Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 77:f89704ed1d8f draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Tue, 10 Jun 2014 10:42:22 -0400 |
| parents | 344f5b5ddfd3 |
| children | bd5fd2f82f3c |
| files | varscan_mpileup2snp_from_bam.xml |
| diffstat | 1 files changed, 10 insertions(+), 1 deletions(-) [+] |
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--- a/varscan_mpileup2snp_from_bam.xml Tue Jun 10 10:08:46 2014 -0400 +++ b/varscan_mpileup2snp_from_bam.xml Tue Jun 10 10:42:22 2014 -0400 @@ -5,7 +5,6 @@ <requirement type="package" version="5.9">ncurses</requirement> <requirement type="package" version="0.1.19a">samtools_parallel_mpileup_0_1_19a</requirement> <requirement type="package" version="2.3.6">varscan</requirement> - <!-- <requirement type="package" version="0.1.19">package_samtools_0_1_19</requirement> --> <requirement type="package" version="5.9">ncurses</requirement> <requirement type="package" version="0.1.19">samtools</requirement> </requirements> @@ -13,6 +12,16 @@ #if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1 echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&2 #else + #import os.path + #for $alignment in $alignments + #if not os.path.isfile(str($alignment)+".bai") + echo "- Indexing alignment file: $alignment.name " ; + samtools index $alignment 2>&1 ; + #else + echo "- Skiping indexing: $alignment.name " ; + #end if + #end for + #if $mpileup_parallelization.mpileup_parallelization_select == "true" samtools-parallel-mpileup mpileup -t $mpileup_parallelization.samtools_threads