Mercurial > repos > matthias > stacks2_ustacks

comparison test-data/gentest.sh @ 6:742c94cfb8cf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
author matthias
date Thu, 20 Jun 2019 08:10:32 -0400
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5:ccbb048a4178 6:742c94cfb8cf
1 #!/usr/bin/env bash
2
3 mkdir stacks_outputs
4
5 denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired &&
6 gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf
7 rm stacks_outputs/catalog.calls
8
9 mv stacks_outputs/PopA_0{1,2}.{tags,snps,alleles}.tsv ustacks/
10 mv stacks_outputs/catalog.{tags,snps,alleles}.tsv cstacks/
11 mv stacks_outputs/PopA_0{1,2}.matches.tsv sstacks/
12 mv stacks_outputs/PopA_0{1,2}.matches.bam tsv2bam/
13 mv stacks_outputs/tsv2bam.log tsv2bam/
14 mv stacks_outputs/catalog.{calls.vcf,fa.gz} gstacks/
15 mv stacks_outputs/gstacks.log* gstacks/
16 mv stacks_outputs/populations.* populations/
17 mv stacks_outputs/denovo_map.log denovo_map/
18
19 rmdir stacks_outputs