RNA-seq issueshttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues2021-07-26T20:37:07-05:00https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues/131Add override (force) for seq-type2021-07-26T20:37:07-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd override (force) for seq-typev2.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues/113Add forward/reverse as expected vals for stranded2021-07-25T20:54:55-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd forward/reverse as expected vals for strandedv2.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues/118Ambiguous species & fastq structure submits blank status detail2021-07-25T20:54:55-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAmbiguous species & fastq structure submits blank status detail# Summary
# Steps to reproduce
v2.0.0rc01 on replicate Q-Y5ER (ambiguous species)
v2.0.0rc01 on replicate Q-Y5HT (fastq structure)
# Observed bug behavior
Blank status detail
# Expected behavior
**Inference of species returns an ambi...# Summary
# Steps to reproduce
v2.0.0rc01 on replicate Q-Y5ER (ambiguous species)
v2.0.0rc01 on replicate Q-Y5HT (fastq structure)
# Observed bug behavior
Blank status detail
# Expected behavior
**Inference of species returns an ambiguous result:** Percent aligned to human = \${align_hu} and percent aligned to mouse = \${align_mo}\
**There is an error with the structure of the fastq**
# Relevant logs and/or screenshots
# Potential fixes
**process *failPreExecutionRun***
```
elif [ ${speciesError} == true ]
then
errorDetails=\$(echo \$(errorDetails)${fastqReadError_details}"\\n")
```
should have `errorDetails=\$(echo \$(errorDetails)${speciesError_details}"\\n")`
AND
```
elif [ ${fastqFileError} == true ]
then
errorDetails=\$(echo \$(errorDetails)${fastqReadError_details}"\\n")
```
should have `errorDetails=\$(echo \$(errorDetails)${fastqFileError_details}"\\n")`
/cc @ghenry @venkat.malladi @s181706v2.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues/134Server changing... need to change .insert calls2021-07-25T20:54:16-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduServer changing... need to change .insert callsBug in server... RCB and RMB columns are available and shouldn't be.
Laura (re: 20210720) will fix bug in a week or 2.
Need to add `nondefaults=["RCB", "RMB"]` to ALL `.insert` calls (python scripts) to the datahubBug in server... RCB and RMB columns are available and shouldn't be.
Laura (re: 20210720) will fix bug in a week or 2.
Need to add `nondefaults=["RCB", "RMB"]` to ALL `.insert` calls (python scripts) to the datahubv2.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues/114Sequencing_Type column change to Experiment_Type2021-02-01T12:06:15-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduSequencing_Type column change to Experiment_Typere-Hongsuda 1/21/21re-Hongsuda 1/21/21v2.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues/115Has_Strand_Specific_Information changed to Strandedness2021-02-01T12:06:14-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduHas_Strand_Specific_Information changed to Strandednessre-Hongsuda 1/21/21re-Hongsuda 1/21/21v2.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues/70Change yes/no metadata to bool2021-02-01T12:06:13-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduChange yes/no metadata to boolre conversation with Hongsuda: 20200817
data-hub in the process of changing yes/no metadata (eg experiment settings) to boolean
be prepared to read submitter metadata as bool and output inferred metadata as boolre conversation with Hongsuda: 20200817
data-hub in the process of changing yes/no metadata (eg experiment settings) to boolean
be prepared to read submitter metadata as bool and output inferred metadata as boolv2.0.0Venkat MalladiGervaise Henrygervaise.henry@utsouthwestern.eduVenkat Malladihttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues/101failPreExecution not running on fastq error2021-01-14T21:33:53-06:00Gervaise Henrygervaise.henry@utsouthwestern.edufailPreExecution not running on fastq error# Summary
If fastqCountError or fastqReadError gets set as true (by getData process), then failPreExecution process should run to create the failed execution run with details. The process is currently set to wait for speciesError channel...# Summary
If fastqCountError or fastqReadError gets set as true (by getData process), then failPreExecution process should run to create the failed execution run with details. The process is currently set to wait for speciesError channel which doesn't get set till after inferMetadata process... but the fastq errors prevent that process from running, so failPreExecution run never happens.
# Steps to reproduce
Run any replicate from study 16-2CNW
# Observed bug behavior
Pipeline successful, but no execution run uploaded.
# Expected behavior
Pipeline successful, execution run uploaded with Error status and detail
# Relevant logs and/or screenshots
# Potential fixes
Split failPreExecution process into 2 (1 dependent on the 2 fastq errors, the other dependent on species error)\
**THIS IS MY PREFERENECE BECAUSE OF EASE AND SPEED OF IMPLEMENTATION** DSL2 will probably make this problem irrelevant anyway, so more complicated fix feels waste of time.
Can also:
* make 1 error variable that any failure sets to true, then have failPreExecution dependent on only that variable
/cc @ghenry @venkat.malladi @s181706v1.0.1https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues/36Alignment output chromosome number replaced with contig ID2020-03-24T10:10:58-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAlignment output chromosome number replaced with contig ID# Summary
Chromosome numbers not being saved, instead it is the contig ID... this is evident in all the bams, but goes all the way back to sam...
# Steps to reproduce
Look at the output of any alignData step and do a `head -n 5` on the ...# Summary
Chromosome numbers not being saved, instead it is the contig ID... this is evident in all the bams, but goes all the way back to sam...
# Steps to reproduce
Look at the output of any alignData step and do a `head -n 5` on the sam
# Observed bug behavior
Instead of chr1 it lists chrNC_000001.11
# Expected behavior
See above
# Relevant logs and/or screenshots
# Potential fixes
This is either a problem with the reference or the hisat2 command
/cc @ghenry @venkat.malladi @s181706 @s189701v0.0.1Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/issues/44inferMetadata stranded logic error2020-03-24T10:10:58-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduinferMetadata stranded logic error# Summary
Infer strandedness outputs wrong
# Steps to reproduce
Run integration tests
# Observed bug behavior
Output unstranded
# Expected behavior
Output stranded
# Relevant logs and/or screenshots
> PairEnd,unstranded,us,0.0974,0.7...# Summary
Infer strandedness outputs wrong
# Steps to reproduce
Run integration tests
# Observed bug behavior
Output unstranded
# Expected behavior
Output stranded
# Relevant logs and/or screenshots
> PairEnd,unstranded,us,0.0974,0.7630,0.1395\
> SingleEnd,unstranded,us,0.0275,0.8993,0.0732
# Potential fixes
Check logic
/cc @ghenry @venkat.malladi @s181706v0.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.edu