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closes #11071
[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 b657a68c9f042926e94f6f5e63889d51aadf3906..d1c7f12c8848663ba6d900fe600a924d022e6e53 100644 (file)
--- a/doc/user/examples/crunch-examples.html.textile.liquid
+++ b/doc/user/examples/crunch-examples.html.textile.liquid
@@ -1,18 +1,16 @@
 ---
 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).
@@ -24,7 +22,7 @@ table(table table-bordered table-condensed).
 
 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).
@@ -35,7 +33,7 @@ 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).
@@ -47,7 +45,7 @@ table(table table-bordered table-condensed).
 
 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).
@@ -63,7 +61,7 @@ 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).
@@ -75,7 +73,7 @@ table(table table-bordered table-condensed).
 
 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).
@@ -90,7 +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).