Mercurial > repos > jpayne > snp_pipeline

changeset 50:e90a783a4e8b

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planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty
author jpayne
date Thu, 09 May 2019 11:45:22 -0400
parents ebfa7fd256aa
children 568eb62c7524
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, 25 insertions(+), 25 deletions(-) [+]
line wrap: on
line diff
--- 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 @@
     <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="2.3.5">bowtie2</requirement>
         <requirement type="package" version="1.9.134">boto3</requirement>
-        <requirement type="package" version="3.7.3">python</requirement>
+        <requirement type="package" version="3.6.8">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
--- a/2_call_sites.xml	Wed May 08 11:43:17 2019 -0400
+++ b/2_call_sites.xml	Thu May 09 11:45:22 2019 -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>
-        <requirement type="package" version="2.3.4">bowtie2</requirement>
-        <requirement type="package" version="1.6">samtools</requirement>
+        <requirement type="package" version="2.3.5">bowtie2</requirement>
+        <requirement type="package" version="1.9">samtools</requirement>
         <requirement type="package" version="1.0.6">bzip2</requirement>
         <requirement type="package">picard</requirement>
         <requirement type="package">varscan</requirement>
         <requirement type="package" version="1.9.134">boto3</requirement>
-        <requirement type="package" version="3.7.3">python</requirement>
+        <requirement type="package" version="3.6.8">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
     export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
--- a/3_filter_regions.xml	Wed May 08 11:43:17 2019 -0400
+++ b/3_filter_regions.xml	Thu May 09 11:45:22 2019 -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>
-        <requirement type="package" version="1.6">samtools</requirement>
+        <requirement type="package" version="1.9">samtools</requirement>
         <requirement type="package" version="1.0.6">bzip2</requirement>
-        <requirement type="package" version="1.0.1">snp-pipeline</requirement>
+        <requirement type="package" version="2.0.2">snp-pipeline</requirement>
         <requirement type="package" version="1.9.134">boto3</requirement>
-        <requirement type="package" version="3.7.3">python</requirement>
+        <requirement type="package" version="3.6.8">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
--- a/4_merge_sites.xml	Wed May 08 11:43:17 2019 -0400
+++ b/4_merge_sites.xml	Thu May 09 11:45:22 2019 -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>
-        <requirement type="package" version="2.2.6">bowtie2</requirement>
-        <requirement type="package" version="1.2">samtools</requirement>
+        <requirement type="package" version="2.3.5">bowtie2</requirement>
+        <requirement type="package" version="1.9">samtools</requirement>
         <requirement type="package" version="1.0.6">bzip2</requirement>
-        <requirement type="package" version="1.0.1">snp-pipeline</requirement>
-        <requirement type="package" version="3.7.3">python</requirement>
+        <requirement type="package" version="2.0.2">snp-pipeline</requirement>
+        <requirement type="package" version="3.6.8">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
--- a/5_call_consensus.xml	Wed May 08 11:43:17 2019 -0400
+++ b/5_call_consensus.xml	Thu May 09 11:45:22 2019 -0400
@@ -2,17 +2,17 @@
     <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="2.0.2">snp-pipeline</requirement>
         <requirement type="package" version="1.9.134">boto3</requirement>
-        <requirement type="package" version="3.7.3">python</requirement>
+        <requirement type="package" version="3.6.8">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
         #set $identifier = $call_pileup.name.split(' ')[0]
-        python3 $__tool_directory__/snp-cache.py snp_consenus_calls
+        python $__tool_directory__/snp-cache.py snp_consenus_calls
             "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)"
             -c "
-                mkdir ./$identifier/
+                mkdir -p ./$identifier/
                 && cp $call_pileup ./$identifier/reads.all.pileup
                 && cfsan_snp_pipeline call_consensus -v 4 -l $snps --vcfFileName "consensus.vcf" ./$identifier/reads.all.pileup 1>&2 && tar zcv ./consensus.vcf ./consensus.fasta
             "
@@ -37,7 +37,7 @@
             <param name="snps" value="snplist.txt" />
             <param name="calls" value="samples/sample1/var.flt.vcf" />
             <param name="call_pileup" value="samples/sample1/reads.all.pileup" />
-            <output name="calls_consensus_vcf" value="samples/sample1/consensus.vcf" lines_diff="6" />
+            <output name="calls_consensus_vcf" value="samples/sample1/consensus.vcf" lines_diff="20" />
             <output name="calls_consensus_fa" value="samples/sample1/consensus.fasta" lines_diff="2" />
         </test>
     </tests>
--- 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 @@
 <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>
-        <requirement type="package" version="1.6">bcftools</requirement>
+        <requirement type="package" version="1.9">bcftools</requirement>
         <requirement type="package" version="1.0.6">bzip2</requirement>
-        <requirement type="package" version="1.0.1">snp-pipeline</requirement>
+        <requirement type="package" version="2.0.2">snp-pipeline</requirement>
         <requirement type="package" version="0.2.5">tabix</requirement>
-        <requirement type="package" version="1.6">htslib</requirement>
-        <requirement type="package" version="3.7.3">python</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[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
@@ -36,7 +36,7 @@
                     <element name="sample4" value="samples/sample4/consensus.vcf" />
                 </collection>
             </param>
-            <output name="snpmav" value="snpma.vcf" lines_diff="2" />
+            <output name="snpmav" value="snpma.vcf" lines_diff="4" />
         </test>
     </tests>
     <help><![CDATA[
--- a/7_smp_matrix.xml	Wed May 08 11:43:17 2019 -0400
+++ b/7_smp_matrix.xml	Thu May 09 11:45:22 2019 -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>
-        <requirement type="package" version="1.6">bcftools</requirement>
+        <requirement type="package" version="1.9">bcftools</requirement>
         <requirement type="package" version="1.0.6">bzip2</requirement>
-        <requirement type="package" version="1.0.1">snp-pipeline</requirement>
+        <requirement type="package" version="2.0.2">snp-pipeline</requirement>
         <requirement type="package" version="0.2.5">tabix</requirement>
-        <requirement type="package" version="3.7.3">python</requirement>
+        <requirement type="package" version="3.6.8">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&