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…talling the Travis build
updated trimming/qc details
First release ready
Fixing linting errors and stuff like that
apeltzer
requested changes
Apr 15, 2019
Applied suggestion from PR review. Co-Authored-By: ignaciot <ignaciot@users.noreply.github.com>
…hange request.
edmundmiller
added a commit
that referenced
this pull request
Sep 30, 2021
commit 009fefb264d08e6c6045d8e010e7c4ad76a0f10b
Merge: 3b8d8ba f23d912
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sun Jan 27 15:33:17 2019 -0600
Merge branch 'develop' into feature/IMR
* develop:
Merge in conda environments (#22) Fix: #20
Initial pos2bed rule and fix file label (#21)
Add Homer Find Peaks Fix: #11 (#15)
Add Homer Find Peaks Fix: #12 (#14)
Add bowtie2 rule for GM Fix: #4 (#10)
Finish Fastqc rule Fix: #3 (#9)
Make travis only build master and develop
commit 3b8d8ba8d548bd86b8b8ad36702746d742149403
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 28 11:23:16 2018 -0600
Rearrange All rule to be cleaner
commit ef707e6357308bea9177895549fd1a40b98da773
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 28 00:48:15 2018 -0600
Add IMR fastqc
commit 7083799daf3d6bf6298b01e192bae67717c95af3
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 28 00:42:00 2018 -0600
Forgot to include new rules
commit b00159779f1fdea9c79da829f788dc781e6fdd89
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 28 00:38:57 2018 -0600
Rename output files
commit e82c8e7585b65a1fab1e7d8958233fc6cd596f9e
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 28 00:36:58 2018 -0600
Fix IMR typo
commit edc7b5bf7dc7adc4dffc7d4329cc39824dfae26a
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 28 00:35:49 2018 -0600
Add Test rules for IMR
commit f2acad2dcfe7bd66bc251912af16d467893b161e
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 28 00:11:31 2018 -0600
Fix merge issue
commit 3eea0a9c5e380ceaf731dbda7341e61e2f1825ca
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 28 00:11:10 2018 -0600
Write eRNA prediction
commit a36fb42d267586119a5c2c347813f402598049c8
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 28 00:04:12 2018 -0600
Add remove Genes Rule
Generalize hg19 refseq Rules
commit 136ca385af4a5aadfb9354f0d91886948f9be061
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 28 00:03:58 2018 -0600
Add findPeaks rule
commit 3120a27077fbe413befd1994f53e8047540333e9
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 23:59:27 2018 -0600
Add rule for Homer makeTagDirectory
commit aa9e3d8667818b56def89bec04ba4eea26f65e12
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 23:57:06 2018 -0600
Add bowtie2 rule for IMR
commit 81bdb22f51a7d65157a30bd1df24122745754f51
Merge: 04fb6ee 61b25e9
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 23:51:46 2018 -0600
Data rewrite #29
Finish #17
* feature/data_rewrite: (38 commits)
Add IMR90 Histones
Add naming to GM histones
Fix File and dir and child of another output
Missed GM
Missed hg19 chrom Length
Add rule to download Peng's eRNAs
Missed GM19 bowtie2 rule
Fix hg18 refseq rule
Add IMR90 Download Rule
Move GM data under it's own dir
Add dummy rule for GM Datasets
Change rule naming convention
Fix new genome.fa.fai rule
Add pull in refseq for hg18
Add hg18 bowtie2 reference
Remove unnecessary dependencies
Finish #5 (#28)
Feature/genes histones (#25)
Squashed commit of the following:
Develop (#24)
...
commit 61b25e9b84aea546e4d354525c4a2c0609b4f3a3
Merge: 7be14ab 04fb6ee
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 23:51:06 2018 -0600
Merge branch 'master' into feature/data_rewrite
* master:
Finish #5 (#28)
Squashed commit of the following:
WIP: Predict eRNAs on hg18 (#19)
Move to the Cookiecutter Snakemake workflow (#8)
Update Dag
Add HistonesIntersect
Add Sort to bed
Split Histones
Add getHistones
Add RemoveGenes
Add slopRefSeq
Add Chromosome sizes
Add Genomehg19
Add dag.png
Remove Makefile
Update Snakefile
Update Snakefile
Update README
Add Snakefile
commit 7be14ab1ee9db69e1a2b283a76be199564582105
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 23:43:39 2018 -0600
Add IMR90 Histones
commit e648135d4e76900eb623806752cae9baacabd335
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 23:36:29 2018 -0600
Add naming to GM histones
commit 195b5b07d634174b31ce21099b0f170642761349
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 23:21:14 2018 -0600
Fix File and dir and child of another output
commit dd9640881b12e1638f52abc2ec90766d94bb13c6
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 23:18:25 2018 -0600
Missed GM
commit 67c3a1a2d56e5358152912c95aff397a2af4e6ff
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 23:14:53 2018 -0600
Missed hg19 chrom Length
commit 77181785e300f5d8407fecb76741960a3f3dc94f
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 23:13:57 2018 -0600
Add rule to download Peng's eRNAs
commit 00783456281a6d855c4208045d70cb17fbb40f99
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 23:11:18 2018 -0600
Missed GM19 bowtie2 rule
commit 05cde3346e3fd92c6160c4ee83ceb5fe061d168c
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 23:08:04 2018 -0600
Fix hg18 refseq rule
commit c10d9d66dedf64ca149caf869dc6de2451ec1bb0
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 23:05:07 2018 -0600
Add IMR90 Download Rule
commit e512aa7a709593f25b3c98d1cbac4f1b3152ef82
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 23:01:48 2018 -0600
Move GM data under it's own dir
commit 127a7f529038c9b3f0d666735d02a743cfc93dd7
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 22:56:42 2018 -0600
Add dummy rule for GM Datasets
commit 90ca78f074f7fab5c97ab4ef3223fd0b2a38f6f9
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 22:49:08 2018 -0600
Change rule naming convention
commit 94e965c4a1575f1727dbff11f4aaf30e11ed652a
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 22:46:39 2018 -0600
Fix new genome.fa.fai rule
commit 8d4fee83494c946ecbc5e78e83a30f2f0c2566da
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 22:45:40 2018 -0600
Add pull in refseq for hg18
commit 2e299e56be630579ea9b35dd1fd790874a68ca7a
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 22:38:54 2018 -0600
Add hg18 bowtie2 reference
commit d3114d5401253b322229653b178accacae2faaab
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 22:37:24 2018 -0600
Remove unnecessary dependencies
commit 04fb6eed22248e5a9fae8494296a27b9c375d42e
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 22:23:36 2018 -0600
Finish #5 (#28)
* Clean up files from GM18 recreation
* Add reference Genomes Rules
* Silence the curls
* Add bowtie2 rule for hg19 and GM
* Add seperate unzip rule
* Add hg19 makeTagDirectory Rule
* Change homer Genome to hg18
Crucial mistake. This could be what's off with the reads and reproducing
the exact amount. Fix #12 related to #6
* Fix naming typo
* Add Homer findPeaks for hg19
* Add pos2bed Rule
* Fix unzipping of the hg19 Reference Genome
* Leave the hg18 Reference genome for another day
* Add rule to download AWS iGenomes script
Needs to be made executable #26
* Fix rule to download hg19 bowtie2 from AWS-iGenome
* Remove conda env because of genome issue
* Add download of refseq
* Add hg19 remove genes
* Add rule to predict eRNAs in hg19
* Add prefixes
* Add test for eRNAs
commit 6d703fd70f4cf12b9761575be782eaa5b179c828
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Mon Nov 26 23:18:35 2018 -0600
Squashed commit of the following:
commit aa0f902b7fff698c230d1b9ebb76f9db72700674
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sun Nov 25 17:13:03 2018 -0600
Add rule to sort liftOver Bed files
commit 61ba3c329fdb471947670948089057876635f6d1
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sun Nov 25 17:06:58 2018 -0600
Fix log typo
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Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sun Nov 25 17:05:33 2018 -0600
Fix liftOver rule
commit 5d6f9dffa76cd4a97f9221bb1a40e915e69769a1
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sat Nov 24 23:46:26 2018 -0600
Move mapchain download to data
commit ea69d805571d88cb6972dcaa99a6b24cf6bdd978
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sat Nov 24 23:30:26 2018 -0600
Sort the Histone Bed file
commit 98792de55a0ec62ef54a326bb7d22f8861ca083d
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sat Nov 24 22:39:22 2018 -0600
Try converting Histones to BED files
commit ba817755a716a05e202f66577677387ae94622b1
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sat Nov 24 22:09:38 2018 -0600
Move back to samtools Sort
Trying to figure out how to sort by chromosome
commit 51ca69e0a7ade4b5c86c10fe25feb1f3e76c336b
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sat Nov 24 22:09:13 2018 -0600
Homer needs to be local to have genomes
commit 09d5f1cab1a7861cf544722fecd737a619d6bc68
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Thu Nov 15 23:42:54 2018 -0600
Change from samtools to picard for sorting
commit 871fbf891628fe8d8ed42054ac4ec14c50c1476f
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 14 15:16:41 2018 -0600
Add rules to pull in fastq data for histones
Squashed commit of the following:
commit d64276ca147a7ab85595e4c76b42d945696e797c
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 14 15:13:26 2018 -0600
Update Histone Intersect Rule for sorted files
commit 749267ec7847a97c8a88cb4cab0255212dea030e
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 14 15:12:53 2018 -0600
Write rule to sort Histones for hg18
commit 08f9c11a6f0cf7bff81d7bb63ccfec7010de54a2
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 14 11:32:57 2018 -0600
Add links to the experiments
In case they're needed in the future so they don't need to be hunted down.
commit 5ac1ac3ca91ab2b563a3af80a4868098f25e1cdd
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 14 11:31:48 2018 -0600
Change to curl
The -L flag handles the redirects
commit 7f5112b8800ec006dc37834d4ab50538b2484980
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 14 10:40:41 2018 -0600
Update rules to wget instead of HTTPRemoteProvider
commit f89233a6d0627e700585c44b7ec0d9ad9449c741
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 13 22:51:27 2018 -0600
Update Histone intersect to new Histone files
commit f0338a815d950e8785be3136da76cde10932a946
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 13 22:50:40 2018 -0600
Write rule to align the histones to hg18
commit 6405b7d1c6e99f70d05483b3e4df6810f35ca3b4
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 13 22:34:27 2018 -0600
Write rules for histone downloads
commit ef0c53f9d03e9fe87a2489f9306dbf5a88a4bc50
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 13 13:26:28 2018 -0600
Add initial rules to get GM Histones
Only the links to the files
commit 1205eab3a4e6ca0bea429e72de49f2c322449b5c
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Mon Nov 12 19:11:49 2018 -0600
Squashed commit of the following:
commit f24e1503e960d90b0a45d9fbfd89cd57f63ef622
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Mon Nov 12 18:58:55 2018 -0600
Seperate out liftOver rule
commit 04e0f93c435e89291f6d36e47e45c7cfe71c049a
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sat Nov 10 20:43:57 2018 -0600
Fix typo
commit d42139271bcf563103a503523fec12bcdeb57b47
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sat Nov 10 00:02:27 2018 -0600
Fix env typo
It's running
commit 1b9adc313e2999a0c07e40213f4d2714bef35f0c
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:54:06 2018 -0600
Change me3 to me1
Thanks Chahat for catching that
commit 15425daa148f30b38e21beaf9b464c376f841ac0
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:53:42 2018 -0600
Fix HTTP by moving to one line
commit aa3ab140e4196dd415196bddd3aff61ec0bcadc0
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:52:41 2018 -0600
Fix hg19 typo
commit ba8881c1cb4d3239215736fb5b21758b37d4b639
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:50:58 2018 -0600
Add date to input file
It's late
commit 82f7a27d4ff3e581b8486b14151f42d1fb4e3e8e
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:50:47 2018 -0600
Fix http
commit 7766951bab4731cfa3e28bd7c60cb12597a85b7a
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:48:48 2018 -0600
Get rid of run commands using conda
commit ebcfba05ae4d5c5d95fe714bd34473bf56747c9b
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:48:36 2018 -0600
Update all rules
commit fe2a6641dc2c92a4ea9bec2e45a0446420691447
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:45:05 2018 -0600
Add rules to test both hg19 liftover and hg18
commit ee3fab0ecabd65dd84061c64421592630b93c362
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:44:32 2018 -0600
Add liftover rule Fix: #23
commit b556f4ce32bc47115f8c36de5fcdfa53d164a295
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:00:06 2018 -0600
Add rule to all to make eRNAs
commit c8a948e7c1b6e549fd941cfd3376d525677986f6
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:00:06 2018 -0600
Add rule to all to make eRNAs
commit 2e73abac401db7426f14430c91eca6e7e83f2fb4
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 22:58:51 2018 -0600
Add initial Histone Intersect rule
commit d1344986f545161976d22f96fb2d1e8059a84302
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 22:46:30 2018 -0600
Add bedtools env and fix rules Fix: #20
commit 2f079a4da9418465533c5a0c06b6b98e9d42cfde
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 22:45:00 2018 -0600
Add bedops env to fix BED
commit 37bd6d428fc6fa2ef3baa88f0bc5ba85f9b26fe6
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 22:44:40 2018 -0600
Fix pos2bed not running
commit 76c8ac7c0f20c650327fdfbfa03c0dccbff67c26
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 10:59:36 2018 -0600
Update all rule
commit 33ecadaca03ffb397d99d8a6d77cfed51ae89db6
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 10:58:17 2018 -0600
Fix awk rule by adding OFS as tabs
commit 4de96d157f5bda14e815af0aa8d8d8d7736001a6
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 00:23:48 2018 -0600
Restructure awk command for readability
commit ac4bdda95a15f303e0257b00c48e6159dffd7e6d
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Thu Nov 8 23:59:27 2018 -0600
Fix awk rule
All {} including the ones inside the awk command need to be double in smk
commit fd4fe69ca62d6cbdd86c7bb3713791eee22f0ab5
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Thu Nov 8 19:13:57 2018 -0600
Add broken awk commmand
commit efbb5ab07e3a0e2cbc828a315e95ab8038333af9
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Thu Nov 8 18:18:12 2018 -0600
Add initial Remove genes rule
Does not run because the BED coordinates are messed up.
commit 0c1c9e2e2b84b8714e1fe3f3fd235aa0bb406a5c
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Thu Nov 8 17:38:31 2018 -0600
Add slopRefSeq rule
Working on #6
commit 382b0c3c49d8d1f2da9bd5c24d4b10ec592a4b6b
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 22:25:22 2018 -0600
Merge in conda environments (#22) Fix: #20
* Add homer conda config
* WIP: Add docker singularity
* Fix homer absolute path
* Use homer env for pos2bed
commit bdb9488eb41a18821f1e2816a9f289983303b300
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Thu Nov 8 13:36:58 2018 -0600
Initial pos2bed rule and fix file label (#21)
commit 2f4420eac5ab8f01542cd9f03caa4bc4f4d58f06
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Thu Nov 8 00:00:29 2018 -0600
Add Homer Find Peaks Fix: #11 (#15)
* Fix wrong output for homer test
* Add initial findPeaks rule
* Tested: Change peaks to create the last file
commit 5364306af98bd9de1a2f610f374e326289d8bad0
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 7 23:11:43 2018 -0600
Add Homer Find Peaks Fix: #12 (#14)
* Add initial Homer Make Tag Dir Rule
* Make Tag Dir Rule runs
At least initially waiting for the reads to align
commit 40246636536e6f88be36a26044e299540676139e
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 7 16:27:10 2018 -0600
Add bowtie2 rule for GM Fix: #4 (#10)
* Add initial bowtie2 rule
WIP
* Testing for just one GM file
Getting error that it must have a 1 or 2 in the format
* Bowtie2 rule is working #4
Just need to add in the wildcards and correct targets
* Change Date of results to relavent date
* Generalize rule for GM
* Fix missed error in Fastqc #3
commit 3bd54b6441a11e5d27f17cddaea93f2696828572
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 7 15:16:41 2018 -0600
Finish Fastqc rule Fix: #3 (#9)
* Add fastqc rule
* Add rules for testing
* Fastqc rule works
commit 9d5268042c049393eb3b2011fedb7d99e6b42902
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Oct 24 12:08:45 2018 -0500
Make travis only build master and develop
PRs will also build
commit 8584f416ad21f9fd3a88cbf273f6ef9b5d720e31
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sun Nov 25 17:18:52 2018 -0600
WIP: Predict eRNAs on hg18 (#19)
* Make travis only build master and develop
PRs will also build
* Finish Fastqc rule Fix: #3 (#9)
* Add fastqc rule
* Add rules for testing
* Fastqc rule works
* Add bowtie2 rule for GM Fix: #4 (#10)
* Add initial bowtie2 rule
WIP
* Testing for just one GM file
Getting error that it must have a 1 or 2 in the format
* Bowtie2 rule is working #4
Just need to add in the wildcards and correct targets
* Change Date of results to relavent date
* Generalize rule for GM
* Fix missed error in Fastqc #3
* Add Homer Find Peaks Fix: #12 (#14)
* Add initial Homer Make Tag Dir Rule
* Make Tag Dir Rule runs
At least initially waiting for the reads to align
* Add Homer Find Peaks Fix: #11 (#15)
* Fix wrong output for homer test
* Add initial findPeaks rule
* Tested: Change peaks to create the last file
* Initial pos2bed rule and fix file label (#21)
* Merge in conda environments (#22) Fix: #20
* Add homer conda config
* WIP: Add docker singularity
* Fix homer absolute path
* Use homer env for pos2bed
commit dda87eeed2a077187c03a99cb8f5a2d9048f9297
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Oct 17 12:03:47 2018 -0500
Move to the Cookiecutter Snakemake workflow (#8)
* Use snakemake cookiecutter
* Comment out .test for now
* Do a dry run
* Comment out config till it's used
* Update README
commit 5554ebd69daaeb1f5533d80aaa72bba233724adf
Author: emiller88 <edmund.a.miller@gmail.com>
Date: Fri Apr 27 01:19:59 2018 -0500
Update Dag
commit 9b55a79808165fc622d7b831bd15a94a52bd900e
Author: emiller88 <edmund.a.miller@gmail.com>
Date: Fri Apr 27 00:59:19 2018 -0500
Add HistonesIntersect
Finish HistonesIntersect
Weird thing is I managed to get less eRNAs this go around. Stay tuned folks.
commit f79412615000b6c72baf376870518356b66bd2f3
Author: emiller88 <edmund.a.miller@gmail.com>
Date: Fri Apr 27 00:58:17 2018 -0500
Add Sort to bed
Adding Sorting to bed files so that it can run with betools intersect
commit b92a9142d21af1cae32fffa5180771b946f892ed
Author: emiller88 <edmund.a.miller@gmail.com>
Date: Fri Apr 27 00:28:03 2018 -0500
Split Histones
For faster download and run time on slow internet connections
commit 6b5647703ef4f530724be2d38373ba4536020125
Author: emiller88 <edmund.a.miller@gmail.com>
Date: Thu Apr 26 23:24:21 2018 -0500
Add getHistones
2017-10-23
commit 053a1e37252a3b796098cff6606257fa1ac48ffe
Author: emiller88 <edmund.a.miller@gmail.com>
Date: Thu Apr 26 22:25:28 2018 -0500
Add RemoveGenes
commit 7d44c600ee37c18ac1318a7c7a0662aae641919f
Author: emiller88 <edmund.a.miller@gmail.com>
Date: Thu Apr 26 22:14:25 2018 -0500
Add slopRefSeq
commit bc0ae1fa9b2a6b8d65bc349eda96a338c59bf0bf
Author: emiller88 <edmund.a.miller@gmail.com>
Date: Thu Apr 26 21:53:46 2018 -0500
Add Chromosome sizes
commit 8e36e3b765355d5c81e205936b4973b4fae2cdd3
Author: emiller88 <edmund.a.miller@gmail.com>
Date: Wed Apr 25 13:23:21 2018 -0500
Add Genomehg19
commit 7c085058ea7b9c231c0bd6d8f9411b8c4e92c449
Author: emiller88 <edmund.a.miller@gmail.com>
Date: Wed Apr 25 11:21:45 2018 -0500
Add dag.png
commit 9b1482793945387dbe87695a0e2e1d6168187150
Author: emiller88 <edmund.a.miller@gmail.com>
Date: Tue Apr 24 22:37:27 2018 -0500
Remove Makefile
Gone over to the snake side
commit cc3def4b15acd70d783df81a3543bdc6836c0254
Author: emiller88 <edmund.a.miller@gmail.com>
Date: Tue Apr 24 09:44:11 2018 -0500
Update Snakefile
commit 8d91ed16f102cf00f756a6f087a9df6d5349cbb1
Author: emiller88 <edmund.a.miller@gmail.com>
Date: Mon Apr 23 15:10:49 2018 -0500
Update Snakefile
Add getIMR90Data, qualityCheck, getRefGenome, working on buildRefGenome
commit f45e479c1bbb66cb01ecab381ef4c5a37db7da83
Author: emiller88 <edmund.a.miller@gmail.com>
Date: Mon Apr 23 14:28:28 2018 -0500
Update README
Add getting started for snakemake workflow
commit f9d886b6d979daa27ec35c1daaa9132d1cb397c2
Author: emiller88 <edmund.a.miller@gmail.com>
Date: Mon Apr 23 12:41:34 2018 -0500
Add Snakefile
commit 3bc9569d45e59329f360250f790ae2e361f4303a
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 27 22:23:36 2018 -0600
Finish #5 (#28)
* Clean up files from GM18 recreation
* Add reference Genomes Rules
* Silence the curls
* Add bowtie2 rule for hg19 and GM
* Add seperate unzip rule
* Add hg19 makeTagDirectory Rule
* Change homer Genome to hg18
Crucial mistake. This could be what's off with the reads and reproducing
the exact amount. Fix #12 related to #6
* Fix naming typo
* Add Homer findPeaks for hg19
* Add pos2bed Rule
* Fix unzipping of the hg19 Reference Genome
* Leave the hg18 Reference genome for another day
* Add rule to download AWS iGenomes script
Needs to be made executable #26
* Fix rule to download hg19 bowtie2 from AWS-iGenome
* Remove conda env because of genome issue
* Add download of refseq
* Add hg19 remove genes
* Add rule to predict eRNAs in hg19
* Add prefixes
* Add test for eRNAs
commit dc94cec4f6f8c33c252eda9b0b90dbd804b22a6d
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Mon Nov 26 23:19:52 2018 -0600
Feature/genes histones (#25)
* Make travis only build master and develop
PRs will also build
* Finish Fastqc rule Fix: #3 (#9)
* Add fastqc rule
* Add rules for testing
* Fastqc rule works
* Add bowtie2 rule for GM Fix: #4 (#10)
* Add initial bowtie2 rule
WIP
* Testing for just one GM file
Getting error that it must have a 1 or 2 in the format
* Bowtie2 rule is working #4
Just need to add in the wildcards and correct targets
* Change Date of results to relavent date
* Generalize rule for GM
* Fix missed error in Fastqc #3
* Add Homer Find Peaks Fix: #12 (#14)
* Add initial Homer Make Tag Dir Rule
* Make Tag Dir Rule runs
At least initially waiting for the reads to align
* Add Homer Find Peaks Fix: #11 (#15)
* Fix wrong output for homer test
* Add initial findPeaks rule
* Tested: Change peaks to create the last file
* Initial pos2bed rule and fix file label (#21)
* Merge in conda environments (#22) Fix: #20
* Add homer conda config
* WIP: Add docker singularity
* Fix homer absolute path
* Use homer env for pos2bed
* Add slopRefSeq rule
Working on #6
* Add initial Remove genes rule
Does not run because the BED coordinates are messed up.
* Add broken awk commmand
* Fix awk rule
All {} including the ones inside the awk command need to be double in smk
* Restructure awk command for readability
* Fix awk rule by adding OFS as tabs
* Update all rule
* Fix pos2bed not running
* Add bedops env to fix BED
* Add bedtools env and fix rules Fix: #20
* Add initial Histone Intersect rule
* Add rule to all to make eRNAs
* Squashed commit of the following:
commit f24e1503e960d90b0a45d9fbfd89cd57f63ef622
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Mon Nov 12 18:58:55 2018 -0600
Seperate out liftOver rule
commit 04e0f93c435e89291f6d36e47e45c7cfe71c049a
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sat Nov 10 20:43:57 2018 -0600
Fix typo
commit d42139271bcf563103a503523fec12bcdeb57b47
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sat Nov 10 00:02:27 2018 -0600
Fix env typo
It's running
commit 1b9adc313e2999a0c07e40213f4d2714bef35f0c
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:54:06 2018 -0600
Change me3 to me1
Thanks Chahat for catching that
commit 15425daa148f30b38e21beaf9b464c376f841ac0
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:53:42 2018 -0600
Fix HTTP by moving to one line
commit aa3ab140e4196dd415196bddd3aff61ec0bcadc0
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:52:41 2018 -0600
Fix hg19 typo
commit ba8881c1cb4d3239215736fb5b21758b37d4b639
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:50:58 2018 -0600
Add date to input file
It's late
commit 82f7a27d4ff3e581b8486b14151f42d1fb4e3e8e
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:50:47 2018 -0600
Fix http
commit 7766951bab4731cfa3e28bd7c60cb12597a85b7a
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:48:48 2018 -0600
Get rid of run commands using conda
commit ebcfba05ae4d5c5d95fe714bd34473bf56747c9b
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:48:36 2018 -0600
Update all rules
commit fe2a6641dc2c92a4ea9bec2e45a0446420691447
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:45:05 2018 -0600
Add rules to test both hg19 liftover and hg18
commit ee3fab0ecabd65dd84061c64421592630b93c362
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:44:32 2018 -0600
Add liftover rule Fix: #23
commit b556f4ce32bc47115f8c36de5fcdfa53d164a295
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:00:06 2018 -0600
Add rule to all to make eRNAs
* Add rules to pull in fastq data for histones
Squashed commit of the following:
commit d64276ca147a7ab85595e4c76b42d945696e797c
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 14 15:13:26 2018 -0600
Update Histone Intersect Rule for sorted files
commit 749267ec7847a97c8a88cb4cab0255212dea030e
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 14 15:12:53 2018 -0600
Write rule to sort Histones for hg18
commit 08f9c11a6f0cf7bff81d7bb63ccfec7010de54a2
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 14 11:32:57 2018 -0600
Add links to the experiments
In case they're needed in the future so they don't need to be hunted down.
commit 5ac1ac3ca91ab2b563a3af80a4868098f25e1cdd
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 14 11:31:48 2018 -0600
Change to curl
The -L flag handles the redirects
commit 7f5112b8800ec006dc37834d4ab50538b2484980
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 14 10:40:41 2018 -0600
Update rules to wget instead of HTTPRemoteProvider
commit f89233a6d0627e700585c44b7ec0d9ad9449c741
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 13 22:51:27 2018 -0600
Update Histone intersect to new Histone files
commit f0338a815d950e8785be3136da76cde10932a946
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 13 22:50:40 2018 -0600
Write rule to align the histones to hg18
commit 6405b7d1c6e99f70d05483b3e4df6810f35ca3b4
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 13 22:34:27 2018 -0600
Write rules for histone downloads
commit ef0c53f9d03e9fe87a2489f9306dbf5a88a4bc50
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 13 13:26:28 2018 -0600
Add initial rules to get GM Histones
Only the links to the files
* Change from samtools to picard for sorting
* Homer needs to be local to have genomes
* Move back to samtools Sort
Trying to figure out how to sort by chromosome
* Try converting Histones to BED files
* Sort the Histone Bed file
* Move mapchain download to data
* Fix liftOver rule
* Fix log typo
* Add rule to sort liftOver Bed files
commit 2fa379f37e10aafaf10ce65a6cb9b503b64dc41d
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Mon Nov 26 23:18:35 2018 -0600
Squashed commit of the following:
commit aa0f902b7fff698c230d1b9ebb76f9db72700674
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sun Nov 25 17:13:03 2018 -0600
Add rule to sort liftOver Bed files
commit 61ba3c329fdb471947670948089057876635f6d1
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sun Nov 25 17:06:58 2018 -0600
Fix log typo
commit 54f3f1d07c25813a8441d8f4282e1d586f4c24bf
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sun Nov 25 17:05:33 2018 -0600
Fix liftOver rule
commit 5d6f9dffa76cd4a97f9221bb1a40e915e69769a1
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sat Nov 24 23:46:26 2018 -0600
Move mapchain download to data
commit ea69d805571d88cb6972dcaa99a6b24cf6bdd978
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sat Nov 24 23:30:26 2018 -0600
Sort the Histone Bed file
commit 98792de55a0ec62ef54a326bb7d22f8861ca083d
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sat Nov 24 22:39:22 2018 -0600
Try converting Histones to BED files
commit ba817755a716a05e202f66577677387ae94622b1
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sat Nov 24 22:09:38 2018 -0600
Move back to samtools Sort
Trying to figure out how to sort by chromosome
commit 51ca69e0a7ade4b5c86c10fe25feb1f3e76c336b
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sat Nov 24 22:09:13 2018 -0600
Homer needs to be local to have genomes
commit 09d5f1cab1a7861cf544722fecd737a619d6bc68
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Thu Nov 15 23:42:54 2018 -0600
Change from samtools to picard for sorting
commit 871fbf891628fe8d8ed42054ac4ec14c50c1476f
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 14 15:16:41 2018 -0600
Add rules to pull in fastq data for histones
Squashed commit of the following:
commit d64276ca147a7ab85595e4c76b42d945696e797c
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 14 15:13:26 2018 -0600
Update Histone Intersect Rule for sorted files
commit 749267ec7847a97c8a88cb4cab0255212dea030e
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 14 15:12:53 2018 -0600
Write rule to sort Histones for hg18
commit 08f9c11a6f0cf7bff81d7bb63ccfec7010de54a2
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 14 11:32:57 2018 -0600
Add links to the experiments
In case they're needed in the future so they don't need to be hunted down.
commit 5ac1ac3ca91ab2b563a3af80a4868098f25e1cdd
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 14 11:31:48 2018 -0600
Change to curl
The -L flag handles the redirects
commit 7f5112b8800ec006dc37834d4ab50538b2484980
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 14 10:40:41 2018 -0600
Update rules to wget instead of HTTPRemoteProvider
commit f89233a6d0627e700585c44b7ec0d9ad9449c741
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 13 22:51:27 2018 -0600
Update Histone intersect to new Histone files
commit f0338a815d950e8785be3136da76cde10932a946
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 13 22:50:40 2018 -0600
Write rule to align the histones to hg18
commit 6405b7d1c6e99f70d05483b3e4df6810f35ca3b4
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 13 22:34:27 2018 -0600
Write rules for histone downloads
commit ef0c53f9d03e9fe87a2489f9306dbf5a88a4bc50
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Tue Nov 13 13:26:28 2018 -0600
Add initial rules to get GM Histones
Only the links to the files
commit 1205eab3a4e6ca0bea429e72de49f2c322449b5c
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Mon Nov 12 19:11:49 2018 -0600
Squashed commit of the following:
commit f24e1503e960d90b0a45d9fbfd89cd57f63ef622
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Mon Nov 12 18:58:55 2018 -0600
Seperate out liftOver rule
commit 04e0f93c435e89291f6d36e47e45c7cfe71c049a
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sat Nov 10 20:43:57 2018 -0600
Fix typo
commit d42139271bcf563103a503523fec12bcdeb57b47
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Sat Nov 10 00:02:27 2018 -0600
Fix env typo
It's running
commit 1b9adc313e2999a0c07e40213f4d2714bef35f0c
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:54:06 2018 -0600
Change me3 to me1
Thanks Chahat for catching that
commit 15425daa148f30b38e21beaf9b464c376f841ac0
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:53:42 2018 -0600
Fix HTTP by moving to one line
commit aa3ab140e4196dd415196bddd3aff61ec0bcadc0
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:52:41 2018 -0600
Fix hg19 typo
commit ba8881c1cb4d3239215736fb5b21758b37d4b639
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:50:58 2018 -0600
Add date to input file
It's late
commit 82f7a27d4ff3e581b8486b14151f42d1fb4e3e8e
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:50:47 2018 -0600
Fix http
commit 7766951bab4731cfa3e28bd7c60cb12597a85b7a
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:48:48 2018 -0600
Get rid of run commands using conda
commit ebcfba05ae4d5c5d95fe714bd34473bf56747c9b
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:48:36 2018 -0600
Update all rules
commit fe2a6641dc2c92a4ea9bec2e45a0446420691447
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:45:05 2018 -0600
Add rules to test both hg19 liftover and hg18
commit ee3fab0ecabd65dd84061c64421592630b93c362
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:44:32 2018 -0600
Add liftover rule Fix: #23
commit b556f4ce32bc47115f8c36de5fcdfa53d164a295
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:00:06 2018 -0600
Add rule to all to make eRNAs
commit c8a948e7c1b6e549fd941cfd3376d525677986f6
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 23:00:06 2018 -0600
Add rule to all to make eRNAs
commit 2e73abac401db7426f14430c91eca6e7e83f2fb4
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 22:58:51 2018 -0600
Add initial Histone Intersect rule
commit d1344986f545161976d22f96fb2d1e8059a84302
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 22:46:30 2018 -0600
Add bedtools env and fix rules Fix: #20
commit 2f079a4da9418465533c5a0c06b6b98e9d42cfde
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 22:45:00 2018 -0600
Add bedops env to fix BED
commit 37bd6d428fc6fa2ef3baa88f0bc5ba85f9b26fe6
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 22:44:40 2018 -0600
Fix pos2bed not running
commit 76c8ac7c0f20c650327fdfbfa03c0dccbff67c26
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 10:59:36 2018 -0600
Update all rule
commit 33ecadaca03ffb397d99d8a6d77cfed51ae89db6
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 10:58:17 2018 -0600
Fix awk rule by adding OFS as tabs
commit 4de96d157f5bda14e815af0aa8d8d8d7736001a6
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 00:23:48 2018 -0600
Restructure awk command for readability
commit ac4bdda95a15f303e0257b00c48e6159dffd7e6d
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Thu Nov 8 23:59:27 2018 -0600
Fix awk rule
All {} including the ones inside the awk
B396
command need to be double in smk
commit fd4fe69ca62d6cbdd86c7bb3713791eee22f0ab5
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Thu Nov 8 19:13:57 2018 -0600
Add broken awk commmand
commit efbb5ab07e3a0e2cbc828a315e95ab8038333af9
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Thu Nov 8 18:18:12 2018 -0600
Add initial Remove genes rule
Does not run because the BED coordinates are messed up.
commit 0c1c9e2e2b84b8714e1fe3f3fd235aa0bb406a5c
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Thu Nov 8 17:38:31 2018 -0600
Add slopRefSeq rule
Working on #6
commit 382b0c3c49d8d1f2da9bd5c24d4b10ec592a4b6b
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Fri Nov 9 22:25:22 2018 -0600
Merge in conda environments (#22) Fix: #20
* Add homer conda config
* WIP: Add docker singularity
* Fix homer absolute path
* Use homer env for pos2bed
commit bdb9488eb41a18821f1e2816a9f289983303b300
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Thu Nov 8 13:36:58 2018 -0600
Initial pos2bed rule and fix file label (#21)
commit 2f4420eac5ab8f01542cd9f03caa4bc4f4d58f06
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Thu Nov 8 00:00:29 2018 -0600
Add Homer Find Peaks Fix: #11 (#15)
* Fix wrong output for homer test
* Add initial findPeaks rule
* Tested: Change peaks to create the last file
commit 5364306af98bd9de1a2f610f374e326289d8bad0
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 7 23:11:43 2018 -0600
Add Homer Find Peaks Fix: #12 (#14)
* Add initial Homer Make Tag Dir Rule
* Make Tag Dir Rule runs
At least initially waiting for the reads to align
commit 40246636536e6f88be36a26044e299540676139e
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 7 16:27:10 2018 -0600
Add bowtie2 rule for GM Fix: #4 (#10)
* Add initial bowtie2 rule
WIP
* Testing for just one GM file
Getting error that it must have a 1 or 2 in the format
* Bowtie2 rule is working #4
Just need to add in the wildcards and correct targets
* Change Date of results to relavent date
* Generalize rule for GM
* Fix missed error in Fastqc #3
commit 3bd54b6441a11e5d27f17cddaea93f2696828572
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Nov 7 15:16:41 2018 -0600
Finish Fastqc rule Fix: #3 (#9)
* Add fastqc rule
* Add rules for testing
* Fastqc rule works
commit 9d5268042c049393eb3b2011fedb7d99e6b42902
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Wed Oct 24 12:08:45 2018 -0500
Make travis only build master and develop
PRs will also build
commit 7b4f6de9f64f00e24e230e30cbedf71cfd1618ee
Author: Edmund Miller <edmund.a.miller@gmail.com>
Date: Mon Nov 26 23:01:44 2018 -0600
Develop (#24)
* Make travis only build master and develop
PRs will also build
* Finish Fastqc rule Fix: #3 (#9)
* Add fastqc rule
* Add rules for testing
* Fastqc rule works
* Add bowtie2 rule for GM Fix: #4 (#10)
* Add initial bowtie2 rule
WIP
* Testing for just one GM file
Getting error that it must have a 1 or 2 in the format
* Bowtie2 rule is working #4
Just need to add in the wildcards and correct targets
* Change Date of results to relavent date
* Generalize rule for GM
* Fix missed error in Fastqc #3
* Add Homer Find Peaks Fix: #12 (#14)
* Add initial Homer Make Tag Dir Rule
* Make Tag Dir Rule runs
At least initially waiting for the reads to align
* Add Homer Find Peaks Fix: #11 (#15)
* Fix wrong output for homer test
* Add initial findPeaks rule
* Tested: Change peaks to create the last file
* Initial pos2bed rule and fix file label (#21)
* Merge in conda environments (#22) Fix: #20
* Add homer conda config
* WIP: Add docker singularity
* Fix homer absolute path
* Use homer env for pos2bed
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Many thanks to contributing to nf-core/nascent!
Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).
PR checklist
nextflow run . -profile test,docker).nf-core lint .).docsis updatedCHANGELOG.mdis updatedREADME.mdis updatedLearn more about contributing: https://github.com/nf-core/nascent/tree/master/.github/CONTRIBUTING.md