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arvados / crunch_scripts @ master

Name Size
  crunchutil
  test
GATK2-VariantFiltration 1.98 KB
GATK2-bqsr 2.77 KB
GATK2-merge-call 7.21 KB
GATK2-realign 5.09 KB
arvados-bcbio-nextgen.py 5.57 KB
arvados_bwa.py 3.66 KB
arvados_gatk2.py 1.6 KB
arvados_ipc.py 1.47 KB
arvados_picard.py 1.34 KB
arvados_samtools.py 3.58 KB
bwa-aln 3.84 KB
bwa-index 1.17 KB
collection-merge 1.17 KB
crunchrunner 157 Bytes
cwl-runner 3.9 KB
decompress-all.py 1.72 KB
file-select 420 Bytes
grep 655 Bytes
hash 1012 Bytes
pgp-survey-import 4.65 KB
pgp-survey-parse 530 Bytes
picard-gatk2-prep 6.6 KB
pyrtg.py 2.37 KB
rtg-fasta2sdf 733 Bytes
rtg-fastq2sdf 1.4 KB
rtg-map 1.13 KB
rtg-snp 988 Bytes
run-command 15.8 KB
split-fastq.py 1.97 KB

Latest revisions

# Date Author Comment
5a0d9381 10/17/2016 05:23 pm Peter Amstutz

10200: Copy cwl-runner crunch script into arvados_cwl package to avoid version skew. Keep old cwl-runner code as a fallback to avoid breaking installations that haven't been updated.

84d86c17 10/04/2016 08:43 pm Peter Amstutz

10165: Add --output-name option to set name of output collection.

ad4344e2 09/30/2016 06:44 pm Peter Amstutz

10165: Always make an output collection when a workflow completes.

e2f3466f 09/28/2016 08:29 pm Peter Amstutz

10151: Ensure that job_order_object is normalized and Directory listings are enumerated.

91528dba 09/26/2016 09:04 pm Peter Amstutz

10081: Fix renamed methods.

c961ea10 08/11/2016 07:50 pm Peter Amstutz

9751: Fix direct to keep directory references.
Add arvados-specific integration test for arvados-cwl-runner.

133c1473 07/15/2016 01:14 pm Peter Amstutz

9570: Just add keep: to input keep locators in cwl-runner.

ec2af1a4 07/15/2016 01:13 pm Peter Amstutz

9570: Update cwl-runner for latest cwltool. Ensure use_container,
tmpdir_prefix and on_error are set.

2f1d6ce8 06/28/2016 05:17 pm Peter Amstutz

9442: Make cwl-runner crunch script backwards compatible (note-6)

fbc5ee76 06/21/2016 04:01 pm Peter Amstutz

8442: cwl-runner crunch script must provide work_api parameter to ArvCwlRunner
constructor.

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