Statistics
| Branch: | Tag: | Revision:

arvados / crunch_scripts @ master

Name Size
  crunchutil
  test
GATK2-VariantFiltration 2.08 KB
GATK2-bqsr 2.87 KB
GATK2-merge-call 7.3 KB
GATK2-realign 5.19 KB
arvados-bcbio-nextgen.py 5.66 KB
arvados_bwa.py 3.75 KB
arvados_gatk2.py 1.7 KB
arvados_ipc.py 1.57 KB
arvados_picard.py 1.44 KB
arvados_samtools.py 3.67 KB
bwa-aln 3.94 KB
bwa-index 1.26 KB
collection-merge 1.27 KB
crunchrunner 255 Bytes
cwl-runner 4 KB
decompress-all.py 1.82 KB
file-select 518 Bytes
grep 753 Bytes
hash 1.08 KB
pgp-survey-import 4.75 KB
pgp-survey-parse 628 Bytes
picard-gatk2-prep 6.7 KB
pyrtg.py 2.47 KB
rtg-fasta2sdf 831 Bytes
rtg-fastq2sdf 1.5 KB
rtg-map 1.22 KB
rtg-snp 1.06 KB
run-command 15.9 KB
split-fastq.py 2.07 KB

Latest revisions

# Date Author Comment
0f644e24 06/28/2017 08:27 pm Tom Clegg

2411: Add copyright notices to everything.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <>

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)

View revisions

Also available in: Atom