h1. Crunch examples
-Several crunch scripts are included with Arvados in the @/crunch_scripts@ directory. They are intended to provide examples and starting points for writing your own scripts.
+Several crunch scripts are included with Arvados in the "/crunch_scripts directory":https://arvados.org/projects/arvados/repository/revisions/master/show/crunch_scripts. They are intended to provide examples and starting points for writing your own scripts.
h4. bwa-aln
-Run the bwa aligner on a set of paired-end fastq files, producing a BAM file for each pair.
+Run the bwa aligner on a set of paired-end fastq files, producing a BAM file for each pair. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/bwa-aln
+
+<div class="offset1">
+table(table table-bordered table-condensed).
+|_Parameter_|_Description_|_Example_|
+|bwa_tbz|Collection with the bwa source distribution.|@8b6e2c4916133e1d859c9e812861ce13+70@|
+|input|Collection with fastq reads (pairs of *_1.fastq.gz and *_2.fastq.gz).|@d0136bc494c21f79fc1b6a390561e6cb+2778@|
+</div>
h4. bwa-index
-Generate an index of a fasta reference genome suitable for use by bwa-aln.
+Generate an index of a fasta reference genome suitable for use by bwa-aln. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/bwa-index
+
+<div class="offset1">
+table(table table-bordered table-condensed).
+|_Parameter_|_Description_|_Example_|
+|bwa_tbz|Collection with the bwa source distribution.|@8b6e2c4916133e1d859c9e812861ce13+70@|
+|input|Collection with reference data (*.fasta.gz, *.fasta.fai.gz, *.dict.gz).|@c361dbf46ee3397b0958802b346e9b5a+925@|
+</div>
h4. picard-gatk2-prep
-Using the FixMateInformation, SortSam, ReorderSam, AddOrReplaceReadGroups, and BuildBamIndex modules from picard, prepare a BAM file for use with the GATK2 tools. Additionally, run picard's CollectAlignmentSummaryMetrics module to produce a @*.casm.tsv@ statistics file for each BAM file.
+Using the FixMateInformation, SortSam, ReorderSam, AddOrReplaceReadGroups, and BuildBamIndex modules from picard, prepare a BAM file for use with the GATK2 tools. Additionally, run picard's CollectAlignmentSummaryMetrics module to produce a @*.casm.tsv@ statistics file for each BAM file. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/picard-gatk2-prep
+
+<div class="offset1">
+table(table table-bordered table-condensed).
+|_Parameter_|_Description_|_Example_|
+|input|Collection containing aligned bam files.||
+|picard_zip|Collection with the picard binary distribution.||
+|reference|Collection with reference data (*.fasta.gz, *.fasta.fai.gz, *.dict.gz).|@c361dbf46ee3397b0958802b346e9b5a+925@|
+</div>
+
+h4. GATK2-realign
+
+Run GATK's RealignerTargetCreator and IndelRealigner modules on a set of BAM files. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-realign
+
+<div class="offset1">
+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.||
+|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.||
+|region_padding|Corresponds to GATK @--interval_padding@ argument. Required if a regions parameter is given.|10|
+</div>
h4. GATK2-bqsr
-Run GATK's BaseQualityScoreRecalibration module on a set of BAM files.
+Run GATK's BaseQualityScoreRecalibration module on a set of BAM files. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-bqsr
+
+<div class="offset1">
+table(table table-bordered table-condensed).
+|_Parameter_|_Description_|_Example_|
+|input|Collection containing bam files.||
+|gatk_tbz|Collection with the GATK2 binary distribution.||
+|gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
+</div>
h4. GATK2-merge-call
-Merge a set of BAM files using picard, and run GATK's UnifiedGenotyper module on the merged set to produce a VCF file.
+Merge a set of BAM files using picard, and run GATK's UnifiedGenotyper module on the merged set to produce a VCF file. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-merge-call
-h4. GATK2-realign
+<div class="offset1">
+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.||
+|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|
+</div>
+
+h4. file-select
-Run GATK's RealignerTargetCreator and IndelRealigner modules on a set of BAM files.
+Pass through the named files from input to output collection, and ignore the rest. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/file-select
+<div class="offset1">
+table(table table-bordered table-condensed).
+|_Parameter_|_Description_|_Example_|
+|names|List of filenames to include in the output.|@["human_g1k_v37.fasta.gz","human_g1k_v37.fasta.fai.gz"]@|
+</div>
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