chore(main): release 1.2.0

[github-actions[bot]]

:robot: I have created a release beep boop

1.2.0 (2023-04-16)

Features

• add a function to extract chromosome names and lengths from a SAM file (413ead9)
• add a rule for genome indexing (f2d596e)
• add a rule to convert BAM files to BED (a948d98)
• add a rule to convert kmers table to PLINK (8c4bfad)
• add error handling (da92bdb)
• add k-mer counts dist. plots (7df4787)
• add k-mer counts dist. plots (79427b4)
• add k-mer counts dist. plots (c45c412)
• add kGWASflow.py (698dcb8)
• add manhattan plot point size parameter (84415fe)
• add manhattan plot point size parameter (cfa961d)
• add missing logs and messages (293b2b6)
• add missing logs and messages (ba23335)
• add new functions, update checkpoints + target outputs (6dac404)
• add rules for converting BAM to BED (33ed058)
• add rules for generating igv reports (igv-report) (2c4b4fe)
• added container to define underlying OS for each job (022ab15)
• added log to merge_read rule (7caf0cf)
• added touch output to kmc rules + add priorities (758c807)
• control y axis limits in manhattan plot (76ec1ed)
• improve the kmers GWAS summary reports (9d5de9e)
• plot the k-mer's position on the chr if only one chr is provided (1fc8e5c)
• udpate config files + add new parameters (38c939b)
• update blast wrapper to v1.25.0 (3da03ba)
• update kmersGWAS to v.0.3 (84cfb9f)
• update to kmc 3.2.1 (c933fda)
• use python qmplot instead of qqman r package for manhattan plots (42dc51b)
• use python qmplot instead of qqman r package for manhattan plots (1dbfae4)

Bug Fixes

• change conda channels order (6b5d561)
• change output, log paths and report caption (827dcad)
• change x and y-axis ticks and labels (c7cdf87)
• changed conda channel_priority to flexible (fda022b)
• changed conda-frontend to conda (0aa0d01)
• changed plot_manhattan default parameter (a8ad464)
• fixed issues with hardcoded param indexes (978ce5b)
• fixed lints in build_kmers_gwas rules (3045d8e)
• fixed lints in combine_and_filter rules (d545a76)
• fixed lints in count_kmers rules (70157d8)
• fixed lints in create_kmers_table rule (dd97786)
• fixed lints in create_kmers_table rule (94018ab)
• fixed lints in fetch_reads rules (19756fd)
• fixed lints in fetch_significant_kmers rule (65d9fd4)
• fixed lints in filter_kmers rules (4824847)
• fixed lints in generate_results_table rule (3288591)
• fixed lints in ref rules (d904046)
• fixed the issues with ends_with_gz function (30f1c41)
• make the script compatible to new kmers GWAS summary reports (3dbecf0)
• remove build info from env yaml (0f5d3e6)
• solve the lib dependency issues with samtools (3695279)
• solve the lib dependency issues with samtools (b5b19af)
• specify the spades version (35d5690)
• update input file paths (05d7e6b)
• update input, ouput and params paths (4637ed6)
• update output directory paths + add touch (a0500c2)
• wrong path fetch_reads (49ec743)

Performance Improvements

• update kGWASflow version to 1.1.0 (178180f)
• update snakemake version to 7.25.0 (5b999c4)
• update to fasterq-dump wrapper v1.23.5 (373b406)
• update to libgcc 7.2.0 + libiconv 1.17 (cdb0e8f)
• update to snakemake 7.18.2 (2feba33)
• update to snakemake 7.18.2 (fdb9255)

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