#!/usr/bin/python
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
import arvados
import subprocess
-import subst
+import crunchutil.subst as subst
import shutil
import os
+import sys
+import time
if len(arvados.current_task()['parameters']) > 0:
p = arvados.current_task()['parameters']
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 $(sam_fa_indices))\n"))
-with open("/tmp/crunch-job/gatk-variant.yaml", "w") as f:
+with open("/tmp/crunch-job/freebayes-variant.yaml", "w") as f:
f.write('''
-# Template for whole genome Illumina variant calling with GATK pipeline
+# Template for whole genome Illumina variant calling with FreeBayes
+# This is a GATK-free pipeline without post-alignment BAM pre-processing
+# (recalibration and realignment)
---
details:
- analysis: variant2
# batch: your-arbitrary-batch-name
algorithm:
aligner: bwa
- mark_duplicates: picard
- recalibrate: gatk
- realign: gatk
- variantcaller: gatk-haplotype
+ mark_duplicates: true
+ recalibrate: false
+ realign: false
+ variantcaller: freebayes
platform: illumina
quality_format: Standard
- coverage_interval: genome
# for targetted projects, set the region
# variant_regions: /path/to/your.bed
''')
+os.unlink("/usr/local/share/bcbio-nextgen/gemini_data")
+os.symlink(arvados.get_job_param_mount("gemini_data"), "/usr/local/share/bcbio-nextgen/gemini_data")
+
os.chdir(arvados.current_task().tmpdir)
-rcode = subprocess.call(["bcbio_nextgen.py", "--workflow", "template", "/tmp/crunch-job/gatk-variant.yaml", "project1",
+rcode = subprocess.call(["bcbio_nextgen.py", "--workflow", "template", "/tmp/crunch-job/freebayes-variant.yaml", "project1",
subst.do_substitution(p, "$(file $(R1))"),
subst.do_substitution(p, "$(file $(R2))")])
print("arvados-bcbio-nextgen: start writing output to keep")
done = False
+ api = arvados.api('v1')
while not done:
try:
out = arvados.CollectionWriter()