mskcc/roslin-cwl issues and pull requests

#42 - Develop

Pull Request - State: closed - Opened by allanbolipata over 4 years ago

#42 - Develop

Pull Request - State: closed - Opened by allanbolipata over 4 years ago

#41 - Feature/add meta input for copy outputs

Pull Request - State: closed - Opened by nikhil over 4 years ago

#40 - Feature/add submodule helix filters

Pull Request - State: closed - Opened by allanbolipata over 4 years ago

#40 - Feature/add submodule helix filters

Pull Request - State: closed - Opened by allanbolipata over 4 years ago

#39 - Exegesis: explicitly list BWA arguments used

Pull Request - State: closed - Opened by soccin over 4 years ago

#39 - Exegesis: explicitly list BWA arguments used

Pull Request - State: closed - Opened by soccin over 4 years ago

#38 - Exegesis: explicitly list BWA arguments used

Pull Request - State: closed - Opened by soccin over 4 years ago - 2 comments

#38 - Exegesis: explicitly list BWA arguments used

Pull Request - State: closed - Opened by soccin over 4 years ago - 2 comments

#37 - Rename pi and pi_email

Pull Request - State: closed - Opened by nikhil over 4 years ago

#37 - Rename pi and pi_email

Pull Request - State: closed - Opened by nikhil over 4 years ago

#36 - Added output folder for intermediate metrics

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

#36 - Added output folder for intermediate metrics

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

#35 - Add module that assesses the health of certain outputs, such as bam

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

#35 - Add module that assesses the health of certain outputs, such as bam

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

#34 - Feature/add testing

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

#33 - Feature/add testing

Pull Request - State: closed - Opened by nikhil over 4 years ago

#33 - Feature/add testing

Pull Request - State: closed - Opened by nikhil over 4 years ago

#32 - Output "intermediate files" that are used as input for ROSLIN QC

Issue - State: closed - Opened by allanbolipata over 4 years ago

#32 - Output "intermediate files" that are used as input for ROSLIN QC

Issue - State: closed - Opened by allanbolipata over 4 years ago

#31 - Find out why bam index files are getting corrupted

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

#31 - Find out why bam index files are getting corrupted

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

#30 - Feature/3.0.0 release

Pull Request - State: closed - Opened by nikhil over 4 years ago

#30 - Feature/3.0.0 release

Pull Request - State: closed - Opened by nikhil over 4 years ago

#29 - Create a generate-qc-sv workflow

Issue - State: closed - Opened by nikhil almost 5 years ago

#29 - Create a generate-qc-sv workflow

Issue - State: closed - Opened by nikhil almost 5 years ago

#28 - Refactor output format for bams, runparams, and assay

Issue - State: closed - Opened by nikhil almost 5 years ago

#28 - Refactor output format for bams, runparams, and assay

Issue - State: closed - Opened by nikhil almost 5 years ago

#27 - Feature/remove cutadapt

Pull Request - State: closed - Opened by nikhil almost 5 years ago

#27 - Feature/remove cutadapt

Pull Request - State: closed - Opened by nikhil almost 5 years ago

#26 - Modify Xmx params being passed

Pull Request - State: closed - Opened by allanbolipata almost 5 years ago

#25 - Added copy_output cwls

Pull Request - State: closed - Opened by nikhil almost 5 years ago

#24 - Remove bait and target files from pair workflows; separate out to QC module

Issue - State: closed - Opened by allanbolipata almost 5 years ago - 1 comment

#24 - Remove bait and target files from pair workflows; separate out to QC module

Issue - State: closed - Opened by allanbolipata almost 5 years ago - 1 comment

#23 - Make facets output optional and not break ROSLIN run

Issue - State: open - Opened by allanbolipata almost 5 years ago

#22 - Feature/update readme

Pull Request - State: closed - Opened by allanbolipata almost 5 years ago - 1 comment

#22 - Feature/update readme

Pull Request - State: closed - Opened by allanbolipata almost 5 years ago - 1 comment

#21 - Needs continuous integration implemented

Issue - State: closed - Opened by allanbolipata almost 5 years ago

#21 - Needs continuous integration implemented

Issue - State: closed - Opened by allanbolipata almost 5 years ago

#20 - In the trimming step of sample-workflow.cwl, file outputs only go by the file name; if they are the same across different paths, they are overwritten

Issue - State: open - Opened by allanbolipata almost 5 years ago - 3 comments
Labels: bug

#20 - In the trimming step of sample-workflow.cwl, file outputs only go by the file name; if they are the same across different paths, they are overwritten

Issue - State: open - Opened by allanbolipata almost 5 years ago - 3 comments
Labels: bug

#19 - duplicate "downsampling_type" keys in mutect.cwl

Issue - State: closed - Opened by stevekm almost 5 years ago
Labels: bug

#19 - duplicate "downsampling_type" keys in mutect.cwl

Issue - State: closed - Opened by stevekm almost 5 years ago
Labels: bug

#18 - Make memory assignment for MarkDuplicates in roslin-cwl configurable

Issue - State: open - Opened by allanbolipata almost 5 years ago

#17 - updated qc and facets versions

Pull Request - State: closed - Opened by timosong almost 5 years ago

#17 - updated qc and facets versions

Pull Request - State: closed - Opened by timosong almost 5 years ago

#16 - Feature/remove pairing file requirement

Pull Request - State: closed - Opened by allanbolipata almost 5 years ago - 1 comment

#16 - Feature/remove pairing file requirement

Pull Request - State: closed - Opened by allanbolipata almost 5 years ago - 1 comment

#15 - Switch to bwa mem 0.7.12

Pull Request - State: closed - Opened by allanbolipata almost 5 years ago

#14 - fix versions in msisensor and conpair

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

#13 - Feature/remove legacy files for qc

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

#12 - Roslin-QC MPGR file removal from pipeline inputs

Issue - State: closed - Opened by allanbolipata about 5 years ago - 1 comment

#11 - Changed cmo fillout to use runtime threads for n_threads

Pull Request - State: closed - Opened by allanbolipata about 5 years ago - 1 comment

#10 - Changed bwa mem memory

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

#9 - Increase ram in bwa-mem 0.7.5a

Issue - State: closed - Opened by allanbolipata about 5 years ago - 1 comment

#8 - Wrong CWL Version cwl:v1.0 should be v1.0

Issue - State: open - Opened by sivkovic about 5 years ago

#7 - Moved project workflow CWLs to top level

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

#6 - 2.6.x

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

#5 - basic filtering steps still using cmo_resources.json

Issue - State: closed - Opened by allanbolipata about 5 years ago - 1 comment

#4 - Change facets_snps in db_files from string to File; are there others?

Issue - State: closed - Opened by allanbolipata about 5 years ago - 1 comment

#3 - Fix java_temp/TMP_DIR designations in CWLs

Issue - State: closed - Opened by allanbolipata about 5 years ago

#2 - Cwl tool fix 1

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

#1 - Remove namespace, schema, foaf and doap

Issue - State: closed - Opened by allanbolipata about 5 years ago - 1 comment

GitHub / mskcc/roslin-cwl issues and pull requests