From d86f4c7485e7338e3725687634014c7711b83bfd Mon Sep 17 00:00:00 2001 From: Tom Clegg Date: Tue, 11 Feb 2014 21:11:45 -0800 Subject: [PATCH] Fill in missing example locators for crunch wrappers. --- .../examples/crunch-examples.html.textile.liquid | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/doc/user/examples/crunch-examples.html.textile.liquid b/doc/user/examples/crunch-examples.html.textile.liquid index 65fd316c10..b657a68c9f 100644 --- a/doc/user/examples/crunch-examples.html.textile.liquid +++ b/doc/user/examples/crunch-examples.html.textile.liquid @@ -18,6 +18,7 @@ Run the bwa aligner on a set of paired-end fastq files, producing a BAM file for table(table table-bordered table-condensed). |_Parameter_|_Description_|_Example_| |bwa_tbz|Collection with the bwa source distribution.|@8b6e2c4916133e1d859c9e812861ce13+70@| +|samtools_tgz|Collection with the samtools source distribution.|@c777e23cf13e5d5906abfdc08d84bfdb+74@| |input|Collection with fastq reads (pairs of *_1.fastq.gz and *_2.fastq.gz).|@d0136bc494c21f79fc1b6a390561e6cb+2778@| @@ -40,7 +41,7 @@ Using the FixMateInformation, SortSam, ReorderSam, AddOrReplaceReadGroups, and B table(table table-bordered table-condensed). |_Parameter_|_Description_|_Example_| |input|Collection containing aligned bam files.|| -|picard_zip|Collection with the picard binary distribution.|| +|picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@| |reference|Collection with reference data (*.fasta.gz, *.fasta.fai.gz, *.dict.gz).|@c361dbf46ee3397b0958802b346e9b5a+925@| @@ -52,8 +53,8 @@ Run GATK's RealignerTargetCreator and IndelRealigner modules on a set of BAM fil table(table table-bordered table-condensed). |_Parameter_|_Description_|_Example_| |input|Collection containing aligned bam files.|| -|picard_zip|Collection with the picard binary distribution.|| -|gatk_tbz|Collection with the GATK2 binary distribution.|| +|picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@| +|gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@| |gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@| |known_sites|List of files in the data bundle to use as GATK @-known@ arguments. Optional. |@["dbsnp_137.b37.vcf","Mills_and_1000G_gold_standard.indels.b37.vcf"]@ (this is the default value)| |regions|Collection with .bed files indicating sequencing target regions. Optional.|| @@ -68,7 +69,7 @@ Run GATK's BaseQualityScoreRecalibration module on a set of BAM files. "View sou table(table table-bordered table-condensed). |_Parameter_|_Description_|_Example_| |input|Collection containing bam files.|| -|gatk_tbz|Collection with the GATK2 binary distribution.|| +|gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@| |gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@| @@ -80,8 +81,8 @@ Merge a set of BAM files using picard, and run GATK's UnifiedGenotyper module on table(table table-bordered table-condensed). |_Parameter_|_Description_|_Example_| |input|Collection containing bam files.|| -|picard_zip|Collection with the picard binary distribution.|| -|gatk_tbz|Collection with the GATK2 binary distribution.|| +|picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@| +|gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@| |gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@| |regions|Collection with .bed files indicating sequencing target regions. Optional.|| |region_padding|Corresponds to GATK @--interval_padding@ argument. Required if a regions parameter is given.|10| -- 2.30.2