diff --git a/tools/picard/picard_AddOrReplaceReadGroups.xml b/tools/picard/picard_AddOrReplaceReadGroups.xml index d70b2294846..cc670abb9f0 100644 --- a/tools/picard/picard_AddOrReplaceReadGroups.xml +++ b/tools/picard/picard_AddOrReplaceReadGroups.xml @@ -1,4 +1,4 @@ - + picard picard_wrapper.py diff --git a/tools/picard/picard_BamIndexStats.xml b/tools/picard/picard_BamIndexStats.xml index 53258ae83cf..8855a91d6a9 100644 --- a/tools/picard/picard_BamIndexStats.xml +++ b/tools/picard/picard_BamIndexStats.xml @@ -1,4 +1,4 @@ - + picard picard_wrapper.py diff --git a/tools/picard/picard_FastqToSam.xml b/tools/picard/picard_FastqToSam.xml index f1674688fb7..2f736b3be96 100644 --- a/tools/picard/picard_FastqToSam.xml +++ b/tools/picard/picard_FastqToSam.xml @@ -1,4 +1,4 @@ - + creates an unaligned BAM file picard java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC diff --git a/tools/picard/picard_MarkDuplicates.xml b/tools/picard/picard_MarkDuplicates.xml index 61835e209e9..5c8cb86ad30 100644 --- a/tools/picard/picard_MarkDuplicates.xml +++ b/tools/picard/picard_MarkDuplicates.xml @@ -1,4 +1,4 @@ - + picard_wrapper.py --input="$input_file" diff --git a/tools/picard/picard_ReorderSam.xml b/tools/picard/picard_ReorderSam.xml index 7fb41a573b3..09d15d1d63c 100644 --- a/tools/picard/picard_ReorderSam.xml +++ b/tools/picard/picard_ReorderSam.xml @@ -1,4 +1,4 @@ - + picard picard_wrapper.py diff --git a/tools/picard/picard_ReplaceSamHeader.xml b/tools/picard/picard_ReplaceSamHeader.xml index 95a584068da..6cd30eb9596 100644 --- a/tools/picard/picard_ReplaceSamHeader.xml +++ b/tools/picard/picard_ReplaceSamHeader.xml @@ -1,4 +1,4 @@ - + picard picard_wrapper.py diff --git a/tools/picard/picard_SamToFastq.xml b/tools/picard/picard_SamToFastq.xml index 2274ad1caed..278f42934c6 100644 --- a/tools/picard/picard_SamToFastq.xml +++ b/tools/picard/picard_SamToFastq.xml @@ -1,4 +1,4 @@ - + creates a FASTQ file picard java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC diff --git a/tools/picard/rgPicardASMetrics.xml b/tools/picard/rgPicardASMetrics.xml index 15381bbfcac..dcd1f998588 100644 --- a/tools/picard/rgPicardASMetrics.xml +++ b/tools/picard/rgPicardASMetrics.xml @@ -1,4 +1,4 @@ - + picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" --datatype "$input_file.ext" diff --git a/tools/picard/rgPicardFixMate.xml b/tools/picard/rgPicardFixMate.xml index 5d7ecb6142e..83859e551df 100644 --- a/tools/picard/rgPicardFixMate.xml +++ b/tools/picard/rgPicardFixMate.xml @@ -1,4 +1,4 @@ - + for paired data picard_wrapper.py -i "$input_file" -o "$out_file" --tmpdir "${__new_file_path__}" -n "$out_prefix" diff --git a/tools/picard/rgPicardGCBiasMetrics.xml b/tools/picard/rgPicardGCBiasMetrics.xml index f5eab53d0de..7adce089f04 100644 --- a/tools/picard/rgPicardGCBiasMetrics.xml +++ b/tools/picard/rgPicardGCBiasMetrics.xml @@ -1,4 +1,4 @@ - + picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --windowsize "$windowsize" --mingenomefrac "$mingenomefrac" -n "$out_prefix" --tmpdir "${__new_file_path__}" diff --git a/tools/picard/rgPicardHsMetrics.xml b/tools/picard/rgPicardHsMetrics.xml index d2d3017befe..56c7ef9123d 100644 --- a/tools/picard/rgPicardHsMetrics.xml +++ b/tools/picard/rgPicardHsMetrics.xml @@ -1,4 +1,4 @@ - + for targeted resequencing data diff --git a/tools/picard/rgPicardInsertSize.xml b/tools/picard/rgPicardInsertSize.xml index 2cbda571a7d..5d188095582 100644 --- a/tools/picard/rgPicardInsertSize.xml +++ b/tools/picard/rgPicardInsertSize.xml @@ -1,4 +1,4 @@ - + for PAIRED data picard diff --git a/tools/picard/rgPicardLibComplexity.xml b/tools/picard/rgPicardLibComplexity.xml index ab252100ec2..3e0fc72775a 100644 --- a/tools/picard/rgPicardLibComplexity.xml +++ b/tools/picard/rgPicardLibComplexity.xml @@ -1,4 +1,4 @@ - + picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --minid "$minIDbases" --maxdiff "$maxDiff" --minmeanq "$minMeanQ" --readregex "$readRegex" --optdupdist "$optDupeDist" diff --git a/tools/picard/rgPicardMarkDups.xml b/tools/picard/rgPicardMarkDups.xml index 5a6947b85a8..07894d90683 100644 --- a/tools/picard/rgPicardMarkDups.xml +++ b/tools/picard/rgPicardMarkDups.xml @@ -1,4 +1,4 @@ - + picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" -o "$out_file" --remdups "$remDups" --assumesorted "$assumeSorted" --readregex "$readRegex" --optdupdist "$optDupeDist"