User: c.clarido

gravatar for c.clarido
c.clarido50
Reputation:
50
Status:
New User
Location:
Netherlands/Rotterdam/Leiden University (Applied Science)
Last seen:
3 weeks, 6 days ago
Joined:
1 year, 8 months ago
Email:
c*************@gmail.com

Posts by c.clarido

<prev • 37 results • page 1 of 4 • next >
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Forum: Recommend papers: automated vs manual downstream analysis
... Hello community, I was just wondering if anyone could recommend me a paper which address the following keywords: 1. reproducibility 2. automation genome downstream analysis: annotation and filtering 3. manual downstream analysis vs automated ...
forum analysis reproducibility manual downstream written 4 weeks ago by c.clarido50 • updated 18 days ago by h.mon25k
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How to run R docker in WDL?
... Hello community, I am building a pipeline in WDL + Cromwell. I have a specific docker for each tasks, or example: version 1.0 import "../tasks/common.wdl" task CallSV { input { IndexedBamFile bamFile Reference reference String out ...
wdl R cromwell docker gatk written 9 weeks ago by c.clarido50
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WDL + cromwell and remote server
... Good day community, I'd like to build a WDL SV calling pipeline that accepts BAM and reference files. I have the files in a remote server which I have mounted with sshfs in my local. When I try to testrun the workflow, I get a warning that hardlinks can not be made. At the end, the run failed bec ...
cromwel sshfs pipeline wdl written 3 months ago by c.clarido50
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WDL: how to use scatter for multiple callers?
... Good day, I have a bam file and 3 callers (delly,clever and lumpy) to detect structural variants and then use a tool (survivor) to merge the files. I was wondering if there is a way to use scatter in WDL so that the three callers will each ouput a VCF file? Kind regards, C.agaser ...
scatter wdl written 3 months ago by c.clarido50
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Comment: C: how to install survivor with conda
... I get this: $ conda search survivor Loading channels: done PackagesNotFoundError: The following packages are not available from current channels: - survivor Current channels: - https://conda.anaconda.org/bioconda/osx-64 - https://conda.anaconda. ...
written 4 months ago by c.clarido50
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how to install survivor with conda
... Hello community, I'm kinda new with installing packages in conda. So I am trying to install the [survivor][1] and I tried both: 1. conda install -c bioconda survivor 2. conda install -c bioconda/label/cf201901 survivor I get: PackagesNotFoundError: The following packages are not available from ...
channel survivor conda instal written 4 months ago by c.clarido50 • updated 4 months ago by Devon Ryan90k
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Comment: C: How to add help function in a snakemake file
... Thank you, I added a rule where I "cat" the help description from a file and it works fine. ...
written 7 months ago by c.clarido50
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How to add help function in a snakemake file
... Hello community, How do you add help function in a snakemake file such that it will print a description of the workflow when you enter: snakemake --snakefile Snakefile help I tried the following: import argparse parser = argparse.ArgumentParser( description='''ENTER DESCRIPTION H ...
snakefile snakemake helpfunction written 7 months ago by c.clarido50 • updated 7 months ago by dariober10k
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Comment: C: Error: Snakemake skiped a rule
... Thank you rizoic, I will definitely try this, In the meantime I used the priority method and it seems to be working ( still processing ). ...
written 8 months ago by c.clarido50
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Comment: C: Error: Snakemake skiped a rule
... In addition I found the following the information from snakemake documentation: Snakemake allows rules to specify numeric priorities: rule: input: ... output: ... priority: 50 shell: ... Per default, each rule has a priority of 0. Any rule that specifies a higher pr ...
written 8 months ago by c.clarido50

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