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closes #11823
[arvados.git] / 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 65fd316c107d8f39cc5cf6191aedad7706c1f093..d1c7f12c8848663ba6d900fe600a924d022e6e53 100644 (file)
--- a/doc/user/examples/crunch-examples.html.textile.liquid
+++ b/doc/user/examples/crunch-examples.html.textile.liquid
@@ -1,29 +1,28 @@
 ---
 layout: default
 navsection: userguide
-navmenu: Examples
-title: "Crunch examples"
-
+title: "Scripts provided by Arvados"
 ...
 
-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
 
 <div class="offset1">
 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@|
 </div>
 
 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
 
 <div class="offset1">
 table(table table-bordered table-condensed).
@@ -34,26 +33,26 @@ 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
 
 <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.||
+|picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@|
 |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
+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
 
 <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.||
+|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 +61,26 @@ 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
 
 <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_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@|
 |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. "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
 
 <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.||
+|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 +88,7 @@ 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
 
 <div class="offset1">
 table(table table-bordered table-condensed).