v3.11.0
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/bwa-mem2/mem-samblaster (#2962) (ff613f3)
- autobump bio/bwa/mem-samblaster (#2961) (83754dd)
- autobump bio/fastq_screen (#2952) (e45fcac)
- autobump bio/freebayes (#2963) (7a0d553)
- 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/ngsderive (#2964) (df82b38)
- autobump bio/open-cravat/module (#2966) (f1ffa3e)
- autobump bio/open-cravat/run (#2965) (9b371ca)
- autobump bio/ptrimmer (#2933) (cd37e0b)
- autobump bio/rasusa (#2967) (9f25643)
- autobump bio/rbt/csvreport (#2956) (b2a469d)
- autobump bio/sambamba/flagstat (#2973) (4575792)
- autobump bio/sambamba/index (#2971) (18359ac)
- autobump bio/sambamba/markdup (#2968) (191542d)
- autobump bio/sambamba/merge (#2975) (adf9a28)
- autobump bio/sambamba/slice (#2972) (88ac3f6)
- autobump bio/sambamba/sort (#2976) (990e841)
- autobump bio/sambamba/view (#2970) (613e55d)
- autobump bio/seqkit (#2969) (e25b840)
- autobump bio/sra-tools/fasterq-dump (#2974) (d8b4b5f)
- 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)