| Previous changeset 49:ebfa7fd256aa (2019-05-08) Next changeset 51:568eb62c7524 (2019-09-17) |
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Commit message:
planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty |
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modified:
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 |
| 1_map_reads.xml |
| diff -r ebfa7fd256aa -r e90a783a4e8b 1_map_reads.xml |
| 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 @@ <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" && |
| 2_call_sites.xml |
| diff -r ebfa7fd256aa -r e90a783a4e8b 2_call_sites.xml |
| 2_call_sites.xml |
| --- 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" && |
| 3_filter_regions.xml |
| diff -r ebfa7fd256aa -r e90a783a4e8b 3_filter_regions.xml |
| 3_filter_regions.xml |
| --- 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" && |
| 4_merge_sites.xml |
| diff -r ebfa7fd256aa -r e90a783a4e8b 4_merge_sites.xml |
| 4_merge_sites.xml |
| --- 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" && |
| 5_call_consensus.xml |
| diff -r ebfa7fd256aa -r e90a783a4e8b 5_call_consensus.xml |
| 5_call_consensus.xml |
| --- 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> |
| 6_merge_vcfs.xml |
| diff -r ebfa7fd256aa -r e90a783a4e8b 6_merge_vcfs.xml |
| 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 @@ <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[ |
| 7_smp_matrix.xml |
| diff -r ebfa7fd256aa -r e90a783a4e8b 7_smp_matrix.xml |
| 7_smp_matrix.xml |
| --- 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" && |