Closed rhshah closed 5 years ago
Started test on: marianas_process_loop_umi_1.8.0
couple of observations:
We should label the files and folder as 1.8.1.
I added the new jar to mskcc/marianas:0.1.0
I was able to run using cwltool:
Version:/home/shahr2/tools/system/miniconda/versions/4.6.14/envs/test_toil/bin/cwltool 1.0.20190228155703
cwltool --singularity --non-strict /home/shahr2/github/cwl-commandlinetools/marianas_process_loop_umi_1.8.0/marianas_process_loop_umi.cwl $PWD/process_loop_umi_inputs.yaml
But failed with toil-cwl-runner:
#Using toil-cwl-runner
toil-cwl-runner --logFile $PWD/processUMILoop_toil.log --jobStore $PWD/processUMILoop_jobstore --batchSystem lsf --workDir $PWD --outdir $PWD --writeLogs $PWD/processUMILoop_toil_log --logLevel DEBUG --stats --retryCount 2 --no-container --disableCaching --maxLogFileSize 20000000000 /home/shahr2/github/cwl-commandlinetools/marianas_process_loop_umi_1.8.0/marianas_process_loop_umi.cwl $PWD/process_loop_umi_inputs.yaml`
Probably failed due to toil version=3.20
.
Anyhow this command works:
mkdir $PWD/processUMILoop_toil_log
toil-cwl-runner --singularity --logFile processUMILoop_toil.log --jobStore $PWD/processUMILoop_jobstore --batchSystem lsf --workDir $PWD/processUMILoop_toil_log --outdir $PWD --writeLogs $PWD/processUMILoop_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /home/shahr2/github/cwl-commandlinetools/marianas_process_loop_umi_1.8.0/marianas_process_loop_umi.cwl $PWD/process_loop_umi_inputs.yaml > processUMILoop_toil.stdout 2> processUMILoop_toil.stderr
also need to modify ramMin
, coreMin
Couple of things that I noticed:
@shalabhsuman & @ionox0
For example:
marianas_process_loop_umi_1.8.1/marianas_process_loop_umi.cwl
Should be:
marianas_process_loop_umi_1.8.1/marianas_process_loop_umi_1.8.1.cwl
@shalabhsuman @ionox0 Another thing while writing readme can you please follow this : https://github.com/mskcc/cwl-commandlinetools/tree/feature/test_modify_cwls/picard_fix_mate_information_1.96 https://github.com/mskcc/cwl-commandlinetools/tree/feature/test_modify_cwls/picard_add_or_replace_read_groups_1.96
We need to test the following CWLS: