Scripts provided by Arvados

Note:

Arvados pipeline templates are deprecated. The recommended way to develop new workflows for Arvados is using the Common Workflow Language.

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.

bwa-aln

Run the bwa aligner on a set of paired-end fastq files, producing a BAM file for each pair. View source.

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`

bwa-index

Generate an index of a fasta reference genome suitable for use by bwa-aln. View source.

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`

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. View source.

Parameter	Description	Example
input	Collection containing aligned bam files.
picard_zip	Collection with the picard binary distribution.	`687f74675c6a0e925dec619cc2bec25f+77`
reference	Collection with reference data (.fasta.gz, .fasta.fai.gz, *.dict.gz).	`c361dbf46ee3397b0958802b346e9b5a+925`

GATK2-realign

Run GATK’s RealignerTargetCreator and IndelRealigner modules on a set of BAM files. View source.

Parameter	Description	Example
input	Collection containing aligned bam files.
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.
region_padding	Corresponds to GATK `--interval_padding` argument. Required if a regions parameter is given.	10

GATK2-bqsr

Run GATK’s BaseQualityScoreRecalibration module on a set of BAM files. View source.

Parameter	Description	Example
input	Collection containing bam files.
gatk_tbz	Collection with the GATK2 binary distribution.	`7e0a277d6d2353678a11f56bab3b13f2+87`
gatk_bundle	Collection with the GATK data bundle.	`d237a90bae3870b3b033aea1e99de4a9+10820`

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. View source.

Parameter	Description	Example
input	Collection containing bam files.
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

file-select

Pass through the named files from input to output collection, and ignore the rest. View source.

Parameter	Description	Example
names	List of filenames to include in the output.	`["human_g1k_v37.fasta.gz","human_g1k_v37.fasta.fai.gz"]`

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