Mercurial > repos > elixir-it > mutect2

comparison mutect2.xml @ 7:2ebf2cd4f18f draft

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Uploaded
author elixir-it
date Tue, 03 Jul 2018 04:46:13 -0400
parents 0cc081cd3992
children 467fcccde14d
comparison
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6:5345d2d688d9 7:2ebf2cd4f18f
17 ## TODO creation of symlinks because mutect2 want the extensions of the file 17 ## TODO creation of symlinks because mutect2 want the extensions of the file
18 ln -s $input1 tumor.bam && 18 ln -s $input1 tumor.bam &&
19 ln -s $input2 normal.bam && 19 ln -s $input2 normal.bam &&
20 ln -s $input1".bai" tumor.bam.bai && 20 ln -s $input1".bai" tumor.bam.bai &&
21 ln -s $input2".bai" normal.bam.bai && 21 ln -s $input2".bai" normal.bam.bai &&
22 #if $reference_source == "history" 22 #if $reference_source.reference_source_selector == "history"
23 ln -s $reference genome.fa && 23 ln -s $reference_source.ref_file_h genome.fa &&
24 ln -s $reference".fai" genome.fa.fai 24 ln -s $reference_source.ref_file_h".fai" genome.fa.fai &&
25 #end if 25 #end if
26 #if $list 26 #if $list
27 ln -s $list position.bed && 27 ln -s $list position.bed &&
28 #end if 28 #end if
29 #if $dbSNP 29 #if $dbSNP
35 #if $alleles 35 #if $alleles
36 ln -s $alleles alleles.vcf 36 ln -s $alleles alleles.vcf
37 #end if 37 #end if
38 38
39 ##TODO creation of .dict file of the genome required by mutect2 to run 39 ##TODO creation of .dict file of the genome required by mutect2 to run
40 #if $reference_source == "history" 40 #if $reference_source.reference_source_selector == "history"
41 java -jar \$CONDA_DEFAULT_ENV/share/picard-2.7.1-2/picard.jar CreateSequenceDictionary R= genome.fa O= genome.dict 2>$log 41 java -jar \$CONDA_DEFAULT_ENV/share/picard-2.7.1-2/picard.jar CreateSequenceDictionary R= genome.fa O= genome.dict 2>$log &&
42 #end if 42 #end if
43 43
44 ##TODO gatk-register take the GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 unzip it 44 ##TODO gatk-register take the GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 unzip it
45 ##and move the .jar file to \$CONDA_DEFAULT_ENV/opt/gatk-3.8/ then the mutect2 command is runned 45 ##and move the .jar file to \$CONDA_DEFAULT_ENV/opt/gatk-3.8/ then the mutect2 command is runned
46 gatk3-register \$_CONDA_DIR/../GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 2>$log ; 46 gatk3-register \$_CONDA_DIR/../GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 2>$log ;
47 java -jar \$CONDA_DEFAULT_ENV/opt/gatk-3.8/GenomeAnalysisTK.jar -nct \${GALAXY_SLOTS:-4} -T MuTect2 -I:tumor tumor.bam -I:normal normal.bam -o $output 47 java -jar \$CONDA_DEFAULT_ENV/opt/gatk-3.8/GenomeAnalysisTK.jar -nct \${GALAXY_SLOTS:-4} -T MuTect2 -I:tumor tumor.bam -I:normal normal.bam -o $output
48 #if $reference_source == "history" 48 #if $reference_source.reference_source_selector == "history"
49 -R genome.fa 49 -R genome.fa
50 #else 50 #end if
51 #if $reference_source.reference_source_selector == "cached"
51 -R $reference_source.ref_file.fields.path 52 -R $reference_source.ref_file.fields.path
52 #end if 53 #end if
53 ## TODO advanced inputs section if the optional inputs are present their options are added to the command 54 ## TODO advanced inputs section if the optional inputs are present their options are added to the command
54 #if $dbSNP 55 #if $dbSNP
55 --dbsnp dbSNP.vcf 56 --dbsnp dbSNP.vcf