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mskcc
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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
0
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