1.5.0

• updated components: seq-data-to-lane-bam, bwa-mem-aligner and payload-gen-dna-seq-qc
• able to handle multiple input BAMs
• able to handle different input BAMs containing read group with same ID
• added tests for the above scenarios

Note:

1. compatible argo-metadata-schema versions: 0.4.0
2. requires Nextflow 20.07.1 or higher

1.4.0

• update to SONG/SCORE utils 2.3.0
• enable DSL2: nextflow.preview.dsl = 2 to nextflow.enable.dsl = 2

Note:

1. compatible argo-metadata-schema versions: 0.4.0
2. requires Nextflow 20.07.1 or higher

1.3.0

• updated payload generation modules to include a new field session_id in SONG metadata
• introduced dependencies among some potential parallel tasks so that they run sequentially, this is to reduce disk IO bottleneck during concurrent reads from very large files (#47)

Note: compatible argo-metadata-schema versions: 0.4.0

1.2.0

• updated payload gen tools to sync with harmonized SONG schemas which support well defined data categories and data types
• updated utils module to 1.1.5
• added default params, especially for second level objects, this can also serves as documentation
• added support for local mode which is greatly useful for testing
• added test that can be run on Travis without SONG/SCORE dependecies

Note: compatible argo-metadata-schema versions: 0.3.0

1.1.1

• update to song-score-util 1.1.1 with song-client 4.2.1
• improved song-submit error handling
• support experimental_strategy in bwa-mem-aligner

Note: compatible argo-metadata-schema versions: 0.2.0

1.1.0

• update payload-gen-dna-alignment and payload-gen-dna-seq-qc with SONG payload schema change
• update score-client docker image to 5.0.0

Note: compatible argo-metadata-schema versions: 0.2.0

1.0.6

• update with song-client docker image 4.2.0 that supports non-root user

Note: compatible argo-metadata-schema versions: 0.1.1, 0.1.0

1.0.5

• update payload-gen-dna-seq-qc which sanitizes lane bam qc metrics file name with : converts to _, but also avoids possible file name collision as a result of the conversion

Note: compatible argo-metadata-schema versions: 0.1.1, 0.1.0

1.0.4

• updated output file naming conventions
• add support for optional tempdir param for aligner and mkdup tools, this enables the possibility to use local scratch storage for large temporatory files

1.0.3

• pickup updated song/score modules that hide api tokens