bwa-mem-aligner.0.1.7.1

• get read group ID from input lane bam header instead of relying on file name which is not reliable due to converion of special chars

bam-merge-sort-markdup.0.1.8.0

• added tool info to extra_info JSON

seq-data-to-lane-bam.0.2.2.0

• update samtools/biobambam

bwa-mem-aligner.0.1.6.0

Merge pull request #86 from icgc-argo/seq-data-to-lane-bam.0.2.2.0

Seq data to lane bam.0.2.2.0

bam-merge-sort-markdup.0.1.7.0

• updated samtools/biobambam
• updated some params in streaming between different tools, such as disable bam compression

bwa-mem-aligner.0.1.5.1

• add input_bam size as a tag

seq-data-to-lane-bam.0.2.1.0

Merge pull request #80 from icgc-argo/bam-merge-sort-markdup.0.1.6.0

Bam merge sort markdup.0.1.6.0

bam-merge-sort-markdup.0.1.6.0

Merge pull request #80 from icgc-argo/bam-merge-sort-markdup.0.1.6.0

Bam merge sort markdup.0.1.6.0

bwa-mem-aligner.0.1.5.0

• cleaned up params
• added mem and cpus params
• populate aligned BAM @RG header using info from SONG metadata when provided

seq-data-to-lane-bam.0.2.0.0

add "samtools split" as default to preprocess the BAM.