User: skanwal

gravatar for skanwal
skanwal50
Reputation:
50
Status:
New User
Location:
Last seen:
9 months ago
Joined:
3 years, 11 months ago
Email:
s******@student.unimelb.edu.au

Posts by skanwal

<prev • 17 results • page 1 of 2 • next >
2
votes
2
answers
441
views
2
answers
Comment: C: CWL: Using the "EnvVarRequirement" to pass an environment variable to a script
... Hi Michael, Thanks a lot for the response. I have edited the bash script to write to the standard output and using `stdout` in the cwl definition to write it to a file. This works as expected. --- Sehrish K ...
written 9 months ago by skanwal50
0
votes
2
answers
441
views
2
answers
Answer: A: CWL: Using the "EnvVarRequirement" to pass an environment variable to a script
... Hi Tom, Thanks for the response. Changing the tool definition according to your suggestion is raising the following issue: > INFO /Users/kanwals/miniconda3/envs/cwl/bin/cwltool 1.0.20190915164430 > INFO Resolved './runFolderCheck.cwl' to > 'file:///Users/kanwals/Documents/UMCCR/git/bcl2fa ...
written 9 months ago by skanwal50
6
votes
2
answers
441
views
2
answers
CWL: Using the "EnvVarRequirement" to pass an environment variable to a script
... Hello, I am running a bash script inside a docker container that expects `DEPLOY_ENV` variable to be set to an appropriate value. However, when running `cwltool ./runFolderCheck.cwl ./runFolderCheck-job.yml`, I get: > INFO /Users/kanwals/miniconda3/envs/cwl/bin/cwltool 1.0.20190915164430 > ...
common workflow language cwl written 9 months ago by skanwal50
0
votes
3
answers
1.3k
views
3
answers
Comment: C: CWL: Getting output file of a CommandLineTool using glob
... Thanks @inutano. It did the trick :) ...
written 23 months ago by skanwal50
0
votes
3
answers
1.3k
views
3
answers
Comment: C: CWL: Getting output file of a CommandLineTool using glob
... Same error: [job kallisto-quant.cwl] Job error: Error collecting output for parameter 'quantification': kallisto-quant.cwl:31:4: Did not find output file with glob pattern: '['*.tsv']' [job kallisto-quant.cwl] completed permanentFail {} Final process status is permanentFail ...
written 23 months ago by skanwal50
0
votes
3
answers
1.3k
views
3
answers
Answer: A: CWL: Getting output file of a CommandLineTool using glob
... Hi Kaushik, Thanks for replying. Yes, I have run this tool a few times, using a conda installation and also it's docker image. The tool produces three files: abundance.h5 abundance.tsv run_info.json The docker command produced by cwltool ((provided in the original question) also loo ...
written 23 months ago by skanwal50
2
votes
3
answers
1.3k
views
3
answers
CWL: Getting output file of a CommandLineTool using glob
... Hi, I am trying to run the following CommandLineTool description: #!/usr/bin/env cwl-runner cwlVersion: v1.0 class: CommandLineTool hints: DockerRequirement: dockerPull: quay.io/biocontainers/kallisto:0.44.0--h7d86c95_2 inputs: fastqs: type: Fil ...
common workflow language cwl written 24 months ago by skanwal50 • updated 23 months ago by inutano30
0
votes
1
answer
1.6k
views
1
answers
Comment: C: fail to open file - bwa mem using CWL
... Thanks for the reply. I have solved this issue by making some changes in the yaml file for workflow. I was not specifying the input path correctly in the job file and had some issues in specifying the array of files as input to bwa-mem. It's finally resolved :) ...
written 3.2 years ago by skanwal50
2
votes
1
answer
1.6k
views
1
answer
fail to open file - bwa mem using CWL
... Hi, I am trying to run simple two step CWL workflow, using v1.0. Step 1: Create sequence dictionary for reference Step 2: Align input fastq reads with reference Step1 runs fine but step 2 (bwa mem) throws the following error: [job bwa-mem] /Users/sehrish/Google Drive/AnalysisGalaxyCpipeCWL/ ...
bwa-mem cwl written 3.2 years ago by skanwal50 • updated 3.2 years ago by solomon.shorser20
0
votes
0
answers
1.9k
views
0
answers
Comment: C: CWL : file could not be created with exception File not found
... Yes, I have tried removing the import but the error is exactly the same. Error: Could not find or load main class org.broadinstitute.sting.gatk.CommandLineGATK Error collecting output for parameter 'output_printReads' ...
written 4.0 years ago by skanwal50

Latest awards to skanwal

Popular Question 19 months ago, created a question with more than 1,000 views. For CWL : file could not be created with exception File not found
Popular Question 23 months ago, created a question with more than 1,000 views. For CWL : file could not be created with exception File not found

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1376 users visited in the last hour