mskcc roslin-cwl issues

mskcc / roslin-cwl

CWLs for the Roslin Variant Pipeline

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#42 allanbolipata closed 4 years ago
0
Feature/add meta input for copy outputs

#41 nikhil closed 4 years ago
0
Feature/add submodule helix filters

#40 allanbolipata closed 4 years ago
0
Exegesis: explicitly list BWA arguments used

#39 soccin closed 4 years ago
0
Exegesis: explicitly list BWA arguments used

#38 soccin closed 4 years ago
2
Rename pi and pi_email

#37 nikhil closed 4 years ago
0
Added output folder for intermediate metrics

#36 nikhil closed 4 years ago
1
Add module that assesses the health of certain outputs, such as bam

#35 allanbolipata opened 4 years ago
0
Feature/add testing

#34 nikhil closed 4 years ago
1
Feature/add testing

#33 nikhil closed 4 years ago
0
Output "intermediate files" that are used as input for ROSLIN QC

#32 allanbolipata closed 4 years ago
0
Find out why bam index files are getting corrupted

#31 allanbolipata opened 4 years ago
0
Feature/3.0.0 release

#30 nikhil closed 4 years ago
0
Create a generate-qc-sv workflow

#29 nikhil closed 4 years ago
0
Refactor output format for bams, runparams, and assay

#28 nikhil closed 4 years ago
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Feature/remove cutadapt

#27 nikhil closed 4 years ago
0
Modify Xmx params being passed

#26 allanbolipata closed 4 years ago
0
Added copy_output cwls

#25 nikhil closed 4 years ago
0
Remove bait and target files from pair workflows; separate out to QC module

#24 allanbolipata closed 4 years ago
1
Make facets output optional and not break ROSLIN run

#23 allanbolipata opened 4 years ago
0
Feature/update readme

#22 allanbolipata closed 4 years ago
1
Needs continuous integration implemented

#21 allanbolipata closed 4 years ago
0
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

#20 allanbolipata opened 4 years ago
3
duplicate "downsampling_type" keys in mutect.cwl

#19 stevekm closed 4 years ago
0
Make memory assignment for MarkDuplicates in roslin-cwl configurable

#18 allanbolipata opened 4 years ago
0
updated qc and facets versions

#17 timosong closed 4 years ago
0
Feature/remove pairing file requirement

#16 allanbolipata closed 4 years ago
1
Switch to bwa mem 0.7.12

#15 allanbolipata closed 4 years ago
0
fix versions in msisensor and conpair

#14 allanbolipata closed 4 years ago
0
Feature/remove legacy files for qc

#13 nikhil closed 4 years ago
0
Roslin-QC MPGR file removal from pipeline inputs

#12 allanbolipata closed 4 years ago
1
Changed cmo fillout to use runtime threads for n_threads

#11 allanbolipata closed 4 years ago
1
Changed bwa mem memory

#10 allanbolipata closed 4 years ago
0
Increase ram in bwa-mem 0.7.5a

#9 allanbolipata closed 4 years ago
1
Wrong CWL Version cwl:v1.0 should be v1.0

#8 sivkovic opened 5 years ago
0
Moved project workflow CWLs to top level

#7 allanbolipata closed 5 years ago
0
2.6.x

#6 nikhil closed 5 years ago
0
basic filtering steps still using cmo_resources.json

#5 allanbolipata closed 5 years ago
1
Change facets_snps in db_files from string to File; are there others?

#4 allanbolipata closed 5 years ago
1
Fix java_temp/TMP_DIR designations in CWLs

#3 allanbolipata closed 5 years ago
0
Cwl tool fix 1

#2 nikhil closed 5 years ago
0
Remove namespace, schema, foaf and doap

#1 allanbolipata closed 5 years ago
1