v0.6.4

Release 0.6.4

In this release, we adjust memory and wallclock requirements for a number of modules, update read_group_from_fastq.py from python2 to python3, and incorporate PRs #4 and #5.

• PR #4 (contributed by @BrianSanderson) adds an optional gene and transcript count merge across samples in the RNA and PDX RNA workflows (merge accessed via including the --merge_rna_counts flag).
• PR #5 (contributed by @alanhoyle) adds a catch for corrupt gzip files in the Bowtie module as used by EMASE/GRBS analyses.

Pipelines Added:

None

Modules Added:

1. utility_modules/merge_rsem_counts.nf

Pipeline Changes:

1. workflows/rnaseq.nf module added to merge gene and transcript expression when --merge_rna_counts is used.
2. workflows/pdx_rnaseq.nf module added to merge gene and transcript expression when --merge_rna_counts is used.

Module Changes:

1. bowtie/bowtie.nf pipefail catch added for corrupt gzip files, per #5.
2. fastp/fastp.nf save json report as well as html report.
3. nygenome/lancet.nf wallclock request increase.
4. picard/picard_markduplicates.nf memory adjustment, and accounting for MarkDuplicates not fully respecting -Xmx memory limits imposed by Java.
5. picard/picard_reordersam.nf memory request increase.
6. picard/picard_sortsam.nf memory request increase.
7. utility_modules/read_groups.nf container changed to py3.

Script Changes:

1. bin/shared/read_group_from_fastq.py update from py2 to py3.