Mercurial > repos > jpayne > snp_pipeline

changeset 12:8764af78e270

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planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Tue, 30 Jan 2018 17:21:24 -0500
parents 772f310d2506
children 6adaecff5f2b
files 1_map_reads.xml 4_merge_sites.xml 5_call_consensus.xml 6_merge_vcfs.xml 7_smp_matrix.xml
diffstat 5 files changed, 5 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/1_map_reads.xml	Tue Jan 30 17:15:09 2018 -0500
+++ b/1_map_reads.xml	Tue Jan 30 17:21:24 2018 -0500
@@ -1,6 +1,7 @@
 <tool id="map_reads" name="1. Map Reads" version="1.0.1" profile="16.10">
     <description>to index, or lookup cached alignment</description>
     <requirements>
+        <requirement type="package" version="1.0.6">bzip2</requirement>
         <requirement type="package" version="2.3.4">bowtie2</requirement>
         <requirement type="package" version="1.5.11">boto3</requirement>
         <requirement type="package" version="3.4">python3</requirement>
--- a/4_merge_sites.xml	Tue Jan 30 17:15:09 2018 -0500
+++ b/4_merge_sites.xml	Tue Jan 30 17:21:24 2018 -0500
@@ -3,6 +3,7 @@
     <requirements>
         <requirement type="package" version="2.2.6">bowtie2</requirement>
         <requirement type="package" version="1.2">samtools</requirement>
+        <requirement type="package" version="1.0.6">bzip2</requirement>
         <requirement type="package">snp-pipeline</requirement>
         <requirement type="package" version="3.4">python3</requirement>
     </requirements>
--- a/5_call_consensus.xml	Tue Jan 30 17:15:09 2018 -0500
+++ b/5_call_consensus.xml	Tue Jan 30 17:21:24 2018 -0500
@@ -1,6 +1,7 @@
 <tool id="call_consensus" name="5. Call consensus SNPs" version="1.0.1" profile="16.10">
     <description>for a sample, or lookup cached consensus SNP calls</description>
     <requirements>
+        <requirement type="package" version="1.0.6">bzip2</requirement>
         <requirement type="package" version="1.0.1">snp-pipeline</requirement>
         <requirement type="package" version="1.5.11">boto3</requirement>
         <requirement type="package" version="3.4">python3</requirement>
--- a/6_merge_vcfs.xml	Tue Jan 30 17:15:09 2018 -0500
+++ b/6_merge_vcfs.xml	Tue Jan 30 17:21:24 2018 -0500
@@ -2,6 +2,7 @@
     <description>into a multi-sample VCF with consensus SNPs</description>
     <requirements>
         <!-- <requirement type="package" version="1.6">bcftools</requirement> -->
+        <requirement type="package" version="1.0.6">bzip2</requirement>
         <requirement type="package" version="1.0.1">snp-pipeline</requirement>
         <requirement type="package">tabix</requirement>
         <requirement type="package" version="3.4">python3</requirement>
--- a/7_smp_matrix.xml	Tue Jan 30 17:15:09 2018 -0500
+++ b/7_smp_matrix.xml	Tue Jan 30 17:21:24 2018 -0500
@@ -1,6 +1,7 @@
 <tool id="snp_matrix" name="7. Create a SNP matrix" version="1.0.1" profile="16.10">
     <description>and associated distance metrics</description>
     <requirements>
+        <requirement type="package" version="1.0.6">bzip2</requirement>
         <requirement type="package" version="1.0.1">snp-pipeline</requirement>
         <requirement type="package">tabix</requirement>
         <requirement type="package" version="3.4">python3</requirement>