VCF Uploader v. 1.1.0

This include QC and timing metrics support from Keiran.

VCF Uploader v. 1.0.0

The VCF uploader works and is able to submit files back to GNOS. However, keep in mind two new features that will be added in a 1.1.0 release next week. 1) better support for QC/timing and 2) validation of VCF files.

2.6.2

Debugging information for GTDownload

Point release to address lack of max-memory parameter for unmapped reads.

This point release adds a new parameter to the workflow ini file that allows setting of maximum memory allocation for the unmapped reads extraction step.

Release candidate 1 for BWA Workflow 2.6.0

2.6.0-rc1

Working on cleaning up for the gtdownload/upload wrapper

2.4.0 BWA Workflow Release

This is the SeqWare BWA-Mem PanCancer Workflow version 2.4.0 available in its packaged form from https://s3.amazonaws.com/oicr.workflow.bundles/released-bundles/Workflow_Bundle_BWA_2.4.0_SeqWare_1.0.13.zip. This workflow can be created from source, see https://github.com/SeqWare/public-workflows. New features for this workflow compared to 2.3 include: 1) a gtdownload wrapper that monitors progress and kills and restarts the job if it freezes and 2) an option for skipping download/upload from/to GNOS and instead use local file paths (GNOS is still used to retrieve metadata). Please note the reference is hs37d, see ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/README_human_reference_20110707 for more information. Briefly this is the integrated reference sequence from the GRCh37 primary assembly (chromosomal plus unlocalized and unplaced contigs), the rCRS mitochondrial sequence (AC:NC_012920), Human herpesvirus 4 type 1 (AC:NC_007605) and the concatenated decoy sequences (hs37d5cs.fa.gz).

2.3.0 BWA Workflow Release

This is the SeqWare BWA-Mem PanCancer Workflow version 2.3.0 available in its packaged form from https://s3.amazonaws.com/oicr.workflow.bundles/released-bundles/Workflow_Bundle_BWA_2.3.0_SeqWare_1.0.13.zip. This workflow can be created from source, see https://github.com/SeqWare/public-workflows. New features for this workflow compared to 2.2 include: 1) update of the PCAP tools to version 1.0.2 (along with the associated tools including BWA-Mem 0.7.8) see https://github.com/ICGC-TCGA-PanCancer/PCAP-core/tree/v1.0.2 and https://github.com/lh3/bwa/archive/0.7.8.tar.gz, and 2) adding the parameters '"calmdnm=1 calmdnmrecompindetonly=1 calmdnmreference=" + reference_path' to bamsort. Please note the reference is hs37d, see ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/README_human_reference_20110707 for more information. Briefly this is the integrated reference sequence from the GRCh37 primary assembly (chromosomal plus unlocalized and unplaced contigs), the rCRS mitochondrial sequence (AC:NC_012920), Human herpesvirus 4 type 1 (AC:NC_007605) and the concatenated decoy sequences (hs37d5cs.fa.gz).

2.2.0 BWA Workflow Release

This is the SeqWare BWA-Mem PanCancer Workflow version 2.2.0 available in its packaged form from https://s3.amazonaws.com/oicr.workflow.bundles/released-bundles/Workflow_Bundle_BWA_2.2.0_SeqWare_1.0.13.zip. This workflow can be created from source, see https://github.com/SeqWare/public-workflows. New features for this workflow compared to 2.1 include: 1) inclusion of QC information in the metadata uploaded to GNOS along with the aligned BAM, 2) cleanup steps added throughout the workflow to reduce the runtime storage footprint, 3) update of the PCAP tools to version 1.0.0 (along with the associated tools including BWA-Mem 0.7.7-r441), 4) improved efficiency with regards to doing more steps in parallel, 5) more consistent encoding of information in the GNOS metadata using JSON values, and 6) improvements and bug fixes to the metadata uploaded to GNOS. Please note the reference is hs37d, see ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/README_human_reference_20110707 for more information. Briefly this is the integrated reference sequence from the GRCh37 primary assembly (chromosomal plus unlocalized and unplaced contigs), the rCRS mitochondrial sequence (AC:NC_012920), Human herpesvirus 4 type 1 (AC:NC_007605) and the concatenated decoy sequences (hs37d5cs.fa.gz).