# HG changeset patch
# User jpayne
# Date 1719548784 14400
# Node ID d497922d6caae8c1577beaf3f7f8687b0edf3962
# Parent  2af5e948dd5c089bba77cac0aaf787f1592966ab
planemo upload

diff -r 2af5e948dd5c -r d497922d6caa 1_map_reads.xml
--- a/1_map_reads.xml	Wed Jun 26 00:58:54 2024 -0400
+++ b/1_map_reads.xml	Fri Jun 28 00:26:24 2024 -0400
@@ -1,10 +1,10 @@
 <tool id="map_reads" name="1. Map Reads" version="1.0.1" profile="16.10">
     <description>to index, or lookup cached alignment</description>
     <requirements>
-        <!-- <container type="docker">quay.io/biocontainers/mulled-v2-d736175c8392ecaa2a26c372df9ad15b78f8d5b8:d59a38d618c862df52cf9dae223ed9d93ed7225b-0</container> -->
-        <requirement type="package" version="1.0.8">bzip2</requirement>
+        <container type="docker">quay.io/staphb/cfsan-snp-pipeline</container>
+        <!-- <requirement type="package" version="1.0.8">bzip2</requirement>
         <requirement type="package" version="2.4.5">bowtie2</requirement>
-        <!-- <requirement type="package" version="1.9.134">boto3</requirement> -->
+        <requirement type="package" version="1.9.134">boto3</requirement> -->
         <!-- <requirement type="package" version="3.6.8">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
diff -r 2af5e948dd5c -r d497922d6caa 2_call_sites.xml
--- a/2_call_sites.xml	Wed Jun 26 00:58:54 2024 -0400
+++ b/2_call_sites.xml	Fri Jun 28 00:26:24 2024 -0400
@@ -1,13 +1,13 @@
 <tool id="call_sites" name="2. Call Sites" version="1.0.1" profile="16.10">
     <description>of high-confidence SNPs, or lookup cached sitecall</description>
     <requirements>
-        <!-- <container type="docker">quay.io/biocontainers/mulled-v2-e518cb713b80020daa244e2ce559c37edb42dcde:5cb90165033bd74a97d0a807f439cf4b1aaabb89-0</container> -->
-        <requirement type="package" version="2.4.5">bowtie2</requirement>
+        <container type="docker">quay.io/staphb/cfsan-snp-pipeline</container>
+        <!-- <requirement type="package" version="2.4.5">bowtie2</requirement>
         <requirement type="package" version="1.9">samtools</requirement>
         <requirement type="package" version="1.0.8">bzip2</requirement>
         <requirement type="package" version="2.27.4">picard</requirement>
         <requirement type="package" version="2.4.4">varscan</requirement>
-        <!-- <requirement type="package" version="1.9.134">boto3</requirement> -->
+        <requirement type="package" version="1.9.134">boto3</requirement> -->
         <!-- <requirement type="package" version="3.6.8">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
diff -r 2af5e948dd5c -r d497922d6caa 3_filter_regions.xml
--- a/3_filter_regions.xml	Wed Jun 26 00:58:54 2024 -0400
+++ b/3_filter_regions.xml	Fri Jun 28 00:26:24 2024 -0400
@@ -1,11 +1,11 @@
 <tool id="filter_regions" name="3. Filter SNP Regions" version="1.0.1" profile="16.10">
     <description>based on SNP location, or lookup cached filtered sitecall</description>
     <requirements>
-        <!-- <container type="docker">quay.io/biocontainers/mulled-v2-b387422e12acd8cf2ba9f5f1b0f12c36f93c00b7:b1c910a35786ca780412af4d314af0670e08604f-0</container> -->
-        <requirement type="package" version="1.9">samtools</requirement>
+        <container type="docker">quay.io/staphb/cfsan-snp-pipeline</container>
+        <!-- <requirement type="package" version="1.9">samtools</requirement>
         <requirement type="package" version="1.0.8">bzip2</requirement>
         <requirement type="package" version="2.2.1">snp-pipeline</requirement>
-        <!-- <requirement type="package" version="1.9.134">boto3</requirement> -->
+        <requirement type="package" version="1.9.134">boto3</requirement> -->
         <!-- <requirement type="package" version="3.6.8">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
diff -r 2af5e948dd5c -r d497922d6caa 4_merge_sites.xml
--- a/4_merge_sites.xml	Wed Jun 26 00:58:54 2024 -0400
+++ b/4_merge_sites.xml	Fri Jun 28 00:26:24 2024 -0400
@@ -1,11 +1,11 @@
 <tool id="merge_sites" name="4. Merge Sites" version="1.0.1" profile="16.10">
     <description>from multiple samples</description>
     <requirements>
-        <!-- <container type="docker">quay.io/biocontainers/mulled-v2-a9689be5d4f7dc232fcd76f2f32bef2b80afcb49:0560aee94873e022862623c7766c9634a09b9513-0</container> -->
-        <requirement type="package" version="2.4.5">bowtie2</requirement>
+        <container type="docker">quay.io/staphb/cfsan-snp-pipeline</container>
+        <!-- <requirement type="package" version="2.4.5">bowtie2</requirement>
         <requirement type="package" version="1.9">samtools</requirement>
         <requirement type="package" version="1.0.8">bzip2</requirement>
-        <requirement type="package" version="2.2.1">snp-pipeline</requirement>
+        <requirement type="package" version="2.2.1">snp-pipeline</requirement> -->
         <!-- <requirement type="package" version="3.6.8">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
diff -r 2af5e948dd5c -r d497922d6caa 5_call_consensus.xml
--- a/5_call_consensus.xml	Wed Jun 26 00:58:54 2024 -0400
+++ b/5_call_consensus.xml	Fri Jun 28 00:26:24 2024 -0400
@@ -1,10 +1,10 @@
 <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>
-        <!-- <container type="docker">quay.io/biocontainers/mulled-v2-fe715cf36e5a6063362b28e50f1f4a1a767770d5:8f94687b7d8826f1473b7e97df0cea2a960b35bf-0</container> -->
-        <requirement type="package" version="1.0.8">bzip2</requirement>
+        <container type="docker">quay.io/staphb/cfsan-snp-pipeline</container>
+        <!-- <requirement type="package" version="1.0.8">bzip2</requirement>
         <requirement type="package" version="2.2.1">snp-pipeline</requirement>
-        <!-- <requirement type="package" version="1.9.134">boto3</requirement> -->
+        <requirement type="package" version="1.9.134">boto3</requirement> -->
         <!-- <requirement type="package" version="3.6.8">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
diff -r 2af5e948dd5c -r d497922d6caa 6_merge_vcfs.xml
--- a/6_merge_vcfs.xml	Wed Jun 26 00:58:54 2024 -0400
+++ b/6_merge_vcfs.xml	Fri Jun 28 00:26:24 2024 -0400
@@ -1,7 +1,7 @@
 <tool id="merge_vcfs" name="6. Merge VCFs" version="1.0.1" profile="16.10">
     <description>into a multi-sample VCF with consensus SNPs</description>
     <requirements>
-        <!-- <container type="docker">quay.io/biocontainers/mulled-v2-72d480da2f80e0804df2fc75273988c6dba1648d:f354c444b518b0ada8e031aa2984346e2f5d8837-0</container> -->
+        <container type="docker">quay.io/staphb/cfsan-snp-pipeline</container>
         <requirement type="package" version="1.9">bcftools</requirement>
         <requirement type="package" version="1.0.8">bzip2</requirement>
         <requirement type="package" version="2.2.1">snp-pipeline</requirement>
diff -r 2af5e948dd5c -r d497922d6caa 7_smp_matrix.xml
--- a/7_smp_matrix.xml	Wed Jun 26 00:58:54 2024 -0400
+++ b/7_smp_matrix.xml	Fri Jun 28 00:26:24 2024 -0400
@@ -1,11 +1,11 @@
 <tool id="snp_matrix" name="7. Create a SNP matrix" version="1.0.1" profile="16.10">
     <description>and associated distance metrics</description>
     <requirements>
-        <!-- <container type="docker">quay.io/biocontainers/mulled-v2-d2e223d7ac457e81243657cd7ae8336bd1c16e8e:81b350b3fbf165cbf5db53022037a2657a660701-0</container> -->
-        <requirement type="package" version="1.9">bcftools</requirement>
+        <container type="docker">quay.io/staphb/cfsan-snp-pipeline</container>
+        <!-- <requirement type="package" version="1.9">bcftools</requirement>
         <requirement type="package" version="1.0.8">bzip2</requirement>
         <requirement type="package" version="2.2.1">snp-pipeline</requirement>
-        <requirement type="package" version="0.2.6">tabix</requirement>
+        <requirement type="package" version="0.2.6">tabix</requirement> -->
         <!-- <requirement type="package" version="3.6.8">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[