hall-lab / sv-pipeline Goto Github PK

Hi,

The script Pre_Merge_SV_Single.wdl fails to import to Dockstore. This error carries over to the Terra workspace (mgi-hall-anvil-terra/svtools_1000Genomes), so I haven't been able to get the example workspace to run.

warning /scripts/Pre_Merge_SV_Single.wdl: Failed to import 'https://raw.githubusercontent.com/hall-lab/sv-pipeline/terra-compatible-hja/scripts/Pre_Merge_SV_per_sample.wdl' (reason 1 of 1): ERROR: Unexpected symbol (line 49, col 5) when parsing '_gen19'. Expected rbrace, got "output_vcf_basename". output_vcf_basename = basename + '.filtered' ^ $e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 )

Link to Dockstore: https://dockstore.org/workflows/github.com/hall-lab/sv-pipeline/pre_merge_sv_single:terra-compatible-hja?tab=files

Thank you,
Laura

Trying to use with non-chr prefixed chromosome names currently fails.

Hi,

I have 100s of CRAM files which was aligned to hg38, and interested to call structural variation. Tried to use docker since it supports hg38 version reference. I get an error while pulling sv docker image in the Centos7 machine.

#docker pull halllab/cadd-b38-v1-6 Using default tag: latest Error response from daemon: manifest for halllab/cadd-b38-v1-6:latest not found: manifest unknown: manifest unknown

Next try:

Because of this issue, tried to run to call SVs by wdl script. The Readme file instructs to use Cromwell version 25 or later (These scripts can be launched using Cromwell (version 25 or later) to execute wdl script. I think version 25 is much older because of the latest release version is 53.1. Which is the stable and newer version of Cromwell can be used to execute WDL script sv-pipeline for SV calling of CRAM files which are aligned to GRCh38?

I am new to this, could anyone help me how to call SVs form CRAM files, tried to install SVtools seprately, it's getting python2 compatible issues. Please suggest to me which type of workflow is best (wdl, docker, or SVtools) to identify the SVs.

Thanks in advance.
Nitha

Hi!

I was directed to your workflow by my colleague Devin Locke and I was excited to finally find a well written WDL workflow that uses runtimes everywhere, rather than some assumed local state. I was also very happy to find that you provide an easily accessible and small test data set and input.json! I really appreciate the ease with which I could assemble a run for your workflow!

Unfortunately when I try and run the workflow on Cromwell 35 it errors out.

ERROR: Two or more calls or values in the workflow have the same name:

Declaration statement here (line 24, column 12):
    String basename = sub(sub(aligned_cram, "^.*/", ""), aligned_cram_suffix + "$", "")
           ^
      
Declaration statement here (line 96, column 12):
    String basename = sub(sub(aligned_cram, "^.*/", ""), aligned_cram_suffix + "$", "")
           ^

Thanks!
-Kaushik

Seeing errors like:

/opt/lumpy-sv/bin/lumpyexpress: line 15: -n: command not found
/opt/lumpy-sv/bin/lumpyexpress: line 16: [: ==: unary operator expected

in my log files.

This results from hexdump not being installed in the container. Thus, the environment variable is undefined and these errors result.

Note that I believe these to be inconsequential and thus may not fix immediately since I'd prefer not to change pipeline versions midstream.

Where can I download ref_cache file?