v0.7.0

Release 0.7.0

In this release we add a new workflow for calling copy number variation (CNV) from raw Illumina IDAT genotype array files. Currently the IlluminaCytoSNP v2.1 array is supported, but support for additional arrays is possible.

We make additional minor changes as described below.

Pipelines Added:

1. CNV calling from Illumina genotype array data (--cnv_array)

Modules Added:

1. modules/bcftools/bcftools_gtct2vcf.nf
2. modules/bcftools/bcftools_query_ascat.nf
3. modules/illumina/iaap_cli.nf
4. modules/ascat/ascat_run.nf
5. modules/ascat/ascat_annotation.nf

Pipeline Changes:

None

Module Changes:

1. Replaced the incorrect ${task.mem} with ${task.memory} in the Nextflow error catch statement in modules related to the SV calling workflows.
2. utility_modules/gzip.nf: Memory request increase

Scripts Added:

1. cnv_array/ASCAT_run.R
2. cnv_array/annotate_ensembl_genes.pl
3. cnv_array/seg_plot.R
4. cnv_array/segment_raw_extend.pl

Script Changes:

None

NF-Test Modules Added:

1. tests/workflows/cnv_array.nf.test