X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/b54d7820e899733ce10b8960b1f04d0481f2e11f..731ff645f6de779a324999f3b78bf90469dbb4fb:/doc/user/examples/crunch-examples.html.textile.liquid
diff --git a/doc/user/examples/crunch-examples.html.textile.liquid b/doc/user/examples/crunch-examples.html.textile.liquid
index 65fd316c10..c93766a0a7 100644
--- a/doc/user/examples/crunch-examples.html.textile.liquid
+++ b/doc/user/examples/crunch-examples.html.textile.liquid
@@ -1,29 +1,33 @@
---
layout: default
navsection: userguide
-navmenu: Examples
-title: "Crunch examples"
-
+title: "Scripts provided by Arvados"
...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
-h1. Crunch examples
+{% include 'pipeline_deprecation_notice' %}
-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.
+Several crunch scripts are included with Arvados in the "/crunch_scripts directory":https://dev.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. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/bwa-aln
+Run the bwa aligner on a set of paired-end fastq files, producing a BAM file for each pair. "View source.":https://dev.arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/bwa-aln
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@|
h4. bwa-index
-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
+Generate an index of a fasta reference genome suitable for use by bwa-aln. "View source.":https://dev.arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/bwa-index
table(table table-bordered table-condensed).
@@ -34,26 +38,26 @@ table(table table-bordered table-condensed).
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. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/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.":https://dev.arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/picard-gatk2-prep
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@|
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
+Run GATK's RealignerTargetCreator and IndelRealigner modules on a set of BAM files. "View source.":https://dev.arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-realign
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.||
@@ -62,26 +66,26 @@ table(table table-bordered table-condensed).
h4. GATK2-bqsr
-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
+Run GATK's BaseQualityScoreRecalibration module on a set of BAM files. "View source.":https://dev.arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-bqsr
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@|
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. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/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.":https://dev.arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-merge-call
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|
@@ -89,7 +93,7 @@ table(table table-bordered table-condensed).
h4. file-select
-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
+Pass through the named files from input to output collection, and ignore the rest. "View source.":https://dev.arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/file-select
table(table table-bordered table-condensed).