# HG changeset patch
# User jpayne
# Date 1557416722 14400
# Node ID e90a783a4e8bd8d5bd67213bde84b52a14e48733
# Parent ebfa7fd256aa0c53554558a2defe37233d744d00
planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty
diff -r ebfa7fd256aa -r e90a783a4e8b 1_map_reads.xml
--- a/1_map_reads.xml Wed May 08 11:43:17 2019 -0400
+++ b/1_map_reads.xml Thu May 09 11:45:22 2019 -0400
@@ -2,9 +2,9 @@
to index, or lookup cached alignment
bzip2
- bowtie2
+ bowtie2
boto3
- python
+ python
of high-confidence SNPs, or lookup cached sitecall
- bowtie2
- samtools
+ bowtie2
+ samtools
bzip2
picard
varscan
boto3
- python
+ python
based on SNP location, or lookup cached filtered sitecall
- samtools
+ samtools
bzip2
- snp-pipeline
+ snp-pipeline
boto3
- python
+ python
from multiple samples
- bowtie2
- samtools
+ bowtie2
+ samtools
bzip2
- snp-pipeline
- python
+ snp-pipeline
+ python
for a sample, or lookup cached consensus SNP calls
bzip2
- snp-pipeline
+ snp-pipeline
boto3
- python
+ python
&2 && tar zcv ./consensus.vcf ./consensus.fasta
"
@@ -37,7 +37,7 @@
-
+
diff -r ebfa7fd256aa -r e90a783a4e8b 6_merge_vcfs.xml
--- a/6_merge_vcfs.xml Wed May 08 11:43:17 2019 -0400
+++ b/6_merge_vcfs.xml Thu May 09 11:45:22 2019 -0400
@@ -1,12 +1,12 @@
into a multi-sample VCF with consensus SNPs
- bcftools
+ bcftools
bzip2
- snp-pipeline
+ snp-pipeline
tabix
- htslib
- python
+ htslib
+ python
-
+
and associated distance metrics
- bcftools
+ bcftools
bzip2
- snp-pipeline
+ snp-pipeline
tabix
- python
+ python