[ARVADOS] updated: 10543be10e5db9721a638d46e40bacc17d7599fe
git at public.curoverse.com
git at public.curoverse.com
Mon Jul 7 13:03:10 EDT 2014
Summary of changes:
crunch_scripts/arvados-bcbio-nextgen.py | 17 +++++++++--------
1 file changed, 9 insertions(+), 8 deletions(-)
via 10543be10e5db9721a638d46e40bacc17d7599fe (commit)
from c0cda7d557efe50ab2e817a0bb920e8f1c8f73f7 (commit)
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commit 10543be10e5db9721a638d46e40bacc17d7599fe
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Jul 7 13:03:01 2014 -0400
Default arvados-bcbio-nextgen pipeline to use freebayes instead of gatk. no issue #
diff --git a/crunch_scripts/arvados-bcbio-nextgen.py b/crunch_scripts/arvados-bcbio-nextgen.py
index 37ac7d3..d53e069 100755
--- a/crunch_scripts/arvados-bcbio-nextgen.py
+++ b/crunch_scripts/arvados-bcbio-nextgen.py
@@ -69,9 +69,11 @@ with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/picard_index.loc", "w
with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/sam_fa_indices.loc", "w") as f:
f.write(subst.do_substitution(p, "index\tGRCh37\t$(file $(sam_fa_indices))\n"))
-with open("/tmp/crunch-job/gatk-variant.yaml", "w") as f:
+with open("/tmp/crunch-job/freebayes-variant.yaml", "w") as f:
f.write('''
-# Template for whole genome Illumina variant calling with GATK pipeline
+# Template for whole genome Illumina variant calling with FreeBayes
+# This is a GATK-free pipeline without post-alignment BAM pre-processing
+# (recalibration and realignment)
---
details:
- analysis: variant2
@@ -81,20 +83,19 @@ details:
# batch: your-arbitrary-batch-name
algorithm:
aligner: bwa
- mark_duplicates: picard
- recalibrate: gatk
- realign: gatk
- variantcaller: gatk-haplotype
+ mark_duplicates: true
+ recalibrate: false
+ realign: false
+ variantcaller: freebayes
platform: illumina
quality_format: Standard
- coverage_interval: genome
# for targetted projects, set the region
# variant_regions: /path/to/your.bed
''')
os.chdir(arvados.current_task().tmpdir)
-rcode = subprocess.call(["bcbio_nextgen.py", "--workflow", "template", "/tmp/crunch-job/gatk-variant.yaml", "project1",
+rcode = subprocess.call(["bcbio_nextgen.py", "--workflow", "template", "/tmp/crunch-job/freebayes-variant.yaml", "project1",
subst.do_substitution(p, "$(file $(R1))"),
subst.do_substitution(p, "$(file $(R2))")])
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