-
Notifications
You must be signed in to change notification settings - Fork 0
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
ChIP-seq update to 2.1.6 #528
Merged
Merged
Changes from all commits
Commits
Show all changes
24 commits
Select commit
Hold shift + click to select a range
0324419
set input files for aln wf as [[File]] rather than [[[File]]] to matc…
clarabakker f74499d
set checks to use new workflows, testing
clarabakker 1d8e127
restore workflow specs (changed wf instead to match existing wf names…
clarabakker e3c640d
added wf v1.1.2-specific parameters, specified new wf uuid in wfrset_…
clarabakker 3697854
bracket mismatch typo
clarabakker 8b14c2f
chip parameter step1/1c typo
clarabakker a1bbbc9
further simplify fastqs input array, set reference files with names w…
clarabakker f837a9b
ChIP check I/O and parameters modifications for aln (ctl) and post-al…
clarabakker 7aeed9a
add back original to accepted versions
clarabakker 34838bc
change chip-seq to use wdl's control parameters (rm ctl prefix from f…
clarabakker d90b16f
override benchmarking for chip ctl wf
clarabakker c4f5514
added bool to get_chip_files to allow different endedness; updated us…
clarabakker 7e46365
change paired array to booleans for ChIP-seq post-align
clarabakker 4e15ca9
update ChIP-seq pipeline versions
clarabakker 4e37bce
Merge branch 'master' into chip-update
clarabakker 04aabe7
adjustments for ChIP-seq benchmarking, new WDL parameters for paired …
clarabakker feb8d65
Merge branch 'master' into chip-update
clarabakker 081242c
qc get failure handling
clarabakker 6a975b0
Merge branch 'master' into chip-update
clarabakker 7755f70
Merge branch 'master' into chip-update
clarabakker 5d4c9ba
Merge branch 'master' into chip-update
ae2a949
identify mixed paired/single ended, general cleanup
d751f15
Merge branch 'master' into chip-update
clarabakker fec266f
version, changelog, minor spacing fix
clarabakker File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -195,9 +195,9 @@ def step_settings(step_name, my_organism, attribution, overwrite=None): | |
}, | ||
{ | ||
"app_name": "encode-chipseq-aln-chip", | ||
"workflow_uuid": "4dn-dcic-lab:wf-encode-chipseq-aln-chip", | ||
"workflow_uuid": "212a9c91-25d6-473f-b56b-8dd93958c580", | ||
"parameters": {}, | ||
"config": {}, | ||
"config": {"ebs_size": 70}, | ||
'custom_pf_fields': { | ||
'chip.first_ta': { | ||
'genome_assembly': genome, | ||
|
@@ -213,9 +213,9 @@ def step_settings(step_name, my_organism, attribution, overwrite=None): | |
}, | ||
{ | ||
"app_name": "encode-chipseq-aln-ctl", | ||
"workflow_uuid": "4dn-dcic-lab:wf-encode-chipseq-aln-ctl", | ||
"workflow_uuid": "4eb427f1-a7d5-4d74-8cfa-4c77f42d5b43", | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Same as previous comment |
||
"parameters": {}, | ||
"config": {}, | ||
"config":{"instance_type": 'c5.2xlarge', "ebs_size": 70}, | ||
'custom_pf_fields': { | ||
'chip.first_ta_ctl': { | ||
'genome_assembly': genome, | ||
|
@@ -226,9 +226,9 @@ def step_settings(step_name, my_organism, attribution, overwrite=None): | |
}, | ||
{ | ||
"app_name": "encode-chipseq-postaln", | ||
"workflow_uuid": "4dn-dcic-lab:wf-encode-chipseq-postaln", | ||
"workflow_uuid": "291d4c64-75de-434a-9d98-01f40d19e15e", | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. see above |
||
"parameters": {}, | ||
"config": {}, | ||
"config": {"instance_type": "c5.2xlarge", "ebs_size": 80}, | ||
'custom_pf_fields': { | ||
'chip.optimal_peak': { | ||
'genome_assembly': genome, | ||
|
@@ -238,7 +238,7 @@ def step_settings(step_name, my_organism, attribution, overwrite=None): | |
'genome_assembly': genome, | ||
'file_type': 'conservative peaks', | ||
'description': 'Conservative peak calls from ENCODE ChIP-Seq Pipeline'}, | ||
'chip.sig_fc': { | ||
'chip.fc_bw': { | ||
'genome_assembly': genome, | ||
'file_type': 'signal fold change', | ||
'description': 'ChIP-seq signal fold change over input control'} | ||
|
@@ -329,6 +329,7 @@ def step_settings(step_name, my_organism, attribution, overwrite=None): | |
'rna.strandedness_direction': '', | ||
'rna.endedness': '' | ||
}, | ||
"config": {"instance_type": ["m5a.4xlarge", "m6a.4xlarge"], "ebs_size": 90}, | ||
'custom_pf_fields': { | ||
'rna.outbam': { | ||
'genome_assembly': genome, | ||
|
Oops, something went wrong.
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
despite the property name, might it be better to use the alias as was formerly done in case the workflow is added to a new environment (with a different uuid being generated) - perhaps unlikely but if at all possible?
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Yes, I was aiming to make it consistent with other workflows, since I made the new UUIDs consistent (for the current envs). The aliases also are the same for both new and old versions, which maybe also was a factor? It needs to know the new and old version are the same workflow, but only run the new one.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Oops, I see your confusion--the aliases are definitely not the same and the app name keeps the versions together. I do think it is more consistent with other workflows to use the uuid. It is also hard to query aliases for someone going from this workflow setting to the workflow on the portal, right?