User: alanh

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alanh80
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Posts by alanh

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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 4 months ago by alanh80 • updated 4 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 5 months ago by alanh80 • updated 5 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 5 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 6 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 6 months ago by alanh80
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Comment: C: Combine subject with sample type in a scatter?
... How about this: sampleName: valueFrom: | ${ if (inputs.subjectName) { return inputs.subjectName + "_" + inputs.sampleName } else { return inputs.sampleName } } ...
written 6 months ago by alanh80
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Comment: C: Combine subject with sample type in a scatter?
... I've tried a bunch of iterations here: `valueFrom: "$(subjectName)_$(self.sample)"` `valueFrom: ${return inputs.subjectName.concat("_",fastqs.sample)}` and they all fail with various issues. ...
written 6 months ago by alanh80
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Comment: C: Combine subject with sample type in a scatter?
... In a later step, the Mutect2 somatic variant caller seems to name the FORMAT data column in its output VCF using the value in the read. In my above example, if the "$(self.sample)" is either "tumor" or "normal" depending on the sample type. The reads get named "tumor" or "normal" based on that. ...
written 6 months ago by alanh80
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Combine subject with sample type in a scatter?
... I have CWL that runs a pair of tumor-normal samples for a given subject. For later variant calling, I want to add the read names to be something like `$(subjectName)_$(fastqs.sample)` The inputs are like this: inputs: fastqs: type: type: array items: ...
cwl written 6 months ago by alanh80
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Comment: C: What are "HET" regions in a genome?
... From https://www.ncbi.nlm.nih.gov/assembly/GCA_000001405.28 clicked on "Download the regions report" on the upper right, which yields this URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.28_GRCh38.p13/GCA_000001405.28_GRCh38.p13_assembly_regions.txt It's line 212 in that ...
written 6 months ago by alanh80

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Scholar 6 months ago, created an answer that has been accepted. For A: Combine subject with sample type in a scatter?

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