43cd7e88c186db7cbd165 *extdata/docopt.R/rsubread/rsubread_idx.doc.R
a140076686646a8a07fe9c9a8ce6cd91 *extdata/docopt.R/test/test.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
5f7aadbd731bcbaec444dc76dd4a095f *extdata/images/GOslimbarplotMF.png
6fae32862d2e4e981bc801939f1e1f42 *extdata/images/SPR_CWL_hello.png
313be5431e860cfdd2c2d78ebd62dc08 *extdata/images/SPR_WF.png
c40ef318f5d78d24d7f2e9646205e56d *extdata/images/SYSargsList.png
087e13be9dfae45df3468f9c0049b90a *extdata/images/SystemPipeR_Workflow.png
c5e3eb8463a841f4122454bcd54692fb *extdata/images/fastqReport.png
f4b8912fa69465c55ec25503a658ada3 *extdata/images/general.png
4c5b733f81d197f0f87b248544e2fd0a *extdata/images/heatmap1.png
65af7fae458e7ff422c18e61c408ae9f *extdata/images/spr_project.png
c8a0d079e025bf352ed9b7096cf68ca1 *extdata/images/targets_con.png
93c120ea6951091a8752b1d4af5b5ac2 *extdata/images/utilities.png
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
cc7aaece6efa6fb1d6546c037f37eaec *extdata/spr_simple_lw.Rmd
b0845ebd6e88957b9a5f56e256d6236b *extdata/spr_simple_wf.Rmd
9cf4caaa9a2dfb19eb995fd70d97e06d *extdata/targets.txt
a258ef22ea89fd10cb48316d8a492ee1 *extdata/targetsPE.txt
d28177ccf41e00d7375d7db800f159c6 *extdata/targetsPE_chip.txt
ecd47d62b4b4f37d60f51b8a58e961b0 *extdata/targets_chip.txt
639ded39a768ddc16f8ef6917f61a32a *extdata/toolsCollection.Rmd
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
43ba9ac340cbc09c3f670265c8129962 *help/AnIndex
2ca86ec122fa8511a4526ecfb0617e35 *help/aliases.rds
9f15304406048f267c9019f9b59d1333 *help/paths.rds
4efd3e0011567f6fd4b347a948be6af5 *help/systemPipeR.rdb
7bfaf4c20ac6550bc9d64dd320e301dc *help/systemPipeR.rdx
0f2c5035b09472984c16cf390c03391f *html/00Index.html
8b9362669af13540a86a3ac6cf22f99d *html/R.css
cb8f9af77ee975a404f6d993be1d6830 *htmlwidgets/lib/plotwf/dom_to_image.js
8f1068bacff9731fe54c62ea63dbf625 *htmlwidgets/lib/plotwf/full.render.js
39fa41b6f252a7842c2d4aa40af81099 *htmlwidgets/lib/plotwf/plotwf.css
a8831f8262f9dd139111681540fe5b99 *htmlwidgets/lib/plotwf/viz.js
5b2057eff7f99d1871f3281b7246aa21 *htmlwidgets/plotwf.js
aba2f1c3ab9b8cb44ac887c7fd352d47 *htmlwidgets/plotwf.yaml
278596bbb69ee85a3bd326a8cb987dd8 *htmlwidgets/plotwf_legend.svg
