User: ttom

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ttom200
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Posts by ttom

<prev • 57 results • page 1 of 6 • next >
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Comment: C: Capture Output files using glob
... Thank you, it worked ...
written 4 months ago by ttom200
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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 4 months ago by ttom200
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Answer: A: Workflow Error - "list indices must be integers, not str"
... The issue was the presence of this line - entry: $(inputs.spladder_bams) ...
written 4 months ago by ttom200
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Comment: C: Workflow Error - "list indices must be integers, not str"
... 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 4 months ago by ttom200
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Workflow Error - "list indices must be integers, not str"
... 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) - ...
cwl written 4 months ago by ttom200
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Comment: C: CWL passing secondary files in a workflow
... Ah.... my bad. I thought I removed it, but hadn't. With that line removed it works. Thank you... ...
written 4 months ago by ttom200
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Comment: C: CWL passing secondary files in a workflow
... 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 4 months ago by ttom200
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Comment: C: Input type array and Output type file, possible in CWL ?
... 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 4 months ago by ttom200
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Comment: C: CWL passing secondary files in a workflow
... **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 4 months ago by ttom200
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Input type array and Output type file, possible in CWL ?
... 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[] ...
cwl written 4 months ago by ttom200

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Popular Question 4 months ago, created a question with more than 1,000 views. For Tool or Script to convert MAF file to VCF ?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Why Does Vcftools Vcf-Annotate Produce An Empty File
Scholar 4 months ago, created an answer that has been accepted. For A: GATK-Depth of Coverage - Issue with per gene coverage
Scholar 5 months ago, created an answer that has been accepted. For A: GATK-Depth of Coverage - Issue with per gene coverage
Great Question 2.3 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 2.3 years ago, created a question with more than 5,000 views. For Vcftools --Geno And --Hwe Filter Options -No Output File Created
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Tool or Script to convert MAF file to VCF ?
Popular Question 3.6 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 3.6 years ago, created a question with more than 1,000 views. For Why Does Vcftools Vcf-Annotate Produce An Empty File
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Split a multisample bam using RG tag information
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Why Does Vcftools Vcf-Annotate Produce An Empty File
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: Vcftools --Geno And --Hwe Filter Options -No Output File Created
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Why Does Vcftools Vcf-Annotate Produce An Empty File
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Vcftools --Geno And --Hwe Filter Options -No Output File Created
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Vcftools --Geno And --Hwe Filter Options -No Output File Created
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Vcftools --Geno And --Hwe Filter Options -No Output File Created
Scholar 4.6 years ago, created an answer that has been accepted. For A: GATK-Depth of Coverage - Issue with per gene coverage

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