User: alanh

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alanh80
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Posts by alanh

<prev • 19 results • page 1 of 2 • next >
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Annotate DNA germline calls: Funcotator? VEP? SnpEff?
... I'm working on a DNAseq germline workflow to make calls for other researchers to use. I note that GATK's Best Practices uses Funcotator to annotate their germline calls, one of my colleagues has used VEP for this purpose, and I know we've also used SnpEff in the past, but it's been a while. Googli ...
dnaseq annotation germline written 25 days ago by alanh80
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Comment: C: randomly shuffle BAM file
... It appears that if you run `samtools bamshuf` on more recent versions of samtools, it translates that to `samtools collate` automatically. ...
written 3 months ago by alanh80
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toil-cwl-runner on slurm: toil.batchSystems.singleMachine maxMemory limit?
... I've written a CWL that I know works on the Arvados CWL runner on our SLURM cluster with Docker. I'm trying to run it using the toil-cwl-runner on the same SLURM cluster using singularity 2.5.x. I've created a virtualenv and ran `pip install toil[cwl]` and it appears to have installed. I'm ...
toil slurm cwl singularity written 17 months ago by alanh80 • updated 17 months ago by Michael R. Crusoe1.8k
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Rename file in CWL ExpressionTool?
... Expanding on https://www.biostars.org/p/343413/ Is there any way to do this after the fact in an ExpressionTool? I'm running a somatic workflow and using Strelka to call germline variants. Inside the CWL, I'm easily able to refer to the outputs as "tumor_germline/variants_vcf" and "normal_germl ...
file management cwl written 17 months ago by alanh80 • updated 17 months ago by Michael R. Crusoe1.8k
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Comment: C: best practice for renaming file in CWL workflow
... Is there any way to do this after the fact in an ExpressionTool? ...
written 17 months ago by alanh80
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Answer: A: Combine subject with sample type in a scatter?
... To specifically put the answer in context, the correct method is to do the following: steps: dna_align_and_sort: run: align_sort.cwl in: reference_fasta: referenceFasta fastq_files: source: fastqs valueFrom: $(self.files) ...
written 18 months ago by alanh80
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Comment: C: Combine subject with sample type in a scatter?
... Thanks, this answered my question and it was hard to shift the contexts in my head. ...
written 18 months ago by alanh80
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Comment: C: Combine subject with sample type in a scatter?
... How about this: sampleName: valueFrom: | ${ if (inputs.subjectName) { return inputs.subjectName + "_" + inputs.sampleName } else { return inputs.sampleName } } ...
written 18 months ago by alanh80
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Comment: C: Combine subject with sample type in a scatter?
... I've tried a bunch of iterations here: `valueFrom: "$(subjectName)_$(self.sample)"` `valueFrom: ${return inputs.subjectName.concat("_",fastqs.sample)}` and they all fail with various issues. ...
written 18 months ago by alanh80
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Comment: C: Combine subject with sample type in a scatter?
... In a later step, the Mutect2 somatic variant caller seems to name the FORMAT data column in its output VCF using the value in the read. In my above example, if the "$(self.sample)" is either "tumor" or "normal" depending on the sample type. The reads get named "tumor" or "normal" based on that. ...
written 18 months ago by alanh80

Latest awards to alanh

Popular Question 3 months ago, created a question with more than 1,000 views. For Use filename found in an input Directory in a CommandLineTool
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: ExpressionTool failing after a scatter: How do I debug the Javascript?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: ExpressionTool failing after a scatter: How do I debug the Javascript?
Scholar 18 months ago, created an answer that has been accepted. For A: Combine subject with sample type in a scatter?

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