| Previous changeset 2:bd79c4d39af0 (2016-06-15) Next changeset 4:b737f6d83f48 (2017-01-13) |
|
Commit message:
Uploaded |
|
modified:
BAMtoscIDX.jar bam_to_scidx.xml |
| b |
| diff -r bd79c4d39af0 -r 11fc60f0e942 BAMtoscIDX.jar |
| b |
| Binary file BAMtoscIDX.jar has changed |
| b |
| diff -r bd79c4d39af0 -r 11fc60f0e942 bam_to_scidx.xml --- a/bam_to_scidx.xml Wed Jun 15 10:50:24 2016 -0400 +++ b/bam_to_scidx.xml Wed Jun 22 09:46:19 2016 -0400 |
| [ |
| @@ -13,8 +13,9 @@ </stdio> <command> <![CDATA[ - ln -f -s "${input_bam.metadata.bam_index}" "${input_bam}.bai" && - java -jar $__tool_directory__/BAMtoscIDX.jar -b "$input_bam" -i "${input_bam}.bai" -p $require_proper_mate_pairing -r $read -m $min_insert_size -M $max_insert_size -o "$output" 1>/dev/null + ln -s "${input_bam}" "localbam.bam" && + ln -f -s "${input_bam.metadata.bam_index}" "localbam.bam.bai" && + java -jar $__tool_directory__/BAMtoscIDX.jar -b localbam.bam -i localbam.bam.bai -p $require_proper_mate_pairing -r $read -m $min_insert_size -M $max_insert_size -o "$output" 1>/dev/null ]]> </command> <inputs> |