Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / datirium/workflows issues and pull requests

#120 - SDAP-1045 germline variant calling workflow

Pull Request - State: closed - Opened by robert-player over 1 year ago

#119 - Make DiffBind to produce files with unique names

Pull Request - State: closed - Opened by michael-kotliar over 1 year ago

#118 - SDAP-1058 cutandrun workflow bifurcation

Pull Request - State: closed - Opened by robert-player over 1 year ago

#117 - Bump werkzeug from 1.0.1 to 2.2.3 in /dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, python

#116 - Bump http-cache-semantics from 4.1.0 to 4.1.1 in /tests

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, javascript

#115 - MA-plot

Pull Request - State: closed - Opened by michael-kotliar almost 2 years ago

#114 - SDAP-1040 fix IGV sample comparison

Pull Request - State: closed - Opened by robert-player almost 2 years ago

#113 - SDAP-1017 metagenomics pipeline

Pull Request - State: closed - Opened by robert-player almost 2 years ago

#112 - Fix bug with Morpheus heatmap row annotations data types SDAP-1007

Pull Request - State: closed - Opened by michael-kotliar almost 2 years ago

#111 - Sdap 1006 cutandrun feedback changes and dna binding wf output variable change

Pull Request - State: closed - Opened by robert-player almost 2 years ago - 2 comments

#110 - Bump setuptools from 44.1.1 to 65.5.1 in /dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, python

#109 - Bump wheel from 0.35.1 to 0.38.1 in /dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, python

#108 - Update GSEAPy to support the latest GCT v1.3

Pull Request - State: closed - Opened by michael-kotliar almost 2 years ago

#107 - Bump numpy from 1.16.6 to 1.22.0 in /dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, python

#106 - Bump pillow from 6.2.2 to 9.3.0 in /dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, python

#105 - Bump lxml from 4.5.2 to 4.9.1 in /dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, python

#104 - Bump urllib3 from 1.25.10 to 1.26.5 in /dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, python

#103 - Bump certifi from 2020.6.20 to 2022.12.7 in /dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, python

#102 - SDAP-863 diffmeth workflow

Pull Request - State: closed - Opened by robert-player almost 2 years ago

#101 - SDAP-863 diffmeth workflow

Pull Request - State: closed - Opened by robert-player almost 2 years ago

#100 - Update volcano plot to use the latest docker image

Pull Request - State: closed - Opened by michael-kotliar almost 2 years ago

#99 - Bump certifi from 2020.6.20 to 2022.12.7 in /tools/dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 3 comments
Labels: dependencies, python

#98 - Bump pillow from 6.2.2 to 9.3.0 in /tools/dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 3 comments
Labels: dependencies, python

#97 - Update standard DESeq pipeline with MDS plot and heatmap

Pull Request - State: closed - Opened by michael-kotliar about 2 years ago

#95 - Sdap 929 seacr fail fix and igv updates

Pull Request - State: closed - Opened by robert-player about 2 years ago

#94 - Update DESeq Multi-Factor Analysis with Heatmap and MDS plots

Pull Request - State: closed - Opened by michael-kotliar about 2 years ago

#93 - Sdap 818 added cutandrun to diffbind

Pull Request - State: closed - Opened by robert-player about 2 years ago

#92 - SDAP-867 DESeq experimental description clarification

Pull Request - State: closed - Opened by robert-player about 2 years ago

#91 - SDAP-847 gsea summary page added

Pull Request - State: closed - Opened by robert-player about 2 years ago

#90 - Sdap 904 hotfix

Pull Request - State: closed - Opened by robert-player about 2 years ago

#89 - Bump scss-tokenizer and node-sass in /tests

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies, javascript

#88 - Update GSEA with the latest MSigDB version, add new genesets

Pull Request - State: closed - Opened by michael-kotliar about 2 years ago

#87 - cutandrun pipeline

Pull Request - State: closed - Opened by robert-player about 2 years ago

#86 - first cutandrun workflow commit

Pull Request - State: closed - Opened by robert-player about 2 years ago

#85 - Bump urllib3 from 1.25.10 to 1.26.5 in /tools/dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 4 comments
Labels: dependencies

#84 - changed bigwig names for IGV

Pull Request - State: closed - Opened by robert-player about 2 years ago

#81 - fix readme for travis-ci. remove unnecessary files from root of repo

Pull Request - State: closed - Opened by scrowley-Datirium over 2 years ago - 1 comment

#79 - For array input testing

Pull Request - State: closed - Opened by michael-kotliar over 2 years ago

#78 - Bump lxml from 4.5.2 to 4.9.1 in /tools/dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#77 - Bump numpy from 1.16.6 to 1.22.0 in /tools/dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#75 - Remove bigwig outputs from Bismark workflows

Pull Request - State: closed - Opened by michael-kotliar over 2 years ago

#74 - Add tab name for Bismark plots outputs

Pull Request - State: closed - Opened by michael-kotliar over 2 years ago

#72 - Not tested but that what Bismark PE complains about

Pull Request - State: closed - Opened by michael-kotliar over 2 years ago

#71 - Add Bismark PE

Pull Request - State: closed - Opened by michael-kotliar over 2 years ago

#70 - Connect Bismark indices to upstreams

Pull Request - State: closed - Opened by michael-kotliar over 2 years ago

#69 - Bump numpy from 1.16.6 to 1.21.0 in /tools/dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#68 - Bump pillow from 6.2.2 to 9.0.1 in /tools/dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#67 - Bump lxml from 4.5.2 to 4.6.5 in /tools/dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#66 - Bump pip from 20.2.3 to 21.1 in /tools/dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#65 - Documentation refactoring. Work in progress.

Pull Request - State: open - Opened by heylel-b-sh over 3 years ago

#64 - Bump lxml from 4.5.2 to 4.6.3 in /tools/dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#63 - Bump jinja2 from 2.11.2 to 2.11.3 in /tools/dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#62 - Bump pillow from 6.2.2 to 8.1.1 in /tools/dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#60 - update 3d scatter output

Pull Request - State: closed - Opened by heylel-b-sh almost 4 years ago

#59 - change deseq scatterplot output

Pull Request - State: closed - Opened by heylel-b-sh almost 4 years ago

#58 - Bump pillow from 6.2.2 to 7.1.0 in /tools/dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies

#57 - Bump lxml from 4.5.2 to 4.6.2 in /tools/dockerfiles/requirements

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies

#56 - Bypasses trimming adapter step if low read counts found

Pull Request - State: closed - Opened by heylel-b-sh almost 4 years ago

#54 - rna-seq-pe workflow is stuck

Issue - State: closed - Opened by Prakash2403 over 4 years ago - 5 comments

#53 - switch to working schema.org URL

Pull Request - State: closed - Opened by mr-c over 4 years ago - 1 comment

#52 - What is the license of this repo?

Issue - State: closed - Opened by mr-c over 4 years ago - 1 comment

#51 - Preseq graph

Issue - State: open - Opened by tyomach over 4 years ago

#50 - Bug fix, alternative option to set chromosome_list input

Pull Request - State: closed - Opened by michael-kotliar about 5 years ago

#49 - Update genome-indices to support fasta, gz, 2bit

Pull Request - State: closed - Opened by michael-kotliar about 5 years ago

#48 - Update genome-indices to produce data for IGV

Pull Request - State: closed - Opened by michael-kotliar about 5 years ago

#47 - Workflow update / refactoring

Pull Request - State: closed - Opened by michael-kotliar about 5 years ago

#46 - Add HOPACH clustering workflow

Pull Request - State: closed - Opened by michael-kotliar over 5 years ago

#45 - Input of type string[ ] is not displayed on the form

Issue - State: closed - Opened by michael-kotliar over 5 years ago - 1 comment

#44 - IGV loads BAM too slow if it's placed before bigWig

Issue - State: closed - Opened by michael-kotliar over 5 years ago - 1 comment

#43 - Add grouping option to deseq

Pull Request - State: closed - Opened by michael-kotliar over 5 years ago

#42 - Add deeptools

Pull Request - State: closed - Opened by michael-kotliar over 5 years ago

#41 - bigWig track is not displayed when output if File[] or some other reason?

Issue - State: closed - Opened by heylel-b-sh over 5 years ago - 1 comment

#40 - File input in `sd:layout advanced: true` causes error in web interface

Issue - State: closed - Opened by heylel-b-sh over 5 years ago - 1 comment

#39 - Add rgt-THOR (not tested)

Pull Request - State: closed - Opened by michael-kotliar over 5 years ago

#38 - Add scatter3d in PCA workflow

Pull Request - State: closed - Opened by michael-kotliar over 5 years ago

#37 - Disable upstream for legend_name input of PCA workflow

Pull Request - State: closed - Opened by michael-kotliar over 5 years ago