Mercurial > repos > jpayne > snp_pipeline

changeset 59:49d672730d3e

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planemo upload
author jpayne
date Mon, 17 Jun 2024 23:57:13 -0400
parents d53281e6edae
children 0b0e3e4376a7
files 1_map_reads.xml 2_call_sites.xml 3_filter_regions.xml 4_merge_sites.xml 5_call_consensus.xml 6_merge_vcfs.xml 7_smp_matrix.xml
diffstat 7 files changed, 14 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/1_map_reads.xml	Mon Jun 17 02:57:10 2024 -0400
+++ b/1_map_reads.xml	Mon Jun 17 23:57:13 2024 -0400
@@ -2,9 +2,9 @@
     <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>
+        <!-- <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[
--- a/2_call_sites.xml	Mon Jun 17 02:57:10 2024 -0400
+++ b/2_call_sites.xml	Mon Jun 17 23:57:13 2024 -0400
@@ -2,12 +2,12 @@
     <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>
+        <!-- <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[
--- a/3_filter_regions.xml	Mon Jun 17 02:57:10 2024 -0400
+++ b/3_filter_regions.xml	Mon Jun 17 23:57:13 2024 -0400
@@ -2,10 +2,10 @@
     <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>
+        <!-- <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[
--- a/4_merge_sites.xml	Mon Jun 17 02:57:10 2024 -0400
+++ b/4_merge_sites.xml	Mon Jun 17 23:57:13 2024 -0400
@@ -2,10 +2,10 @@
     <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>
+        <!-- <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[
--- a/5_call_consensus.xml	Mon Jun 17 02:57:10 2024 -0400
+++ b/5_call_consensus.xml	Mon Jun 17 23:57:13 2024 -0400
@@ -2,9 +2,9 @@
     <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>
+        <!-- <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[
--- a/6_merge_vcfs.xml	Mon Jun 17 02:57:10 2024 -0400
+++ b/6_merge_vcfs.xml	Mon Jun 17 23:57:13 2024 -0400
@@ -2,11 +2,11 @@
     <description>into a multi-sample VCF with consensus SNPs</description>
     <requirements>
         <container type="docker">quay.io/biocontainers/mulled-v2-72d480da2f80e0804df2fc75273988c6dba1648d:f354c444b518b0ada8e031aa2984346e2f5d8837-0</container>
-        <requirement type="package" version="1.9">bcftools</requirement>
+        <!-- <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="1.9">htslib</requirement>
+        <requirement type="package" version="1.9">htslib</requirement> -->
         <!-- <requirement type="package" version="3.6.8">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
--- a/7_smp_matrix.xml	Mon Jun 17 02:57:10 2024 -0400
+++ b/7_smp_matrix.xml	Mon Jun 17 23:57:13 2024 -0400
@@ -2,10 +2,10 @@
     <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>
+        <!-- <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[