User: ttom
ttom • 210
- Reputation:
- 210
- Status:
- Trusted
- Location:
- Last seen:
- 2 months, 3 weeks ago
- Joined:
- 6 years, 6 months ago
- Email:
- t*************@gmail.com
about me
Posts by ttom
<prev
• 57 results •
page 1 of 6 •
next >
0
votes
1
answer
525
views
1
answers
Comment:
C: Capture Output files using glob
... Thank you, it worked ...
written 13 months ago by
ttom • 210
0
votes
1
answer
525
views
1
answers
Comment:
C: Capture Output files using glob
... One more question on this.
With the given below lines in the code, `splad_outDir` has to be existing for this to work, but will create `splad_outDir/splad`
requirements:
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.splad_outDir)
writable: true
In ...
written 13 months ago by
ttom • 210
3
votes
1
answer
731
views
1
answers
... The issue was the presence of this line
- entry: $(inputs.spladder_bams) ...
written 13 months ago by
ttom • 210
0
votes
1
answer
731
views
1
answers
... Yes, I tried the changes mentioned in both the CWL and YAML files. But getting the same error.
I have given File list like below in other YAML files and they seemed to work. Also here when spladder bams is changed to type `File` and given just one `bam` as input, instead of `File[]`, it is working
...
written 13 months ago by
ttom • 210
3
votes
1
answer
731
views
1
answer
... Not sure, what I am missing here or doing wrong here
**cat spladder.cwl**
cwlVersion: v1.0
class: CommandLineTool
baseCommand: [python, spladder.py]
requirements:
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.spladder_outDir)
- ...
written 13 months ago by
ttom • 210
0
votes
1
answer
1.2k
views
1
answers
... Ah.... my bad. I thought I removed it, but hadn't.
With that line removed it works. Thank you... ...
written 14 months ago by
ttom • 210
0
votes
1
answer
1.2k
views
1
answers
... Yes, makes sense to use the pre-written codes. Thank you !!
By adding `InitialWorkDirRequirement`, the script `index_bam.cwl ` could capture `bam` and `bai` outputs
**cat index_bam.cwl**
requirements:
InitialWorkDirRequirement:
listing: [ $(inputs.bam) ]
inputs:
b ...
written 14 months ago by
ttom • 210
1
vote
1
answer
664
views
1
answers
... Yes, true. The scatter creates multiple jobs and each job output gets written to different file, although the output file is the same. Each time a file gets created, overwriting the previous one.
As a solution, writing the output of the scatter to different output files and then another step to `ca ...
written 14 months ago by
ttom • 210
0
votes
1
answer
1.2k
views
1
answers
... **Option 1**
The script used in `degradation.cwl` does not have an option to give `bai` files as an input explicitly. It rather needs/searches for the `bai` file within the same path where the `bam` file exists. Hence giving `bai` as secondary file worked.
**Option 2 Trial**
`index_bam.cwl` only re ...
written 14 months ago by
ttom • 210
3
votes
1
answer
664
views
1
answer
... Using scatter to run `fastqc_check` step in the workflow where input is an array. Trying to capture all the results to one file. When the output file is kept as File, only the results from last file in the input array gets stored in the output file.
fastqc_check_out:
type: File[]
...
written 14 months ago by
ttom • 210
Latest awards to ttom
Popular Question
4 months ago,
created a question with more than 1,000 views.
For cramtools Java NoClassDefFoundError
Great Question
13 months ago,
created a question with more than 5,000 views.
For Vcftools --Geno And --Hwe Filter Options -No Output File Created
Popular Question
13 months ago,
created a question with more than 1,000 views.
For Tool or Script to convert MAF file to VCF ?
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: Why Does Vcftools Vcf-Annotate Produce An Empty File
Scholar
13 months ago,
created an answer that has been accepted.
For A: GATK-Depth of Coverage - Issue with per gene coverage
Scholar
14 months ago,
created an answer that has been accepted.
For A: GATK-Depth of Coverage - Issue with per gene coverage
Great Question
3.1 years ago,
created a question with more than 5,000 views.
For R : File Do Not Exists Error. Isilon File Path Not Recognized In R
Great Question
3.1 years ago,
created a question with more than 5,000 views.
For Vcftools --Geno And --Hwe Filter Options -No Output File Created
Popular Question
3.1 years ago,
created a question with more than 1,000 views.
For Tool or Script to convert MAF file to VCF ?
Popular Question
4.4 years ago,
created a question with more than 1,000 views.
For R : File Do Not Exists Error. Isilon File Path Not Recognized In R
Popular Question
4.4 years ago,
created a question with more than 1,000 views.
For Why Does Vcftools Vcf-Annotate Produce An Empty File
Popular Question
4.4 years ago,
created a question with more than 1,000 views.
For Split a multisample bam using RG tag information
Teacher
4.4 years ago,
created an answer with at least 3 up-votes.
For A: Why Does Vcftools Vcf-Annotate Produce An Empty File
Appreciated
4.8 years ago,
created a post with more than 5 votes.
For A: Vcftools --Geno And --Hwe Filter Options -No Output File Created
Popular Question
4.8 years ago,
created a question with more than 1,000 views.
For Why Does Vcftools Vcf-Annotate Produce An Empty File
Popular Question
5.0 years ago,
created a question with more than 1,000 views.
For Vcftools --Geno And --Hwe Filter Options -No Output File Created
Popular Question
5.1 years ago,
created a question with more than 1,000 views.
For Vcftools --Geno And --Hwe Filter Options -No Output File Created
Teacher
5.3 years ago,
created an answer with at least 3 up-votes.
For A: Vcftools --Geno And --Hwe Filter Options -No Output File Created
Scholar
5.3 years ago,
created an answer that has been accepted.
For A: GATK-Depth of Coverage - Issue with per gene coverage
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1457 users visited in the last hour