chore: release 3.11.0

[github-actions]

🤖 I have created a release *beep* *boop*

3.11.0 (2024-05-29)

Features

• add samtools markdup wrapper (#2926) (3c86bae)
• Add support for regions file and arbitrary FAI/GZI paths (#2936) (445b35f)
• add wrapper to samtools collate (#2929) (0c7ae27)
• All ngsderive subcommands (#2732) (847ab1d)
• auto infer run mode (#2937) (08bd3cd)
• Goleft indexcov (#2734) (ebef6f8)

Bug Fixes

• bamcoverage without effective genome size (#2941) (b6ad55f)
• issue #366 and #2649 (#2928) (e10ab57)
• remove NA string replacement, fixed upstream (#2940) (8f4d223)

Performance Improvements

• autobump bio/bismark/bam2nuc (#2943) (9228479)
• autobump bio/bismark/bismark (#2948) (d9abb20)
• autobump bio/bismark/bismark_genome_preparation (#2945) (899ae0d)
• autobump bio/bismark/bismark_methylation_extractor (#2944) (1b232d2)
• autobump bio/bismark/bismark2bedGraph (#2947) (ab29098)
• autobump bio/bismark/bismark2report (#2951) (13dd155)
• autobump bio/bismark/bismark2summary (#2946) (bfb3d30)
• autobump bio/bismark/deduplicate_bismark (#2950) (bcf3c06)
• autobump bio/bowtie2/align (#2949) (6b0593f)
• autobump bio/bowtie2/build (#2942) (5b3ca20)
• autobump bio/fastq_screen (#2952) (e45fcac)
• autobump bio/gatk/applybqsr (#2938) (498c67f)
• autobump bio/gatk3/realignertargetcreator (#2931) (2d2835c)
• autobump bio/gdc-api/bam-slicing (#2954) (32d25c1)
• autobump bio/goleft/indexcov (#2930) (5ccbdb0)
• autobump bio/gseapy/gsea (#2953) (dda3d16)
• autobump bio/hifiasm (#2932) (3722de7)
• autobump bio/multiqc (#2955) (91ad107)
• autobump bio/ptrimmer (#2933) (cd37e0b)
• autobump bio/rbt/csvreport (#2956) (b2a469d)
• autobump bio/unicycler (#2957) (185ce7e)
• autobump bio/vep/annotate (#2958) (728658d)
• autobump bio/vep/cache (#2959) (f4e5b66)
• autobump bio/whatshap/haplotag (#2934) (f0b638a)
• Update Datavzrd to 2.36.12 (#2924) (beb9d22)
• Use samtools collate in fastq separate wrapper (#2960) (9c8cf81)

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