User: mkher

gravatar for mkher
mkher50
Reputation:
50
Status:
New User
Location:
Last seen:
10 months, 3 weeks ago
Joined:
3 years, 6 months ago
Email:
m****@nygenome.org

Posts by mkher

<prev • 10 results • page 1 of 1 • next >
2
votes
2
answers
417
views
2
answers
Comment: C: CWL: Array of strings in workflow
... I'm sorry, my mistake. I missed your second suggestion of adding StepInputExpressionRequirement. That looks like exactly what I'm missing. ...
written 11 months ago by mkher50
0
votes
2
answers
417
views
2
answers
Answer: A: CWL: Array of strings in workflow
... Thank you, but that is not what I want to do. The tool is used in multiple contexts and the list of programs varies in each context. In my workflow there's a step where I call it with programs set to [CollectAlignementSummaryMetrics] and another step which calls the same tool with programs set to [M ...
written 11 months ago by mkher50
3
votes
2
answers
417
views
2
answers
CWL: Array of strings in workflow
... I have a command line tool that expect an input that is an array of strings. programs: type: type: array items: string inputBinding: {prefix: PROGRAM=, separate: false} inputBinding: position: 10 I can run this with a job yaml file: ...
cwl written 11 months ago by mkher50
2
votes
1
answer
670
views
1
answer
CWL multidimensional arrays or arrays of tuples
... Does CWL support multidimensional arrays? Is there a way to specify a list of paired fastq files? I am specifying them as two arrays of files, one for read1 and another for reaad2. This is awkward and I haven't figured out how to do crossproducts using them. I have an input that is a list of tuple ...
cwl written 2.3 years ago by mkher50 • updated 2.2 years ago by bogdan.gavrilovic230
0
votes
0
answers
1.4k
views
0
answers
Comment: C: Specify reference to samtools index
... The cram is coordinate-sorted. How can I check if it has M5 tags and what the value is? I am quite confused about what REF_PATH should be set to. ...
written 2.5 years ago by mkher50
0
votes
0
answers
1.4k
views
0
answers
Specify reference to samtools index
... I generated a cram using samtools: samtools view -C -T -o sample.cram sample.bam Now I want to index the cram and the reference file is not in the same location. I get errors like Failed to populate reference for id 91 Failed to populate reference for id 92 I suspect they're beca ...
samtools cram written 2.5 years ago by mkher50
2
votes
1
answer
1.2k
views
1
answer
CWL: Arguments vs Inputs in CommandLineTool.
... I am trying to understand the difference between arguments and inputs in a command line tool. I can see that input files are inputs, but what about other parameters to the tool? The distinction seems somewhat arbitrary. Are there any guidelines for recommended usage? Thank you Manisha ...
common workflow language cwl written 2.7 years ago by mkher50 • updated 2.4 years ago by farahk20
0
votes
2
answers
3.2k
views
2
answers
Comment: C: CWL: How do I use pipes?
... Thank you. I do want to do it as a workflow with separate steps for the two tools. Maybe not for this example of zcat and grep, but in more complex cases. The streamable keyword is what I need. ...
written 3.4 years ago by mkher50
3
votes
2
answers
2.5k
views
2
answers
CWL: How to refer to input or scattered value of a step
... I have a workflow that scatters a step over an array input called intervals. I want to use the value interval[i] to construct another parameter to the step. cwlVersion: v1.0 class: Workflow requirements: - class: ScatterFeatureRequirement - class: StepInputExpressionRequir ...
cwl written 3.4 years ago by mkher50 • updated 18 months ago by jshelton0
9
votes
2
answers
3.2k
views
5 follow
2
answers
CWL: How do I use pipes?
... I want to stream the output of one command as the input to the second command. How do I do that using CWL? For example: zcat sample.fastq.gz | grep ... My attempt to use stdout captured that stdout to a tmp file. Thank you Manisha ...
cwl written 3.5 years ago by mkher50 • updated 3.4 years ago by karl.sebby80

Latest awards to mkher

Popular Question 2.3 years ago, created a question with more than 1,000 views. For CWL: How do I use pipes?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For CWL: How do I use pipes?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1379 users visited in the last hour