From 904a85a7c9758c362fa2ac8562664b6f730bc75e Mon Sep 17 00:00:00 2001
From: Peter Ebert <pebert@mpi-inf.mpg.de>
Date: Fri, 30 Dec 2016 15:14:42 +0100
Subject: [PATCH] MAINT: changed identifier naming

---
 docs/alignment/bisulfite/BALv1.xml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/docs/alignment/bisulfite/BALv1.xml b/docs/alignment/bisulfite/BALv1.xml
index dee515a..0abc256 100644
--- a/docs/alignment/bisulfite/BALv1.xml
+++ b/docs/alignment/bisulfite/BALv1.xml
@@ -46,13 +46,13 @@
 	<!-- Following section: list output files of process [e.g. bed files, wiggle tracks] -->
 	<outputs>
 		<filetype>
-			<identifier>DEEPID.PROC.DATE.aln</identifier>
+			<identifier>DEEPID.PROC.DATE.bam</identifier>
 			<format>BAM</format>
 			<quantity>single</quantity>
 			<comment>Final Bam file with reconverted Cs</comment>
 		</filetype>
 		<filetype>
-			<identifier>DEEPID.PROC.DATE.idx</identifier>
+			<identifier>DEEPID.PROC.DATE.bai</identifier>
 			<format>BAI</format>
 			<quantity>single</quantity>
 			<comment>Corresponding BAM index file</comment>
@@ -191,7 +191,7 @@
 			<version>1.61</version>
 			<command_line>
                 <![CDATA[
-                    java -Xmx50G picard-1.61.jar MarkDuplicates I=sorted_lane_bamfile OUTPUT={DEEPID.PROC.DATE.aln}
+                    java -Xmx50G picard-1.61.jar MarkDuplicates I=sorted_lane_bamfile OUTPUT={DEEPID.PROC.DATE.bam}
 			        TMP_DIR={TMP_DIR} VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=FALSE ASSUME_SORTED=TRUE CREATE_INDEX=TRUE
 			        MAX_RECORDS_IN_RAM=12500000 METRICS_FILE={DEEPID.PROC.DATE.PicardMarkDupmetrics}
 			    ]]>
@@ -202,7 +202,7 @@
 		<tool>
 			<name>samtools</name>
 			<version>0.1.19</version>
-			<command_line><![CDATA[ samtools flagstat {DEEPID.PROC.DATE.aln} > {DEEPID.PROC.DATE.flagstats} ]]></command_line>
+			<command_line><![CDATA[ samtools flagstat {DEEPID.PROC.DATE.bam} > {DEEPID.PROC.DATE.flagstats} ]]></command_line>
             <loop>no looping</loop>
 			<comment></comment>
 		</tool>
@@ -211,7 +211,7 @@
 			<version>1.61</version>
 			<command_line>
                 <![CDATA[
-                    java -Xmx4G picard-1.61.jar CollectMultipleMetrics INPUT={DEEPID.PROC.DATE.aln}
+                    java -Xmx4G picard-1.61.jar CollectMultipleMetrics INPUT={DEEPID.PROC.DATE.bam}
                     REFERENCE_SEQUENCE={reference_genome} ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT
                     OUTPUT={DEEPID.PROC.DATE.PicardInsertSizemetrics} PROGRAM=CollectAlignmentSummaryMetrics
                     PROGRAM=CollectInsertSizeMetrics PROGRAM=QualityScoreDistribution PROGRAM=MeanQualityByCycle
@@ -226,7 +226,7 @@
 			<command_line>
                 <![CDATA[
                     python bcall.py -r {CHROM} --trimPE --snv --zero -e 5 {reference_genome.pos}
-                    -m {DEEPID.PROC.DATE.CHROM_CG_CH.mcall.metrics} {DEEPID.PROC.DATE.aln}
+                    -m {DEEPID.PROC.DATE.CHROM_CG_CH.mcall.metrics} {DEEPID.PROC.DATE.bam}
                     {DEEPID.PROC.DATE.CHROM_CG_CH.mcall}
                 ]]>
             </command_line>