Changelog

3.9.0 (2024-04-22)

Features

• Add wrapper for defining columns in TTree in ROOT (#2898) (48730cd)

• Emu support (#2792) (149ef14)

Bug Fixes

• deeptools bamcoverage fix (#2719) (206425b)

• empty emu combined output (#2899) (7b10806)

Performance Improvements

• autobump bio/bcftools/call (#2828) (cd25cc8)

• autobump bio/bcftools/concat (#2832) (785cd77)

• autobump bio/bcftools/filter (#2821) (c4c2315)

• autobump bio/bcftools/index (#2829) (3ea7efb)

• autobump bio/bcftools/merge (#2827) (b1aee95)

• autobump bio/bcftools/mpileup (#2817) (9b9c0ea)

• autobump bio/bcftools/norm (#2819) (7126185)

• autobump bio/bcftools/reheader (#2822) (a77fa02)

• autobump bio/bcftools/sort (#2825) (7c9bb6d)

• autobump bio/bcftools/stats (#2813) (78e1ed6)

• autobump bio/bcftools/view (#2837) (ba4cb3b)

• autobump bio/bellerophon (#2834) (f9c272e)

• autobump bio/benchmark/chm-eval-sample (#2830) (9911338)

• autobump bio/bgzip (#2839) (8b1d2d7)

• autobump bio/bismark/bam2nuc (#2815) (1462242)

• autobump bio/bismark/bismark (#2812) (62ee915)

• autobump bio/bismark/bismark_genome_preparation (#2820) (108387c)

• autobump bio/bismark/bismark_methylation_extractor (#2814) (47a2c50)

• autobump bio/bismark/bismark2bedGraph (#2831) (556aadd)

• autobump bio/bismark/bismark2report (#2808) (b788b96)

• autobump bio/bismark/bismark2summary (#2809) (ff32047)

• autobump bio/bismark/deduplicate_bismark (#2841) (d897740)

• autobump bio/bowtie2/align (#2810) (f9b273e)

• autobump bio/bwa-mem2/mem (#2824) (a4451ea)

• autobump bio/bwa-meme/mem (#2836) (7f2a24b)

• autobump bio/bwa-memx/index (#2816) (d218b2b)

• autobump bio/bwa-memx/mem (#2826) (e7baf43)

• autobump bio/bwa/aln (#2833) (b41d0b4)

• autobump bio/bwa/index (#2838) (946d5c3)

• autobump bio/bwa/mem (#2818) (2d49db7)

• autobump bio/bwa/mem-samblaster (#2840) (0fc7d78)

• autobump bio/bwa/sampe (#2811) (a6367ba)

• autobump bio/bwa/samse (#2823) (6d2b199)

• autobump bio/bwa/samxe (#2835) (a375c11)

• autobump bio/cnvkit/antitarget (#2848) (91354dc)

• autobump bio/cnvkit/batch (#2849) (9fae85d)

• autobump bio/cnvkit/call (#2844) (5437973)

• autobump bio/cnvkit/diagram (#2846) (bcfcbed)

• autobump bio/cnvkit/export (#2843) (c499d71)

• autobump bio/cnvkit/target (#2847) (a41c0a0)

• autobump bio/cutadapt/pe (#2845) (77a7990)

• autobump bio/cutadapt/se (#2842) (d258f5b)

• autobump bio/deeptools/bamcoverage (#2851) (35d5649)

• autobump bio/delly (#2850) (3fa1540)

• autobump bio/emu/abundance (#2853) (fc3d8b6)

• autobump bio/emu/collapse-taxonomy (#2855) (2ec61a4)

• autobump bio/emu/combine-outputs (#2854) (ce414e9)

• autobump bio/encode_fastq_downloader (#2852) (b71c6d6)

• autobump bio/freebayes (#2856) (6f33607)

• autobump bio/gatk3/printreads (#2857) (e42c565)

• autobump bio/hisat2/align (#2858) (b354fc1)

• autobump bio/hisat2/index (#2860) (5d6bdd1)

• autobump bio/homer/makeTagDirectory (#2859) (b3b9dfd)

• autobump bio/lofreq/call (#2861) (3f66fd1)

• autobump bio/lofreq/indelqual (#2862) (736bc9c)

• autobump bio/minimap2/aligner (#2863) (0fdbb99)

• autobump bio/paladin/align (#2865) (50b5c90)

• autobump bio/paladin/index (#2867) (9d31d8d)

• autobump bio/paladin/prepare (#2866) (e327ba7)

• autobump bio/picard/markduplicates (#2864) (f5ddedc)

• autobump bio/pretext/map (#2868) (68ba090)

• autobump bio/rbt/collapse_reads_to_fragments-bam (#2870) (8b36d24)

• autobump bio/reference/ensembl-variation (#2869) (c8df691)

• autobump bio/samtools/calmd (#2885) (031bdfa)

• autobump bio/samtools/depth (#2875) (16a53d6)

• autobump bio/samtools/faidx (#2874) (6a1b758)

• autobump bio/samtools/fastx (#2884) (60b6495)

• autobump bio/samtools/fixmate (#2872) (6a14082)

• autobump bio/samtools/flagstat (#2880) (b5b67be)

• autobump bio/samtools/idxstats (#2876) (1f5f13e)

• autobump bio/samtools/index (#2890) (f3f5be3)

• autobump bio/samtools/merge (#2883) (162ab43)

• autobump bio/samtools/mpileup (#2877) (376b565)

• autobump bio/samtools/sort (#2886) (da3cc4c)

• autobump bio/samtools/stats (#2888) (5a11e6a)

• autobump bio/samtools/view (#2878) (d54caec)

• autobump bio/snpeff/annotate (#2871) (3732019)

• autobump bio/snpeff/download (#2889) (6700901)

• autobump bio/snpsift/annotate (#2879) (8b5882d)

• autobump bio/snpsift/dbnsfp (#2881) (af992da)

• autobump bio/snpsift/genesets (#2882) (c58973e)

• autobump bio/snpsift/gwascat (#2873) (bd82454)

• autobump bio/spades/metaspades (#2887) (a678d26)

• autobump bio/tabix/index (#2892) (91122a4)

• autobump bio/tabix/query (#2891) (67caa45)

• autobump bio/umis/bamtag (#2894) (50d9fba)

• autobump bio/unicycler (#2893) (591095b)

• autobump bio/vep/annotate (#2896) (85acb44)

• autobump bio/vep/cache (#2897) (529d832)

• autobump bio/vep/plugins (#2895) (e2045c6)

3.8.0 (2024-04-12)

Features

• add fgbio sorting to bwa mem (#2805) (af98a55)

• Add wrapper for ROOT hadd (#2785) (3e82e9c)

Bug Fixes

• bcftool stats bug (#2806) (e7ff82c)

Performance Improvements

• autobump bio/busco (#2787) (ebe243e)

• autobump bio/deeptools/plotfingerprint (#2776) (214ea28)

• autobump bio/deeptools/plotheatmap (#2788) (81ee08b)

• autobump bio/ega/fetch (#2789) (fd83ecb)

• autobump bio/freebayes (#1850) (795e778)

• autobump bio/freebayes (#2790) (fe5de66)

• autobump bio/gdc-api/bam-slicing (#2778) (9375ca8)

• autobump bio/minimap2/aligner (#2780) (23fd5a3)

• autobump bio/minimap2/index (#2779) (8f5d611)

• autobump bio/plass (#2791) (11f34ca)

• autobump bio/rseqc/read_gc (#2781) (842998d)

• autobump bio/seqkit (#2795) (1b2e7ba)

• autobump bio/sourmash/compute (#2794) (8a37a3e)

• autobump bio/tabix/query (#2796) (e21217e)

• autobump bio/tmb/pytmb (#2797) (28ae8a8)

• autobump bio/ucsc/gtfToGenePred (#2782) (4e8c925)

• autobump bio/unicycler (#2316) (0d1486b)

• autobump bio/vembrane/filter (#2783) (bb271ab)

• autobump bio/vembrane/table (#2784) (491d5b6)

• autobump bio/vg/construct (#2798) (25300e4)

• autobump bio/vg/ids (#2804) (4162ce1)

• autobump bio/vg/kmers (#2802) (9ddb88d)

• autobump bio/vg/merge (#2800) (5ba8325)

• autobump bio/vg/prune (#2801) (2061beb)

• autobump bio/vg/sim (#2799) (dfb0d6b)

• autobump bio/vsearch (#2803) (7070607)

3.7.0 (2024-03-27)

Features

• pyTMB (#2739) (0ffbed9)

Bug Fixes

• path of .fai file in ensembl-variation wrapper (#2773) (af63b5b)

3.6.0 (2024-03-26)

Features

• Taxonkit wrapper (#2755) (576ddb9)

3.5.3 (2024-03-22)

Performance Improvements

• autobump bio/busco (#2760) (96a5ee7)

• autobump bio/cutadapt/pe (#2762) (7326a2b)

• autobump bio/cutadapt/se (#2761) (2df0403)

• autobump bio/mapdamage2 (#2765) (03e2812)

• autobump bio/mosdepth (#2764) (b8b54ee)

• autobump bio/rseqc/infer_experiment (#2767) (dfd6ce4)

• autobump bio/rseqc/read_distribution (#2766) (7f32bdf)

• autobump bio/salmon/index (#2769) (f27e290)

• autobump bio/salmon/quant (#2768) (74e93c2)

• autobump bio/sourmash/compute (#2770) (19a8a84)

• autobump utils/csvtk (#2763) (d3fc9d3)

• Update Datavzrd to 2.36.9 (#2758) (efb4337)

3.5.2 (2024-03-18)

Bug Fixes

• output file handling in ensembl-variation wrapper in combination with remote storage or absolute output file paths (#2753) (5bbb7b2)

3.5.1 (2024-03-15)

Performance Improvements

• autobump bio/deeptools/alignmentsieve (#2741) (ce63735)

• autobump bio/deeptools/computematrix (#2740) (c3416a0)

• autobump bio/deeptools/plotcoverage (#2742) (ec1b4e3)

• autobump bio/deeptools/plotprofile (#2743) (1773265)

• autobump bio/entrez/efetch (#2745) (43deba3)

• autobump bio/fgbio/setmateinformation (#2746) (6768125)

• autobump bio/gatk/genotypegvcfs (#2747) (37c7361)

• autobump bio/minimap2/aligner (#2748) (04eca33)

• autobump bio/minimap2/index (#2749) (60aac91)

• autobump bio/rseqc/read_duplication (#2750) (78f15d1)

• autobump bio/seqkit (#2751) (5a4705e)

• autobump bio/ucsc/genePredToBed (#2752) (72ea812)

3.5.0 (2024-03-13)

Features

• Genepred to bed (#2726) (3998574)

• MultiQC automatically detects configuration from input file(s) (#2722) (f61238d)

• Rseqc distribution (#2737) (c732ff0)

• Rseqc infer experiment (#2730) (c597f2b)

• Rseqc read duplication (#2731) (2d5f9e7)

• Rseqc read gc (#2729) (739d809)

• run Mutect2 multiple with input bam files (#2736) (7b42689)

Performance Improvements

• autobump bio/gseapy/gsea (#2727) (400db30)

• autobump bio/sra-tools/fasterq-dump (#2728) (92c9521)

• Update Datavzrd (#2735) (41b562c)

• Update Datavzrd to 2.36.4 (#2720) (7611d30)

• Update Datavzrd to 2.36.5 (#2733) (2fad8a1)

• Update Datavzrd to 2.36.8 (#2738) (8c86447)

3.4.1 (2024-03-01)

Performance Improvements

• autobump bio/gatk/applyvqsr (#2705) (8c90ec7)

• autobump bio/gatk/baserecalibrator (#2704) (0d6c664)

• autobump bio/gatk/collectalleliccounts (#2699) (9018e05)

• autobump bio/gatk/haplotypecaller (#2698) (aa76a60)

• autobump bio/gatk/intervallisttobed (#2700) (3d35d2b)

• autobump bio/gatk/printreadsspark (#2703) (a62781c)

• autobump bio/gatk/selectvariants (#2707) (9815aa5)

• autobump bio/gatk/variantstotable (#2697) (0e6c7ef)

• autobump bio/gatk3/baserecalibrator (#2702) (90a833a)

• autobump bio/gatk3/indelrealigner (#2701) (c13c656)

• autobump bio/gatk3/realignertargetcreator (#2706) (4f3e20b)

• autobump bio/multiqc (#2708) (4d60b0f)

• autobump bio/open-cravat/module (#2709) (c8ec2ae)

• autobump bio/open-cravat/run (#2710) (4268a26)

• autobump bio/picard/collectinsertsizemetrics (#2711) (a2b2d66)

• autobump bio/vg/construct (#2715) (7b1cde1)

• autobump bio/vg/ids (#2717) (e7b495b)

• autobump bio/vg/kmers (#2716) (e5d6785)

• autobump bio/vg/merge (#2713) (2609163)

• autobump bio/vg/prune (#2714) (3abe763)

• autobump bio/vg/sim (#2712) (79dfbef)

• Update datavzrd to 2.36.2 (#2694) (b1ea355)

• Update Datavzrd to 2.36.3 (#2696) (baa8376)

3.4.0 (2024-02-27)

Features

• Add csvtk wrapper (#2681) (495053e)

• MultiQC temp folder, specify outdir/filename, infer options, and bump version (#2639) (1edbead)

3.3.7 (2024-02-27)

Bug Fixes

• account for memory overhead (#2648) (6a05aad)

Performance Improvements

• autobump bio/bbtools (#2627) (7f5b520)

• autobump bio/diamond/blastp (#2630) (3911776)

• autobump bio/diamond/blastx (#2629) (faf5de8)

• autobump bio/diamond/makedb (#2628) (7ddca67)

• autobump bio/encode_fastq_downloader (#2682) (eb4a093)

• autobump bio/fgbio/collectduplexseqmetrics (#2631) (7a58ee9)

• autobump bio/galah (#2670) (8972be1)

• autobump bio/gatk/applybqsr (#2662) (2d1ff8e)

• autobump bio/gatk/applybqsrspark (#2669) (46a8acd)

• autobump bio/gatk/baserecalibratorspark (#2651) (3b4f517)

• autobump bio/gatk/calculatecontamination (#2673) (056c9a0)

• autobump bio/gatk/callcopyratiosegments (#2655) (b1932ae)

• autobump bio/gatk/cleansam (#2660) (3802099)

• autobump bio/gatk/collectreadcounts (#2666) (0aa2cce)

• autobump bio/gatk/combinegvcfs (#2686) (a903745)

• autobump bio/gatk/denoisereadcounts (#2685) (1e8498b)

• autobump bio/gatk/depthofcoverage (#2658) (1f43492)

• autobump bio/gatk/estimatelibrarycomplexity (#2650) (e9395ff)

• autobump bio/gatk/filtermutectcalls (#2684) (b239e62)

• autobump bio/gatk/genomicsdbimport (#2665) (a38b278)

• autobump bio/gatk/getpileupsummaries (#2657) (7523193)

• autobump bio/gatk/learnreadorientationmodel (#2653) (773e78c)

• autobump bio/gatk/leftalignandtrimvariants (#2656) (183950c)

• autobump bio/gatk/markduplicatesspark (#2659) (706cda3)

• autobump bio/gatk/modelsegments (#2663) (bc40698)

• autobump bio/gatk/mutect (#2661) (0e1d98a)

• autobump bio/gatk/scatterintervalsbyns (#2674) (e49b027)

• autobump bio/gatk/splitintervals (#2667) (332eed5)

• autobump bio/gatk/splitncigarreads (#2672) (dabbc1e)

• autobump bio/gatk/variantannotator (#2664) (2142589)

• autobump bio/gatk/varianteval (#2654) (9d4ffea)

• autobump bio/gatk/variantfiltration (#2668) (5cf5407)

• autobump bio/gatk/variantrecalibrator (#2652) (714ae91)

• autobump bio/gatk3/printreads (#2683) (c15b388)

• autobump bio/gatk3/realignertargetcreator (#2671) (103425a)

• autobump bio/igv-reports (#2641) (4bac92e)

• autobump bio/infernal/cmpress (#2676) (7e690c7)

• autobump bio/infernal/cmscan (#2675) (89eac39)

• autobump bio/jellyfish/count (#2643) (68d8bd6)

• autobump bio/jellyfish/dump (#2645) (d3823f8)

• autobump bio/jellyfish/histo (#2642) (26c3123)

• autobump bio/jellyfish/merge (#2644) (2acb46b)

• autobump bio/last/lastal (#2632) (0090d1a)

• autobump bio/last/lastal (#2646) (aecf702)

• autobump bio/last/lastal (#2687) (c252386)

• autobump bio/last/lastdb (#2633) (0adfac7)

• autobump bio/last/lastdb (#2647) (9797636)

• autobump bio/last/lastdb (#2688) (3dec479)

• autobump bio/multiqc (#2677) (197ef10)

• autobump bio/seqkit (#2635) (8ed8105)

• autobump bio/sourmash/compute (#2678) (1ba1a52)

• autobump bio/spades/metaspades (#2689) (35e4c20)

• autobump bio/star/align (#2634) (0cb085a)

• autobump bio/star/index (#2636) (e8df2fe)

• autobump bio/ucsc/gtfToGenePred (#2679) (20682f2)

• autobump bio/vep/cache (#2690) (0ea80f3)

• autobump bio/vep/plugins (#2691) (1b0108f)

• autobump bio/whatshap/haplotag (#2637) (5705ffc)

• Update datavzrd to v2.36.1 (#2692) (cba4946)

3.3.6 (2024-01-26)

Performance Improvements

• autobump bio/bellerophon (#2583) (b0d51ea)

• autobump bio/benchmark/chm-eval-sample (#2581) (d6d37a2)

• autobump bio/bgzip (#2584) (f239106)

• autobump bio/bismark/bam2nuc (#2566) (a892f71)

• autobump bio/bismark/bismark (#2582) (5cb0282)

• autobump bio/bismark/bismark_genome_preparation (#2567) (73059b9)

• autobump bio/bismark/bismark_methylation_extractor (#2576) (c97b557)

• autobump bio/bismark/bismark2bedGraph (#2575) (4bbae6a)

• autobump bio/bismark/bismark2report (#2572) (b018012)

• autobump bio/bismark/bismark2summary (#2574) (ab1c8af)

• autobump bio/bismark/deduplicate_bismark (#2571) (a3d2e1a)

• autobump bio/bowtie2/align (#2578) (e9e6d1e)

• autobump bio/bwa-mem2/mem (#2569) (84ef50c)

• autobump bio/bwa-meme/mem (#2579) (2bc7f68)

• autobump bio/bwa-memx/mem (#2577) (c96c94b)

• autobump bio/bwa/mem (#2573) (191155a)

• autobump bio/bwa/sampe (#2580) (0115a7c)

• autobump bio/bwa/samse (#2568) (9709ef4)

• autobump bio/bwa/samxe (#2570) (c1bf514)

• autobump bio/cnvkit/export (#2585) (e213c0f)

• autobump bio/fastq_screen (#2586) (bfc9e1d)

• autobump bio/gatk/applybqsr (#2587) (d2ddd0b)

• autobump bio/gatk/applybqsrspark (#2588) (b189fab)

• autobump bio/hisat2/align (#2590) (9701b79)

• autobump bio/hisat2/index (#2589) (bd7c9cf)

• autobump bio/homer/makeTagDirectory (#2591) (228cc4e)

• autobump bio/igv-reports (#2592) (b22c843)

• autobump bio/last/lastal (#2595) (2148e09)

• autobump bio/last/lastdb (#2594) (e0d4413)

• autobump bio/lofreq/call (#2596) (533b0ab)

• autobump bio/lofreq/indelqual (#2593) (7741cda)

• autobump bio/minimap2/aligner (#2597) (832d386)

• autobump bio/paladin/align (#2599) (0537271)

• autobump bio/paladin/index (#2601) (b823df4)

• autobump bio/paladin/prepare (#2600) (1b08512)

• autobump bio/picard/markduplicates (#2602) (3186986)

• autobump bio/pretext/map (#2598) (29de6ab)

• autobump bio/samtools/calmd (#2603) (933e7c5)

• autobump bio/samtools/depth (#2610) (94d3b46)

• autobump bio/samtools/faidx (#2608) (895739f)

• autobump bio/samtools/fastx (#2612) (bc81be6)

• autobump bio/samtools/fixmate (#2614) (ecb6d9d)

• autobump bio/samtools/flagstat (#2615) (3117a6a)

• autobump bio/samtools/idxstats (#2604) (bc779d3)

• autobump bio/samtools/index (#2613) (8fc34c5)

• autobump bio/samtools/merge (#2607) (6c94a03)

• autobump bio/samtools/mpileup (#2605) (6c2cbe5)

• autobump bio/samtools/sort (#2606) (23c86ba)

• autobump bio/samtools/stats (#2609) (bdaa3c6)

• autobump bio/samtools/view (#2611) (b18a52c)

• autobump bio/tabix/index (#2616) (32bb492)

• autobump bio/ucsc/bedGraphToBigWig (#2618) (a5a6056)

• autobump bio/ucsc/twoBitInfo (#2619) (2b8b6ad)

• autobump bio/umis/bamtag (#2617) (15bb341)

• autobump bio/vg/construct (#2625) (a8e1d8b)

• autobump bio/vg/ids (#2620) (ef17328)

• autobump bio/vg/kmers (#2624) (0334cc3)

• autobump bio/vg/merge (#2622) (d224795)

• autobump bio/vg/prune (#2621) (d30b324)

• autobump bio/vg/sim (#2626) (a2e60d6)

• autobump bio/vsearch (#2623) (f1e2f24)

• Update datavzrd to v2.35.4 (#2564) (d73914d)

3.3.5 (2024-01-23)

Performance Improvements

• Update datavzrd version to 2.35.3 (#2562) (766a490)

3.3.4 (2024-01-19)

Bug Fixes

• plotting with no model in nonpareil (#2536) (1ac6350)

• test case for reference-ensembl-sequence wrapper (#2522) (46bac2e)

Performance Improvements

• autobump bio/bismark/bam2nuc (#2551) (d15ce0b)

• autobump bio/bismark/bismark (#2553) (8fe6734)

• autobump bio/bismark/bismark_genome_preparation (#2554) (ab64460)

• autobump bio/bismark/bismark_methylation_extractor (#2555) (d468bbf)

• autobump bio/bismark/bismark2bedGraph (#2548) (708070c)

• autobump bio/bismark/bismark2report (#2550) (e78cdc4)

• autobump bio/bismark/bismark2summary (#2549) (aeb56e8)

• autobump bio/bismark/deduplicate_bismark (#2547) (d8cbfba)

• autobump bio/bowtie2/align (#2552) (85c799e)

• autobump bio/bowtie2/build (#2557) (3d51b99)

• autobump bio/busco (#2556) (90a30bc)

• autobump bio/bustools/count (#2524) (456e00d)

• autobump bio/bustools/sort (#2526) (0dc2402)

• autobump bio/bustools/text (#2525) (c6a41f1)

• autobump bio/dada2/add-species (#2528) (436567a)

• autobump bio/dada2/assign-species (#2527) (7786476)

• autobump bio/dada2/collapse-nomismatch (#2531) (46a9bf0)

• autobump bio/dada2/filter-trim (#2532) (3b18635)

• autobump bio/dada2/learn-errors (#2538) (3c8d713)

• autobump bio/dada2/quality-profile (#2530) (40a65c7)

• autobump bio/dada2/sample-inference (#2529) (b35731c)

• autobump bio/delly (#2558) (70a1a17)

• autobump bio/deseq2/deseqdataset (#2539) (2353167)

• autobump bio/fgbio/annotatebamwithumis (#2533) (187aa85)

• autobump bio/fgbio/callmolecularconsensusreads (#2540) (4d3c481)

• autobump bio/fgbio/filterconsensusreads (#2541) (bd43470)

• autobump bio/fgbio/groupreadsbyumi (#2559) (ff568c8)

• autobump bio/gatk/applybqsrspark (#2542) (b2023c1)

• autobump bio/gatk3/baserecalibrator (#2543) (c4e2a35)

• autobump bio/gatk3/indelrealigner (#2534) (9bd6dba)

• autobump bio/mashmap (#2544) (caee69d)

• autobump bio/rasusa (#2535) (caa3b3f)

• autobump bio/tximport (#2545) (fcb1f94)

• autobump bio/vep/annotate (#2561) (9acd1ca)

• autobump bio/vep/cache (#2560) (1f8fe5f)

3.3.3 (2023-12-29)

Performance Improvements

• autobump bio/dada2/assign-taxonomy (#2512) (a6c4b5d)

• autobump bio/dada2/dereplicate-fastq (#2507) (9a4a66a)

• autobump bio/dada2/make-table (#2509) (3560de8)

• autobump bio/dada2/merge-pairs (#2510) (423f296)

• autobump bio/dada2/remove-chimeras (#2511) (b672a0e)

• autobump bio/deseq2/deseqdataset (#2513) (408003b)

• autobump bio/deseq2/wald (#2508) (3c2f4e5)

• autobump bio/ega/fetch (#2497) (2cfba15)

• autobump bio/encode_fastq_downloader (#2514) (d66107e)

• autobump bio/fgbio/callmolecularconsensusreads (#2498) (851f091)

• autobump bio/gatk3/printreads (#2515) (8ca1cee)

• autobump bio/gseapy/gsea (#2499) (34ca621)

• autobump bio/igv-reports (#2516) (7cb25c5)

• autobump bio/last/lastal (#2500) (421a62d)

• autobump bio/last/lastal (#2517) (c6300a1)

• autobump bio/last/lastdb (#2501) (bfc91b0)

• autobump bio/last/lastdb (#2518) (82aa2b2)

• autobump bio/mashmap (#2502) (9153838)

• autobump bio/minimap2/aligner (#2504) (f7968db)

• autobump bio/multiqc (#2503) (c9eda7f)

• autobump bio/sourmash/compute (#2505) (d776e51)

• autobump bio/spades/metaspades (#2519) (6b88e9f)

• autobump bio/sra-tools/fasterq-dump (#2506) (5132a1d)

• autobump bio/vep/cache (#2520) (79f83c7)

• autobump bio/vep/plugins (#2521) (1adf343)

• autobump utils/datavzrd (#2495) (30fa79c)

3.3.2 (2023-12-21)

Bug Fixes

• fix title in ega/fetch metadata (c8305af)

• for vsearch, fixed bug with bz2 output and added general log (#1775) (28e76d0)

3.3.1 (2023-12-15)

Miscellaneous Chores

• release 3.3.1 (530381f)

3.3.0 (2023-12-15)

Features

• add wrapper for fetching files from EGA (#2488) (3d29dcf)

Bug Fixes

• add error handling to entrez wrapper (#2489) (7d654d5)

Performance Improvements

• autobump bio/bcftools/call (#2431) (3fb48df)

• autobump bio/bcftools/concat (#2413) (5bf2d39)

• autobump bio/bcftools/filter (#2428) (6819cb8)

• autobump bio/bcftools/index (#2418) (53259a7)

• autobump bio/bcftools/merge (#2432) (778ea14)

• autobump bio/bcftools/mpileup (#2437) (304d0b8)

• autobump bio/bcftools/norm (#2442) (17a025a)

• autobump bio/bcftools/reheader (#2427) (d737204)

• autobump bio/bcftools/sort (#2421) (a6e4426)

• autobump bio/bcftools/stats (#2441) (8c6f632)

• autobump bio/bcftools/view (#2423) (ba73c90)

• autobump bio/bellerophon (#2439) (439488e)

• autobump bio/benchmark/chm-eval-sample (#2440) (fd6981a)

• autobump bio/bgzip (#2429) (8f3b527)

• autobump bio/bismark/bam2nuc (#2416) (32f9515)

• autobump bio/bismark/bismark (#2443) (2c156a9)

• autobump bio/bismark/bismark_genome_preparation (#2434) (4a1b858)

• autobump bio/bismark/bismark_methylation_extractor (#2415) (ae1848d)

• autobump bio/bismark/bismark2bedGraph (#2435) (ddbc964)

• autobump bio/bismark/bismark2report (#2422) (b3b1f78)

• autobump bio/bismark/bismark2summary (#2420) (31a87bf)

• autobump bio/bismark/deduplicate_bismark (#2426) (490e276)

• autobump bio/bowtie2/align (#2414) (8fe3716)

• autobump bio/bwa-mem2/mem (#2430) (8ae7338)

• autobump bio/bwa-meme/mem (#2433) (2389bba)

• autobump bio/bwa-memx/mem (#2424) (ad72b7b)

• autobump bio/bwa/mem (#2417) (bb679e9)

• autobump bio/bwa/sampe (#2438) (ddefb15)

• autobump bio/bwa/samse (#2436) (a845fa4)

• autobump bio/bwa/samxe (#2425) (973ac6f)

• autobump bio/cnvkit/export (#2444) (36a3d1e)

• autobump bio/fgbio/annotatebamwithumis (#2446) (e896272)

• autobump bio/fgbio/collectduplexseqmetrics (#2448) (2abdd7f)

• autobump bio/fgbio/filterconsensusreads (#2447) (96ad8bc)

• autobump bio/fgbio/groupreadsbyumi (#2445) (d8bc1d7)

• autobump bio/fgbio/setmateinformation (#2449) (866cedc)

• autobump bio/gatk/applybqsr (#2450) (63c744a)

• autobump bio/hisat2/align (#2452) (3549c8e)

• autobump bio/hisat2/index (#2453) (017190a)

• autobump bio/homer/makeTagDirectory (#2451) (22d8f8d)

• autobump bio/lofreq/call (#2454) (08bac48)

• autobump bio/lofreq/indelqual (#2455) (2637859)

• autobump bio/mosdepth (#2456) (3caefb0)

• autobump bio/paladin/align (#2457) (32fb56f)

• autobump bio/paladin/index (#2461) (e3bc12a)

• autobump bio/paladin/prepare (#2459) (bb0f509)

• autobump bio/picard/markduplicates (#2460) (778f1fd)

• autobump bio/pretext/map (#2458) (8535686)

• autobump bio/reference/ensembl-variation (#2462) (26c321a)

• autobump bio/samtools/calmd (#2463) (d1c7b4a)

• autobump bio/samtools/depth (#2477) (da2a62b)

• autobump bio/samtools/faidx (#2470) (7298ed1)

• autobump bio/samtools/fastx (#2474) (ddbfa88)

• autobump bio/samtools/fixmate (#2481) (71ecb0d)

• autobump bio/samtools/flagstat (#2471) (93c93e3)

• autobump bio/samtools/idxstats (#2480) (304c854)

• autobump bio/samtools/index (#2473) (eed7721)

• autobump bio/samtools/merge (#2479) (d6995ca)

• autobump bio/samtools/mpileup (#2475) (c3707b0)

• autobump bio/samtools/sort (#2468) (f04208c)

• autobump bio/samtools/stats (#2466) (82c5af8)

• autobump bio/samtools/view (#2469) (5ecc368)

• autobump bio/snpeff/annotate (#2472) (41cbb4d)

• autobump bio/snpeff/download (#2478) (e8d0586)

• autobump bio/snpsift/annotate (#2464) (7123087)

• autobump bio/snpsift/dbnsfp (#2467) (4071e38)

• autobump bio/snpsift/genesets (#2476) (8db87de)

• autobump bio/snpsift/gwascat (#2465) (74a030f)

• autobump bio/tabix/query (#2483) (1e15361)

• autobump bio/tximport (#2482) (e97353f)

• autobump bio/umis/bamtag (#2484) (d0501aa)

• autobump bio/vembrane/filter (#2486) (b0b3cc9)

• autobump bio/vembrane/table (#2485) (a34fd66)

• autobump bio/vep/annotate (#2487) (530fe3f)

3.2.0 (2023-12-14)

Features

• add entrez/efetch wrapper (#2411) (9f0ad09)

Bug Fixes

• Add json output to Nonpareil and extra plot options (#2393) (c43af99)

3.1.0 (2023-12-11)

Features

• datavzrd to 2.33.2 (#2408) (8cd3c57)

Performance Improvements

• autobump bio/cutadapt/pe (#2395) (1e23b52)

• autobump bio/cutadapt/se (#2396) (948d27e)

• autobump bio/enhancedvolcano (#2398) (8bf91e8)

• autobump bio/gdc-api/bam-slicing (#2399) (5826e30)

• autobump bio/last/lastal (#2400) (c705bda)

• autobump bio/last/lastdb (#2401) (5315ac4)

• autobump bio/vg/construct (#2403) (fb600b4)

• autobump bio/vg/ids (#2406) (a00c987)

• autobump bio/vg/kmers (#2407) (561ccaf)

• autobump bio/vg/merge (#2404) (49d66d3)

• autobump bio/vg/prune (#2402) (51102d9)

• autobump bio/vg/sim (#2405) (5710671)

3.0.4 (2023-12-07)

Bug Fixes

• add support for multiple samples to bcftools mpileup (#2391) (1296a9c)

3.0.3 (2023-12-05)

Bug Fixes

• issue 2295 (#2390) (42906ac)

Performance Improvements

• autobump bio/last/lastal (#2387) (ff512fb)

• autobump bio/last/lastdb (#2388) (0dea6a1)

3.0.2 (2023-11-29)

Performance Improvements

• autobump bio/sra-tools/fasterq-dump (#2385) (2a92a50)

• autobump bio/vsearch (#2386) (702f980)

• autobump utils/datavzrd (#2383) (0d64202)

3.0.1 (2023-11-29)

Performance Improvements

• autobump bio/qualimap/bamqc (#2379) (a3709f0)

• autobump bio/qualimap/rnaseq (#2378) (61b6658)

• autobump bio/seqkit (#2380) (20c22b7)

3.0.0 (2023-11-23)

⚠ BREAKING CHANGES

• replace all bbtool wrappers with one bbtool wrapper for all subcommands (#1322)

Features

• allow for specifying multiple chromosomes in ensembl reference dna sequence download wrapper (#2376) (c5590f0)

• replace all bbtool wrappers with one bbtool wrapper for all subcommands (#1322) (6eb3c22)

Bug Fixes

• Update MultiQC to 1.18 (#2377) (03bf2d9)

Performance Improvements

• autobump bio/bbtools (#2325) (bf09e80)

• autobump bio/bedtools/bamtobed (#2334) (91b8054)

• autobump bio/bedtools/complement (#2341) (d0b9659)

• autobump bio/bedtools/coveragebed (#2342) (8c25388)

• autobump bio/bedtools/genomecov (#2336) (2ba070e)

• autobump bio/bedtools/intersect (#2338) (b299438)

• autobump bio/bedtools/merge (#2330) (8c6ae83)

• autobump bio/bedtools/slop (#2324) (dfef51e)

• autobump bio/bedtools/sort (#2328) (fde082e)

• autobump bio/bedtools/split (#2326) (7663786)

• autobump bio/blast/blastn (#2335) (518a30a)

• autobump bio/blast/makeblastdb (#2329) (f24d810)

• autobump bio/bustools/count (#2339) (f8598f8)

• autobump bio/bwa-mem2/mem (#2323) (c751efd)

• autobump bio/bwa-meme/mem (#2331) (ae28cb4)

• autobump bio/bwa-memx/mem (#2337) (1fe5ba7)

• autobump bio/bwa/mem (#2333) (e24ce7c)

• autobump bio/bwa/sampe (#2327) (70a1ac3)

• autobump bio/bwa/samse (#2332) (61c0e6d)

• autobump bio/bwa/samxe (#2340) (d0865bc)

• autobump bio/cooltools/dots (#2344) (c55e268)

• autobump bio/cooltools/eigs_cis (#2348) (1b7d26e)

• autobump bio/cooltools/eigs_trans (#2346) (f00f77b)

• autobump bio/cooltools/expected_cis (#2347) (f4c8924)

• autobump bio/cooltools/expected_trans (#2350) (7e3f763)

• autobump bio/cooltools/insulation (#2343) (77e4ef5)

• autobump bio/cooltools/pileup (#2345) (6c6b0b1)

• autobump bio/cooltools/saddle (#2349) (9f0f802)

• autobump bio/gseapy/gsea (#2351) (b3b3c94)

• autobump bio/hmmer/hmmbuild (#2355) (2744f59)

• autobump bio/hmmer/hmmpress (#2354) (3f379bc)

• autobump bio/hmmer/hmmscan (#2353) (50c6425)

• autobump bio/hmmer/hmmsearch (#2352) (ed2bbcc)

• autobump bio/last/lastal (#2357) (2589f18)

• autobump bio/last/lastdb (#2356) (4cee71f)

• autobump bio/picard/addorreplacereadgroups (#2370) (cf1cef0)

• autobump bio/picard/bedtointervallist (#2360) (b71d414)

• autobump bio/picard/collectalignmentsummarymetrics (#2359) (8873d75)

• autobump bio/picard/collectgcbiasmetrics (#2366) (f6d5248)

• autobump bio/picard/collecthsmetrics (#2369) (f730d54)

• autobump bio/picard/collectinsertsizemetrics (#2373) (a952ad4)

• autobump bio/picard/collectmultiplemetrics (#2364) (b21473a)

• autobump bio/picard/collectrnaseqmetrics (#2361) (2b36e3c)

• autobump bio/picard/collecttargetedpcrmetrics (#2358) (babe13e)

• autobump bio/picard/createsequencedictionary (#2372) (70630ac)

• autobump bio/picard/markduplicates (#2365) (66bea69)

• autobump bio/picard/mergesamfiles (#2362) (b1e64e2)

• autobump bio/picard/mergevcfs (#2363) (2ca8f9e)

• autobump bio/picard/revertsam (#2367) (8a54527)

• autobump bio/picard/samtofastq (#2371) (62ae9e5)

• autobump bio/picard/sortsam (#2368) (1a359a4)

• autobump bio/sortmerna (#2374) (e0920c9)

• autobump bio/vsearch (#2375) (c59fbc8)

2.13.0 (2023-11-13)

Features

• sortmerna wrapper (#2320) (599165b)

2.12.0 (2023-11-10)

Features

• update datavzrd wrapper to datavzrd v2.31.0 (#2318) (a142594)

2.11.1 (2023-11-10)

Performance Improvements

• autobump utils/nextflow (#2120) (45ea105)

2.11.0 (2023-11-10)

Features

• Gatk short-variants-calling meta-wrapper (#1778) (4099e4b)

Performance Improvements

• autobump bio/gatk/applybqsr (#2300) (eb86cea)

• autobump bio/gatk/callcopyratiosegments (#2303) (a079efa)

• autobump bio/gatk/filtermutectcalls (#2304) (14cdc1f)

• autobump bio/gatk/haplotypecaller (#2307) (ff59451)

• autobump bio/gatk/leftalignandtrimvariants (#2302) (998385d)

• autobump bio/gatk/printreadsspark (#2308) (2aa9b79)

• autobump bio/gatk/scatterintervalsbyns (#2305) (9ddace9)

• autobump bio/gatk/variantannotator (#2306) (2d43be9)

• autobump bio/gatk/varianteval (#2301) (a987c19)

• autobump bio/genomepy (#2299) (cfc3db3)

• autobump bio/gridss/preprocess (#2298) (7cddab3)

• autobump bio/hifiasm (#2309) (2d52e06)

• autobump bio/kallisto/index (#2246) (29b1c32)

• autobump bio/last/lastal (#2310) (0c4ff31)

• autobump bio/last/lastdb (#2093) (d055ba9)

• autobump bio/pbmm2/align (#2313) (d977038)

• autobump bio/pbmm2/index (#2312) (8c714a6)

• autobump bio/pyroe/makesplicedintronic (#2314) (dcb1810)

• autobump bio/pyroe/makeunspliceunspliced (#2311) (295df81)

• autobump bio/seqkit (#2315) (5d8cd40)

2.10.0 (2023-11-08)

Features

• update datavzrd 2.29.0 (#2288) (02ca59a)

• update datavzrd 2.30.0 (#2294) (6c1750d)

Bug Fixes

• bug when renaming samples (#2293) (8c217f8)

• fix datavzrd version pinning (#2290) (2f0cee7)

Performance Improvements

• autobump bio/bustools/sort (#2234) (3ce66d6)

• autobump bio/bustools/text (#2233) (88185ac)

• autobump bio/deseq2/deseqdataset (#2237) (dfc5575)

• autobump bio/deseq2/wald (#2236) (8657895)

• autobump bio/fastp (#2239) (8b5947d)

• autobump bio/fastq_screen (#2238) (c75f5a2)

• autobump bio/fastqc (#2240) (5b46013)

• autobump bio/fgbio/annotatebamwithumis (#2243) (f7b8427)

• autobump bio/fgbio/callmolecularconsensusreads (#2244) (0def80b)

• autobump bio/fgbio/filterconsensusreads (#2242) (aed8b65)

• autobump bio/fgbio/groupreadsbyumi (#2245) (98ca646)

• autobump bio/filtlong (#2241) (2a5123f)

• autobump bio/paladin/align (#2270) (e1d5293)

• autobump bio/paladin/prepare (#2277) (5615116)

• autobump bio/pbmm2/align (#2269) (6f2f6cf)

• autobump bio/pbmm2/index (#2273) (95eea96)

• autobump bio/pear (#2266) (294be33)

• autobump bio/picard/addorreplacereadgroups (#2259) (bc422f3)

• autobump bio/picard/bedtointervallist (#2272) (203b36a)

• autobump bio/picard/collectalignmentsummarymetrics (#2262) (41e8dde)

• autobump bio/picard/collectgcbiasmetrics (#2256) (80b3cf6)

• autobump bio/picard/collecthsmetrics (#2257) (ae663c2)

• autobump bio/picard/collectinsertsizemetrics (#2261) (ef362b3)

• autobump bio/picard/collectmultiplemetrics (#2248) (f73efb6)

• autobump bio/picard/collectrnaseqmetrics (#2250) (c4f541b)

• autobump bio/picard/collecttargetedpcrmetrics (#2263) (2fb4af9)

• autobump bio/picard/markduplicates (#2276) (93933d4)

• autobump bio/picard/mergevcfs (#2271) (302d1ff)

• autobump bio/picard/revertsam (#2285) (eee4daf)

• autobump bio/picard/samtofastq (#2280) (803ddec)

• autobump bio/picard/sortsam (#2258) (118b70d)

• autobump bio/pindel/call (#2275) (45c52d3)

• autobump bio/pindel/pindel2vcf (#2281) (5ffe4bc)

• autobump bio/plass (#2264) (0d8ca7f)

• autobump bio/preseq/lc_extrap (#2254) (538e322)

• autobump bio/pretext/graph (#2251) (f3c7296)

• autobump bio/pretext/map (#2265) (c6c35f8)

• autobump bio/pretext/snapshot (#2282) (a7358b9)

• autobump bio/prosolo/control-fdr (#2268) (c55a9ec)

• autobump bio/prosolo/single-cell-bulk (#2253) (03d4f9f)

• autobump bio/ptrimmer (#2284) (105ffd9)

• autobump bio/purge_dups/calcuts (#2249) (72397c2)

• autobump bio/purge_dups/get_seqs (#2252) (25a113c)

• autobump bio/purge_dups/ngscstat (#2267) (f4e2068)

• autobump bio/purge_dups/pbcstat (#2283) (3893aa0)

• autobump bio/purge_dups/purge_dups (#2278) (a08e8f8)

• autobump bio/purge_dups/split_fa (#2279) (26dbb9e)

• autobump bio/pyroe/idtoname (#2274) (76b9d89)

• autobump bio/pyroe/makesplicedintronic (#2255) (436c1f8)

• autobump bio/pyroe/makeunspliceunspliced (#2260) (1da192d)

• autobump bio/ucsc/faToTwoBit (#2286) (93ba408)

• autobump bio/ucsc/twoBitToFa (#2287) (03447e8)

2.9.1 (2023-11-01)

Performance Improvements

• autobump bio/adapterremoval (#1914) (ca25e3d)

• autobump bio/arriba (#1915) (a4d53df)

• autobump bio/art/profiler_illumina (#1913) (8beb04c)

• autobump bio/assembly-stats (#1916) (e7e4bb9)

• autobump bio/bamtools/filter (#1935) (92b7ce5)

• autobump bio/bamtools/filter_json (#1960) (b4d740e)

• autobump bio/bamtools/split (#1944) (1860890)

• autobump bio/bamtools/stats (#1968) (a221925)

• autobump bio/barrnap (#1921) (52a7360)

• autobump bio/bazam (#1950) (6daa3ad)

• autobump bio/bcftools/call (#1954) (4827897)

• autobump bio/bcftools/concat (#1958) (db356f5)

• autobump bio/bcftools/filter (#1947) (43d2237)

• autobump bio/bcftools/index (#1937) (6cd5422)

• autobump bio/bcftools/merge (#1930) (aa26661)

• autobump bio/bcftools/mpileup (#1949) (df4469e)

• autobump bio/bcftools/norm (#1975) (769e84e)

• autobump bio/bcftools/reheader (#1926) (767f5f8)

• autobump bio/bcftools/sort (#1962) (d113d02)

• autobump bio/bcftools/stats (#1932) (ac1725b)

• autobump bio/bcftools/view (#1936) (34b12ac)

• autobump bio/bedtools/bamtobed (#1956) (0a50372)

• autobump bio/bedtools/complement (#1925) (2116c8b)

• autobump bio/bedtools/coveragebed (#1970) (3a04846)

• autobump bio/bedtools/genomecov (#1938) (92c9e9d)

• autobump bio/bedtools/intersect (#1976) (c90f102)

• autobump bio/bedtools/merge (#1963) (e5ac112)

• autobump bio/bedtools/slop (#1955) (569c089)

• autobump bio/bedtools/sort (#1971) (5687f4f)

• autobump bio/bedtools/split (#1939) (333dbcd)

• autobump bio/bellerophon (#1969) (cd4cc86)

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• autobump bio/gseapy/gsea (#2058) (9eb8b6b)

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• autobump bio/sourmash/compute (#2157) (b4cf7d6)

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• autobump bio/sra-tools/fasterq-dump (#2169) (c0a9f8a)

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• autobump bio/star/index (#2154) (04d580e)

• autobump bio/strelka/germline (#2184) (68d5fda)

• autobump bio/strelka/somatic (#2155) (4609785)

• autobump bio/strling/call (#2176) (fe0a308)

• autobump bio/strling/extract (#2168) (67778b6)

• autobump bio/strling/index (#2152) (37038ed)

• autobump bio/strling/merge (#2164) (ec23c18)

• autobump bio/subread/featurecounts (#2185) (fcdd09e)

• autobump bio/tabix/index (#2196) (baf8370)

• autobump bio/tabix/query (#2195) (0197350)

• autobump bio/transdecoder/longorfs (#2193) (44405ff)

• autobump bio/transdecoder/predict (#2194) (c736c92)

• autobump bio/trim_galore/pe (#2197) (7b18aa9)

• autobump bio/trim_galore/se (#2198) (d0006df)

• autobump bio/trinity (#2199) (4db0e23)

• autobump bio/tximport (#2200) (59213ac)

• autobump bio/ucsc/bedGraphToBigWig (#2207) (d9802d5)

• autobump bio/ucsc/faToTwoBit (#2206) (6df0294)

• autobump bio/ucsc/gtfToGenePred (#2203) (caff71e)

• autobump bio/ucsc/twoBitInfo (#2202) (5b3026b)

• autobump bio/ucsc/twoBitToFa (#2201) (feeb125)

• autobump bio/umis/bamtag (#2205) (450649a)

• autobump bio/unicycler (#2204) (c057410)

• autobump bio/vardict (#2212) (eb59fd5)

• autobump bio/varscan/mpileup2indel (#2208) (3c79afb)

• autobump bio/varscan/mpileup2snp (#2214) (89f1a73)

• autobump bio/varscan/somatic (#2223) (3a423db)

• autobump bio/vcftools/filter (#2209) (3bac802)

• autobump bio/vembrane/filter (#2218) (01c8cf5)

• autobump bio/vembrane/table (#2220) (94fd729)

• autobump bio/vep/annotate (#2217) (7821c79)

• autobump bio/vep/cache (#2210) (12d3ebd)

• autobump bio/vep/plugins (#2213) (a52a0e3)

• autobump bio/verifybamid/verifybamid2 (#2219) (96fd2f4)

• autobump bio/vg/construct (#2216) (263ce06)

• autobump bio/vg/ids (#2224) (e870ebc)

• autobump bio/vg/kmers (#2225) (299fb69)

• autobump bio/vg/merge (#2215) (bbbe6f8)

• autobump bio/vg/prune (#2211) (eff9123)

• autobump bio/vg/sim (#2222) (9a15f42)

• autobump bio/vsearch (#2221) (e5da30c)

• autobump bio/wgsim (#2226) (6406049)

• autobump bio/whatshap/haplotag (#2227) (00c9ff2)

• autobump utils/cairosvg (#1996) (17a0166)

• autobump utils/datavzrd (#2009) (bda71cb)

• autobump utils/xsv (#2228) (05af587)

2.9.0 (2023-10-30)

Features

• CNV Facets (#1773) (74f5e4a)

• encode fastq downloader (#1798) (1cc3e00)

• for bwa, auto infer block size, extra tests, code cleanup and add docs (#1774) (66940e3)

• Gseapy (#1822) (2a50eb0)

• unaligned bam input support for minimap2 alignment (#1863) (76280a5)

Bug Fixes

• for nonpareil, use pigz and pbzip2 and auto infer of -X (#1776) (45860bf)

• moving to utils (#1770) (b5c0c01)

Performance Improvements

• autopin bio/bwa/mem (#1907) (99e9f60)

• autopin bio/multiqc (#1906) (6c67666)

2.8.0 (2023-10-26)

Features

• methyldackel extract (#1823) (930d64e)

• Unified seqtk wrapper (#1777) (0e7fff5)

Bug Fixes

• add readthedocs config file v2 (#1902) (bb29891)

2.7.0 (2023-10-23)

Features

• Cnvkit call wrapper (#1879) (db073db)

• cnvkit diagram wrapper (#1881) (d3cfc11)

• Cnvkit target wrapper (#1878) (07f3b16)

• whatshap haplotag (#1862) (d55ed6a)

• wrapper for cnvkit batch (#1877) (40bfc5d)

Bug Fixes

• Update environment.yaml of MultiQC (#1873) (bcd4a24)

Performance Improvements

• autobump bio/bcftools/call (#1855) (ef3ba47)

• autobump bio/bcftools/filter (#1889) (088aa72)

• autobump bio/bcftools/merge (#1887) (43781d6)

• autobump bio/bcftools/mpileup (#1896) (0dcb3cc)

• autobump bio/bcftools/norm (#1884) (30a9f95)

• autobump bio/bcftools/reheader (#1841) (f450530)

• autobump bio/bcftools/stats (#1883) (9ac746c)

• autobump bio/bcftools/view (#1842) (19e89ab)

• autobump bio/bismark/bam2nuc (#1867) (f29483a)

• autobump bio/bismark/bismark (#1853) (6babc2a)

• autobump bio/bismark/bismark2bedGraph (#1894) (6bd04db)

• autobump bio/bismark/bismark2report (#1871) (c5003d5)

• autobump bio/bismark/bismark2summary (#1882) (3256aa1)

• autobump bio/bismark/deduplicate_bismark (#1846) (b18c5c7)

• autobump bio/bowtie2/build (#1893) (dc2f765)

• autobump bio/bwa-meme/mem (#1861) (31be794)

• autobump bio/bwa/samxe (#1895) (929ddd6)

• autobump bio/deeptools/computematrix (#1848) (0fdcd5a)

• autobump bio/gatk/applybqsr (#1866) (201dea6)

• autobump bio/gatk3/baserecalibrator (#1847) (80edec6)

• autobump bio/gatk3/indelrealigner (#1890) (7803fbe)

• autobump bio/gatk3/printreads (#1869) (58fe71a)

• autobump bio/lofreq/call (#1860) (ca5409d)

• autobump bio/mashmap (#1886) (4d277b2)

• autobump bio/paladin/align (#1897) (7b5dc11)

• autobump bio/pandora/index (#1868) (bc7b88a)

• autobump bio/picard/collecthsmetrics (#1865) (6028b5d)

• autobump bio/picard/collectrnaseqmetrics (#1844) (bd4ac2f)

• autobump bio/pretext/map (#1851) (f4bb492)

• autobump bio/salmon/quant (#1888) (af65c24)

• autobump bio/samtools/calmd (#1843) (3c5bd68)

• autobump bio/samtools/faidx (#1891) (2d4444e)

• autobump bio/samtools/index (#1849) (2dd024c)

• autobump bio/snpeff/download (#1892) (920eb68)

• autobump bio/snpsift/dbnsfp (#1852) (f8453d6)

• autobump bio/snpsift/dbnsfp (#1898) (3b48591)

• autobump bio/snpsift/gwascat (#1870) (c55a0b5)

• autobump bio/snpsift/varType (#1885) (b456dc5)

• autobump bio/spades/metaspades (#1859) (ef24b5d)

• autobump bio/tabix/query (#1858) (59a11ca)

• autobump bio/umis/bamtag (#1872) (c44ef6b)

• autobump bio/vg/construct (#1857) (addcbdc)

• autobump bio/vg/ids (#1854) (ea9934c)

• autobump utils/datavzrd (#1856) (723fd8b)

2.6.1 (2023-10-04)

Bug Fixes

• build docs on fork (#1800) (d859765)

• fix freebayes parallel (#1807) (2aa2f62)

• Fix MultiQC output file issues (#1796) (ecc45e8)

• genomepy wrapper (#1795) (53231a0)

• gffread - properly generate fasta output (#1797) (89ea854)

Performance Improvements

• autobump bio/blast/makeblastdb (#1786) (a5db830)

• autobump bio/bwa-mem2/mem (#1826) (37665c1)

• autobump bio/bwa-memx/mem (#1802) (9ceb997)

• autobump bio/bwa/samse (#1831) (8f93262)

• autobump bio/bwa/samxe (#1833) (95799fc)

• autobump bio/deeptools/alignmentsieve (#1790) (cfa4cf7)

• autobump bio/deeptools/alignmentsieve (#1832) (2623b3a)

• autobump bio/deeptools/computematrix (#1784) (ccb2958)

• autobump bio/deeptools/plotcoverage (#1815) (693e904)

• autobump bio/deeptools/plotprofile (#1830) (6f49c46)

• autobump bio/deseq2/wald (#1804) (fbc6345)

• autobump bio/gatk/combinegvcfs (#1817) (1cc8adc)

• autobump bio/gatk3/baserecalibrator (#1792) (7b1b2c3)

• autobump bio/gatk3/indelrealigner (#1835) (3d3d31c)

• autobump bio/gatk3/printreads (#1839) (c1d182a)

• autobump bio/gatk3/realignertargetcreator (#1814) (0936b25)

• autobump bio/gdc-api/bam-slicing (#1806) (f723338)

• autobump bio/igv-reports (#1788) (3ecdb17)

• autobump bio/meryl/count (#1787) (486d99b)

• autobump bio/multiqc (#1811) (221db0b)

• autobump bio/pbmm2/align (#1783) (756a11d)

• autobump bio/pbmm2/index (#1801) (a91b214)

• autobump bio/picard/collectalignmentsummarymetrics (#1803) (3d727b4)

• autobump bio/picard/collectmultiplemetrics (#1791) (a289b27)

• autobump bio/picard/collecttargetedpcrmetrics (#1810) (c64d4fd)

• autobump bio/picard/createsequencedictionary (#1812) (3477e80)

• autobump bio/picard/markduplicates (#1837) (4e6af3d)

• autobump bio/picard/mergesamfiles (#1818) (0768970)

• autobump bio/picard/revertsam (#1825) (042589a)

• autobump bio/picard/samtofastq (#1824) (7a30dd8)

• autobump bio/picard/sortsam (#1819) (a7e1233)

• autobump bio/samtools/idxstats (#1780) (01985b9)

• autobump bio/samtools/merge (#1838) (8a3c3c9)

• autobump bio/seqkit (#1805) (923c7ba)

• autobump bio/spades/metaspades (#1820) (755343f)

• autobump bio/sra-tools/fasterq-dump (#1793) (873937e)

• autobump bio/sra-tools/fasterq-dump (#1813) (ffdb0a4)

• autobump bio/star/align (#1829) (524917b)

• autobump bio/star/index (#1836) (0530063)

• autobump bio/varscan/mpileup2indel (#1821) (cb2adbe)

• autobump bio/varscan/mpileup2snp (#1827) (40545ad)

• autobump bio/varscan/somatic (#1834) (a830aa7)

• autobump bio/vg/construct (#1779) (0a9bf2d)

• autobump bio/vg/ids (#1781) (eb1e70e)

• autobump bio/vg/kmers (#1828) (5903848)

• autobump bio/vg/merge (#1816) (6feb18f)

• autobump bio/vg/sim (#1785) (951ca2f)

2.6.0 (2023-08-25)

Features

• add galah wrapper (#1754) (083688a)

• Enhanced-volcano (#1521) (0bd316d)

• Immunedeconv (#1741) (97b5bde)

Bug Fixes

• Bwa mem threads (#1743) (e35e312)

Performance Improvements

• autobump bio/hifiasm (#1768) (5795e2c)

• autobump bio/sourmash/compute (#1767) (412f289)

• autobump bio/vg/prune (#1769) (fe30289)

• update datavzrd 2.23.8 (#1764) (2f76671)

2.5.0 (2023-08-24)

Features

• bedtools split wrapper (#1744) (bad454d)

Bug Fixes

• ensembl-variation - remove index (#1760) (702a85b)

Performance Improvements

• bump datavzrd to 2.23.6 (#1757) (c500eb9)

• update datavzrd 2.23.7 (#1763) (b19813d)

• update picard markduplicates (#1761) (0c8aad0)

• update snakemake wrapper utils (#1762) (371f337)

• update vep annotate (#1759) (f7e372f)

2.4.0 (2023-08-21)

Features

• Add support for threads to GATK genomicsdbimport (#1742) (b312e5c)

• add test for datavzrd (#1755) (996bdcf)

Performance Improvements

• autobump bio/bcftools/stats (#1751) (56843f8)

• autobump bio/bismark/bismark2bedGraph (#1747) (d954019)

• autobump bio/busco (#1739) (d04d8d7)

• autobump bio/delly (#1735) (479ac84)

• autobump bio/fastqc (#1750) (8856ac6)

• autobump bio/gatk/estimatelibrarycomplexity (#1736) (b318de6)

• autobump bio/gatk3/printreads (#1731) (b6fff95)

• autobump bio/mashmap (#1737) (ae721ec)

• autobump bio/picard/bedtointervallist (#1734) (13e5cad)

• autobump bio/qualimap/rnaseq (#1746) (36835c5)

• autobump bio/samtools/depth (#1738) (5d0f676)

• autobump bio/snpsift/dbnsfp (#1749) (cdfa888)

• autobump bio/sra-tools/fasterq-dump (#1732) (06e7b87)

• autobump bio/vg/kmers (#1752) (cf84881)

• autobump bio/vg/merge (#1748) (78f6716)

• autobump utils/cairosvg (#1733) (3a48cd7)

• bump datavzrd to 2.23.2 (#1729) (55a7066)

• bump datavzrd to 2.23.3 (#1745) (dff136b)

• bump datavzrd to 2.23.4 (#1753) (1b729e1)

2.3.2 (2023-08-07)

Bug Fixes

• fgbio annotatebamwithumis allow multiple umi fastq files (#1726) (101744d)

2.3.1 (2023-08-04)

Performance Improvements

• bump datavzrd to 2.23.1 (#1723) (b0d79d8)

2.3.0 (2023-08-04)

Features

• Bowtie2 meta (#1586) (d8edd7b)

• enable output of unmapped reads (#1549) (bff21bc)

• Gatk calculate contamination (#1547) (4f73135)

Bug Fixes

• freebayes wrapper (#1715) (8656035)

Performance Improvements

• autobump bio/bazam (#1555) (9c5d121)

• autobump bio/bcftools/call (#1691) (c6b88eb)

• autobump bio/bcftools/call (#1710) (7430a6f)

• autobump bio/bcftools/concat (#1531) (d6edd85)

• autobump bio/bcftools/concat (#1603) (5b72872)

• autobump bio/bcftools/concat (#1630) (cd70d77)

• autobump bio/bcftools/concat (#1661) (4455dcc)

• autobump bio/bcftools/concat (#1692) (a7ece62)

• autobump bio/bcftools/filter (#1609) (30d5d64)

• autobump bio/bcftools/filter (#1637) (772a77b)

• autobump bio/bcftools/filter (#1676) (1e69c25)

• autobump bio/bcftools/filter (#1703) (c5224a5)

• autobump bio/bcftools/index (#1537) (d403067)

• autobump bio/bcftools/index (#1602) (45e0d82)

• autobump bio/bcftools/merge (#1558) (18ec70f)

• autobump bio/bcftools/mpileup (#1620) (6bc5006)

• autobump bio/bcftools/mpileup (#1683) (dc033c5)

• autobump bio/bcftools/norm (#1680) (0f32280)

• autobump bio/bcftools/norm (#1706) (6822f7a)

• autobump bio/bcftools/reheader (#1595) (83455a3)

• autobump bio/bcftools/reheader (#1638) (6c63212)

• autobump bio/bcftools/sort (#1575) (92b11ed)

• autobump bio/bcftools/view (#1618) (e7c3390)

• autobump bio/bcftools/view (#1631) (0756847)

• autobump bio/bellerophon (#1614) (d9c9b0b)

• autobump bio/bellerophon (#1646) (5c47391)

• autobump bio/bgzip (#1652) (3cc38ac)

• autobump bio/bismark/bismark2report (#1714) (6d95e56)

• autobump bio/bismark/bismark2summary (#1594) (c7a0448)

• autobump bio/bismark/bismark2summary (#1679) (135dabc)

• autobump bio/bismark/bismark2summary (#1687) (3cf315a)

• autobump bio/bowtie2/align (#1634) (477d1ab)

• autobump bio/bustools/sort (#1688) (7d37969)

• autobump bio/bustools/text (#1523) (08f0e0a)

• autobump bio/bwa-mem2/mem (#1669) (92ba532)

• autobump bio/bwa/mem (#1656) (03224f2)

• autobump bio/dada2/add-species (#1522) (2f2ccc6)

• autobump bio/dada2/assign-species (#1563) (adf781e)

• autobump bio/dada2/assign-taxonomy (#1551) (31c3b9a)

• autobump bio/dada2/collapse-nomismatch (#1554) (db5b2ea)

• autobump bio/dada2/dereplicate-fastq (#1671) (2386b66)

• autobump bio/dada2/filter-trim (#1641) (c58bcfb)

• autobump bio/dada2/learn-errors (#1574) (da832b1)

• autobump bio/dada2/make-table (#1678) (a235b2f)

• autobump bio/dada2/merge-pairs (#1588) (17d69a0)

• autobump bio/dada2/merge-pairs (#1689) (ef65a5f)

• autobump bio/dada2/merge-pairs (#1712) (bc6d079)

• autobump bio/dada2/quality-profile (#1534) (05d12b3)

• autobump bio/dada2/remove-chimeras (#1541) (7282994)

• autobump bio/dada2/sample-inference (#1702) (a82d8fc)

• autobump bio/deeptools/alignmentsieve (#1635) (b01bb82)

• autobump bio/deeptools/plotheatmap (#1561) (faf49e2)

• autobump bio/deseq2/deseqdataset (#1633) (176be53)

• autobump bio/diamond/blastp (#1570) (3f61c8f)

• autobump bio/diamond/blastx (#1670) (0eaf267)

• autobump bio/diamond/makedb (#1711) (e4bc2e4)

• autobump bio/fastqc (#1540) (1e0d23e)

• autobump bio/fgbio/annotatebamwithumis (#1572) (47e4c62)

• autobump bio/fgbio/collectduplexseqmetrics (#1648) (e8fd7f0)

• autobump bio/gatk/applybqsr (#1589) (5ebf186)

• autobump bio/gatk/applybqsrspark (#1578) (007a4d1)

• autobump bio/gatk/applyvqsr (#1544) (0c45d39)

• autobump bio/gatk/baserecalibrator (#1535) (0d006e0)

• autobump bio/gatk/baserecalibrator (#1581) (153b20b)

• autobump bio/gatk/baserecalibratorspark (#1600) (2d5a263)

• autobump bio/gatk/baserecalibratorspark (#1649) (207026c)

• autobump bio/gatk/callcopyratiosegments (#1527) (5a4741a)

• autobump bio/gatk/callcopyratiosegments (#1557) (4c788df)

• autobump bio/gatk/cleansam (#1599) (a58bbfe)

• autobump bio/gatk/cleansam (#1659) (299198f)

• autobump bio/gatk/collectalleliccounts (#1719) (bf74f2f)

• autobump bio/gatk/collectreadcounts (#1684) (dae6459)

• autobump bio/gatk/denoisereadcounts (#1704) (c398633)

• autobump bio/gatk/depthofcoverage (#1601) (45248d4)

• autobump bio/gatk/depthofcoverage (#1667) (7ffe876)

• autobump bio/gatk/filtermutectcalls (#1668) (8924792)

• autobump bio/gatk/filtermutectcalls (#1713) (30c7e9b)

• autobump bio/gatk/genomicsdbimport (#1722) (eef7b43)

• autobump bio/gatk/genotypegvcfs (#1560) (b64e056)

• autobump bio/gatk/haplotypecaller (#1705) (ec9815e)

• autobump bio/gatk/intervallisttobed (#1622) (3d5215d)

• autobump bio/gatk/intervallisttobed (#1647) (e4c13a2)

• autobump bio/gatk/intervallisttobed (#1663) (9654834)

• autobump bio/gatk/intervallisttobed (#1693) (8acf652)

• autobump bio/gatk/learnreadorientationmodel (#1625) (bd0fa42)

• autobump bio/gatk/learnreadorientationmodel (#1653) (c2c64ea)

• autobump bio/gatk/leftalignandtrimvariants (#1639) (c3f89ea)

• autobump bio/gatk/leftalignandtrimvariants (#1697) (c4b738a)

• autobump bio/gatk/markduplicatesspark (#1467) (1d383b7)

• autobump bio/gatk/modelsegments (#1543) (f26ea4a)

• autobump bio/gatk/modelsegments (#1611) (77ff014)

• autobump bio/gatk/mutect (#1526) (4789991)

• autobump bio/gatk/mutect (#1696) (666ba69)

• autobump bio/gatk/printreadsspark (#1699) (1aee674)

• autobump bio/gatk/scatterintervalsbyns (#1597) (214c231)

• autobump bio/gatk/scatterintervalsbyns (#1682) (42e0238)

• autobump bio/gatk/selectvariants (#1695) (fb5b42d)

• autobump bio/gatk/splitintervals (#1591) (67ccba6)

• autobump bio/gatk/splitncigarreads (#1536) (68b02fe)

• autobump bio/gatk/splitncigarreads (#1562) (c27f4a6)

• autobump bio/gatk/variantannotator (#1582) (2b41efe)

• autobump bio/gatk/varianteval (#1545) (1b70868)

• autobump bio/gatk/varianteval (#1619) (78c57d1)

• autobump bio/gatk/varianteval (#1677) (29eb05c)

• autobump bio/gatk/variantfiltration (#1577) (0dabdf1)

• autobump bio/gatk/variantstotable (#1539) (00d5abd)

• autobump bio/gatk/variantstotable (#1559) (eba4873)

• autobump bio/gatk3/baserecalibrator (#1642) (782593d)

• autobump bio/gatk3/indelrealigner (#1636) (ab6be44)

• autobump bio/gatk3/realignertargetcreator (#1587) (1e320ac)

• autobump bio/gatk3/realignertargetcreator (#1650) (66bfa88)

• autobump bio/gdc-api/bam-slicing (#1552) (9760140)

• autobump bio/gdc-api/bam-slicing (#1627) (14ff838)

• autobump bio/genomepy (#1542) (f615808)

• autobump bio/hifiasm (#1672) (7ad6d77)

• autobump bio/hifiasm (#1694) (a99f0ef)

• autobump bio/jannovar (#1640) (cf6d9d4)

• autobump bio/kallisto/index (#1708) (a84c0ab)

• autobump bio/kallisto/quant (#1629) (d076334)

• autobump bio/last/lastal (#1666) (1aababe)

• autobump bio/last/lastal (#1709) (fa7a100)

• autobump bio/macs2/callpeak (#1662) (e175ce2)

• autobump bio/mashmap (#1474) (bf67fcd)

• autobump bio/minimap2/aligner (#1592) (c2c611c)

• autobump bio/mosdepth (#1720) (828f780)

• autobump bio/nonpareil/infer (#1606) (a19604d)

• autobump bio/nonpareil/infer (#1681) (e81c291)

• autobump bio/nonpareil/infer (#1701) (0fa0b21)

• autobump bio/open-cravat/module (#1664) (58047f7)

• autobump bio/open-cravat/run (#1596) (acdb91e)

• autobump bio/pbmm2/align (#1553) (03be953)

• autobump bio/picard/addorreplacereadgroups (#1571) (a68069e)

• autobump bio/picard/collectalignmentsummarymetrics (#1716) (f10e617)

• autobump bio/picard/collectgcbiasmetrics (#1660) (aa83b56)

• autobump bio/picard/collecthsmetrics (#1565) (58ebb45)

• autobump bio/picard/collectinsertsizemetrics (#1616) (83bbae5)

• autobump bio/picard/collectmultiplemetrics (#1533) (6163ba6)

• autobump bio/picard/collectmultiplemetrics (#1579) (0009a9b)

• autobump bio/picard/collectrnaseqmetrics (#1567) (8d6a569)

• autobump bio/picard/collecttargetedpcrmetrics (#1584) (60c1626)

• autobump bio/picard/createsequencedictionary (#1643) (ddb979d)

• autobump bio/picard/mergesamfiles (#1690) (cf90f0d)

• autobump bio/picard/mergevcfs (#1718) (4681800)

• autobump bio/picard/revertsam (#1580) (8c9aa09)

• autobump bio/picard/samtofastq (#1569) (9157dea)

• autobump bio/picard/sortsam (#1530) (075a64f)

• autobump bio/pretext/map (#1721) (b13f290)

• autobump bio/pyroe/makesplicedintronic (#1564) (de214c6)

• autobump bio/pyroe/makeunspliceunspliced (#1566) (422e811)

• autobump bio/qualimap/bamqc (#1621) (6806b8a)

• autobump bio/salmon/index (#1532) (dad1a25)

• autobump bio/samtools/calmd (#1576) (76c7661)

• autobump bio/samtools/faidx (#1698) (665c9c4)

• autobump bio/samtools/fastx (#1644) (26fef49)

• autobump bio/samtools/fixmate (#1686) (3de2261)

• autobump bio/samtools/flagstat (#1612) (85c89a1)

• autobump bio/samtools/sort (#1528) (11453ad)

• autobump bio/samtools/sort (#1707) (2a9efe5)

• autobump bio/samtools/stats (#1615) (6b1bb79)

• autobump bio/samtools/stats (#1628) (6895834)

• autobump bio/samtools/stats (#1674) (7bd8a71)

• autobump bio/samtools/view (#1525) (2755074)

• autobump bio/samtools/view (#1608) (f582deb)

• autobump bio/seqkit (#1610) (cabdc5a)

• autobump bio/seqkit (#1673) (13261f8)

• autobump bio/seqtk/mergepe (#1585) (c671e66)

• autobump bio/snpeff/annotate (#1624) (34a1005)

• autobump bio/snpeff/annotate (#1685) (a7b797d)

• autobump bio/snpeff/download (#1626) (9a649d3)

• autobump bio/snpsift/annotate (#1593) (bc9c1a6)

• autobump bio/snpsift/annotate (#1645) (be76f44)

• autobump bio/snpsift/annotate (#1675) (baee34b)

• autobump bio/snpsift/gwascat (#1613) (1764ca5)

• autobump bio/snpsift/gwascat (#1657) (8cc8988)

• autobump bio/snpsift/varType (#1583) (ad5d062)

• autobump bio/sra-tools/fasterq-dump (#1655) (ceb9ed8)

• autobump bio/tabix/index (#1658) (3bcd66d)

• autobump bio/transdecoder/longorfs (#1617) (39bb6fc)

• autobump bio/transdecoder/predict (#1568) (1d19059)

• autobump bio/tximport (#1632) (bbbb631)

• autobump bio/varscan/mpileup2indel (#1556) (5d4f281)

• autobump bio/varscan/mpileup2snp (#1665) (4171043)

• autobump bio/varscan/somatic (#1598) (0a86cbc)

• autobump bio/vembrane/filter (#1623) (47e6d58)

• autobump bio/vembrane/table (#1605) (9c616da)

• autobump bio/vep/cache (#1604) (1681978)

• autobump bio/vg/construct (#1529) (6206f18)

• autobump bio/vg/sim (#1573) (7c2b587)

• autobump bio/vsearch (#1590) (ed2e49b)

• autobump bio/vsearch (#1700) (92f42fc)

• autobump utils/datavzrd (#1538) (10a6b0b)

• autobump utils/datavzrd (#1717) (3ab8832)

• set version for coolpuppy and update versions for some cooltools wrappers (#1546) (41ef6d0)

2.2.1 (2023-07-07)

Performance Improvements

• autobump bio/bcftools/call (#1508) (4732e05)

• autobump bio/bismark/bismark_genome_preparation (#1512) (531493a)

• autobump bio/bustools/count (#1516) (4f3925a)

• autobump bio/delly (#1505) (6b12ad1)

• autobump bio/deseq2/wald (#1510) (3ab5304)

• autobump bio/gatk/getpileupsummaries (#1506) (ed84924)

• autobump bio/gatk/haplotypecaller (#1504) (b45b7fd)

• autobump bio/gatk/selectvariants (#1501) (8557991)

• autobump bio/picard/collectinsertsizemetrics (#1517) (b9749bb)

• autobump bio/picard/markduplicates (#1511) (6e4f778)

• autobump bio/salmon/quant (#1513) (a2c9c37)

• autobump bio/snpeff/annotate (#1507) (b0acd16)

• autobump bio/snpsift/genesets (#1514) (41edbc7)

• autobump bio/subread/featurecounts (#1509) (83256f1)

• autobump bio/trinity (#1503) (84c1bef)

• autobump bio/tximport (#1520) (26e8842)

• autobump bio/vg/merge (#1515) (a85a6c9)

• autobump bio/vg/prune (#1519) (93099d3)

2.2.0 (2023-07-06)

Features

• Deseq2 wald (#1428) (e0d2831)

• Pyroe id-to-name (#1499) (6e1d31d)

2.1.1 (2023-06-30)

Bug Fixes

• bug with -O being used for gap opening penalty and samtools output directory (#1450) (c3f227f)

Performance Improvements

• autobump bio/bcftools/mpileup (#1483) (438c39b)

• autobump bio/bcftools/view (#1469) (1025cee)

• autobump bio/bedtools/coveragebed (#1487) (b9b6123)

• autobump bio/bismark/bam2nuc (#1491) (b7fe91a)

• autobump bio/diamond/makedb (#1495) (5885a0e)

• autobump bio/freebayes (#1478) (dd4c02b)

• autobump bio/gatk/applybqsr (#1470) (7aca9d9)

• autobump bio/gatk/estimatelibrarycomplexity (#1484) (b06df5f)

• autobump bio/gatk/genomicsdbimport (#1492) (826e722)

• autobump bio/gatk/intervallisttobed (#1473) (214dd6b)

• autobump bio/gatk/learnreadorientationmodel (#1494) (e2623fd)

• autobump bio/gatk/splitintervals (#1481) (444dda4)

• autobump bio/gatk/variantannotator (#1489) (03b3fb5)

• autobump bio/gatk/variantrecalibrator (#1496) (3748dec)

• autobump bio/minimap2/aligner (#1477) (75c6265)

• autobump bio/picard/collectalignmentsummarymetrics (#1475) (06e9c4b)

• autobump bio/picard/mergevcfs (#1465) (dbbc182)

• autobump bio/pretext/map (#1493) (7fcae7f)

• autobump bio/qualimap/bamqc (#1471) (4fe5fdc)

• autobump bio/samtools/depth (#1486) (6d23daf)

• autobump bio/samtools/stats (#1468) (adc059b)

• autobump bio/snpsift/annotate (#1480) (a60f667)

• autobump bio/snpsift/dbnsfp (#1490) (8e8af31)

• autobump bio/varscan/mpileup2indel (#1472) (c0a7c47)

• autobump bio/varscan/mpileup2snp (#1476) (a439e5f)

• autobump bio/varscan/somatic (#1482) (18671ad)

• autobump bio/vg/kmers (#1479) (aa00d14)

• autobump bio/xsv (#1485) (a0baa27)

• update datavzrd (#1497) (143a9c8)

2.1.0 (2023-06-29)

Features

• barrnap-wrapper (#1448) (34e4e2c)

• Xsv (complete subcomand suite) (#1430) (da81a5a)

Bug Fixes

• add threads to trim_galore (#1452) (96a3958)

• inconsistent output filenames trim-galore (#1451) (b915e37)

• Nonpareil tweaks (#1449) (b32b341)

Performance Improvements

• autobump bio/bedtools/bamtobed (#1462) (fafb668)

• autobump bio/benchmark/chm-eval-sample (#1438) (3e62178)

• autobump bio/bismark/bismark (#1445) (2110b31)

• autobump bio/bismark/deduplicate_bismark (#1460) (e19ac1c)

• autobump bio/blast/makeblastdb (#1439) (477dc3f)

• autobump bio/cutadapt/se (#1436) (f0b1c63)

• autobump bio/deeptools/plotcoverage (#1443) (369bf8c)

• autobump bio/deeptools/plotprofile (#1461) (7d378c1)

• autobump bio/deseq2/deseqdataset (#1447) (969113f)

• autobump bio/fastp (#1456) (deea9b6)

• autobump bio/gatk/variantstotable (#1459) (d942d2b)

• autobump bio/gatk3/indelrealigner (#1437) (11b52bf)

• autobump bio/hap.py/hap.py (#1435) (2669467)

• autobump bio/minimap2/index (#1433) (77c690d)

• autobump bio/pbmm2/index (#1442) (cbbe8b8)

• autobump bio/pyroe/makesplicedintronic (#1382) (2509e69)

• autobump bio/spades/metaspades (#1463) (064acf8)

• autobump bio/ucsc/bedGraphToBigWig (#1441) (a587628)

• autobump bio/ucsc/twoBitInfo (#1458) (ba6cba8)

• autobump bio/unicycler (#1446) (2edc574)

• autobump bio/vembrane/filter (#1444) (59a0c94)

• autobump bio/vembrane/table (#1457) (058f164)

• autobump bio/vep/plugins (#1440) (37ad96d)

• autobump bio/vg/ids (#1454) (bfc78d2)

• autobump utils/cairosvg (#1455) (326e20b)

2.0.0 (2023-06-13)

⚠ BREAKING CHANGES

• replace individual seqkit wrappers with a single wrapper for all seqkit commands (#1426)

Features

• remove existing run directory option for strelka (#1297) (6f384dd)

• replace individual seqkit wrappers with a single wrapper for all seqkit commands (#1426) (c7a4d96)

Performance Improvements

• update datavzrd to 2.21.0 (#1424) (c7d757a)

1.32.1 (2023-06-09)

Performance Improvements

• autobump bio/bedtools/slop (#1419) (68c27c9)

• autobump bio/bismark/bismark_methylation_extractor (#1418) (fa75c52)

• autobump bio/blast/blastn (#1416) (9a73c52)

• autobump bio/freebayes (#1420) (3d8a9ef)

• autobump bio/gatk/cleansam (#1421) (bcbbcee)

• autobump bio/hap.py/pre.py (#1414) (307bd02)

• autobump bio/open-cravat/run (#1413) (58c1065)

• autobump bio/seqtk/seq (#1423) (cc1a6bf)

• autobump bio/tximport (#1422) (7557c08)

• autobump bio/vg/kmers (#1417) (0d849eb)

1.32.0 (2023-06-07)

Features

• add ragtag wrapper (#1397) (6a967c5)

• add wrapper to plot nonpareil results (#1398) (1b31bd5)

Bug Fixes

• bug with SE reads (#1395) (f44c6a0)

• fastqc doesn’t know how to process multiple files. (#1327) (b5b9878)

• indexed bam files can now be put as input (#1378) (7c53b89)

Performance Improvements

• autobump bio/bcftools/filter (#1383) (dab7630)

• autobump bio/bcftools/view (#1394) (8a8d877)

• autobump bio/bedtools/complement (#1392) (7284ac2)

• autobump bio/bedtools/intersect (#1403) (6a839c1)

• autobump bio/bustools/sort (#1411) (54e2956)

• autobump bio/bwa-mem2/mem (#1389) (9a5828c)

• autobump bio/bwa/samse (#1405) (476f722)

• autobump bio/cutadapt/pe (#1401) (38dfed4)

• autobump bio/deeptools/bamcoverage (#1409) (426852b)

• autobump bio/deeptools/computematrix (#1373) (6f3e9b5)

• autobump bio/deseq2/deseqdataset (#1369) (8ca67e8)

• autobump bio/fastq_screen (#1375) (abb82c4)

• autobump bio/gatk/learnreadorientationmodel (#1407) (614f343)

• autobump bio/gatk/scatterintervalsbyns (#1387) (61944c3)

• autobump bio/gatk/selectvariants (#1376) (e2962a1)

• autobump bio/gatk/variantrecalibrator (#1374) (341ccaa)

• autobump bio/gatk3/indelrealigner (#1371) (6ef06a1)

• autobump bio/hisat2/index (#1370) (b5e37ab)

• autobump bio/last/lastdb (#1400) (db60b46)

• autobump bio/open-cravat/module (#1399) (fc2b86a)

• autobump bio/paladin/index (#1379) (598d8e7)

• autobump bio/picard/bedtointervallist (#1408) (b0f6786)

• autobump bio/picard/revertsam (#1384) (007cbd1)

• autobump bio/pyroe/makeunspliceunspliced (#1406) (61d8377)

• autobump bio/samtools/sort (#1410) (935a677)

• autobump bio/snpsift/annotate (#1390) (f59bb6b)

• autobump bio/spades/metaspades (#1385) (df5c0d1)

• autobump bio/sra-tools/fasterq-dump (#1380) (8b007a5)

• autobump bio/strling/merge (#1404) (f62427b)

• autobump bio/ucsc/faToTwoBit (#1388) (8356b4f)

• autobump bio/ucsc/gtfToGenePred (#1391) (32aa42f)

• autobump bio/ucsc/twoBitToFa (#1393) (ae1453a)

• autobump bio/vep/annotate (#1386) (3365493)

• autobump bio/vg/construct (#1381) (0785aac)

• autobump bio/vg/ids (#1354) (3743f2e)

• autobump bio/vg/prune (#1377) (7dc7890)

• autobump bio/vg/sim (#1402) (3bf4bf7)

1.31.1 (2023-05-17)

Bug Fixes

• fix snpsift annotate output compression (bcf and vcf.gz) (#1367) (7b46592)

1.31.0 (2023-05-16)

Features

• add nonpareil wrapper (#1294) (53318ed)

Bug Fixes

• removed unnecessary dependencies (#1366) (4262cea)

1.30.0 (2023-05-12)

Features

• add memory inference to samtools sort (#1208) (d70a806)

• deeptools bamcoverage (#1237) (ee2413b)

• deeptools plotcoverage (#1241) (d08e4c6)

• DeseqDataSet from multiple input (#1326) (25d8a07)

• Gffread (#1291) (d613ddf)

• Salmon-Tximport meta-wrapper (#1270) (1e31da2)

Bug Fixes

• auto memory calculation (#1210) (b08081f)

• ensembl annotation GRCh37 gft release (#1296) (d5be001)

• fixed bug when formatting string in GATK denoisereadcounts (#1343) (8cc5d91)

Performance Improvements

• autobump bio/bcftools/call (#1349) (064d4a4)

• autobump bio/bcftools/reheader (#1362) (bc4bb1d)

• autobump bio/bcftools/stats (#1361) (444b198)

• autobump bio/bedtools/genomecov (#1351) (f39d37d)

• autobump bio/bedtools/merge (#1348) (46ba353)

• autobump bio/bedtools/sort (#1357) (e17cb5a)

• autobump bio/bismark/bam2nuc (#1341) (ce2b39e)

• autobump bio/bismark/bismark2report (#1334) (d497124)

• autobump bio/bowtie2/align (#1356) (0e6cc68)

• autobump bio/busco (#1359) (41f1185)

• autobump bio/bwa/samxe (#1335) (8042216)

• autobump bio/deeptools/plotfingerprint (#1345) (39f88b7)

• autobump bio/gatk/applybqsr (#1339) (ec62a41)

• autobump bio/gatk/splitncigarreads (#1350) (7a7eb1e)

• autobump bio/gatk/variantfiltration (#1340) (d108c9c)

• autobump bio/manta (#1342) (a23858a)

• autobump bio/minimap2/aligner (#1329) (45c53eb)

• autobump bio/open-cravat/run (#1330) (fc82508)

• autobump bio/picard/addorreplacereadgroups (#1333) (d273596)

• autobump bio/picard/collectinsertsizemetrics (#1352) (ae1e2bd)

• autobump bio/rasusa (#1353) (3c41241)

• autobump bio/samtools/fastx (#1347) (d6e6329)

• autobump bio/seqkit/fx2tab (#1338) (53922ca)

• autobump bio/snpeff/annotate (#1363) (9ba0b3d)

• autobump bio/snpeff/download (#1358) (2c5a385)

• autobump bio/sourmash/compute (#1360) (1ec19c2)

• autobump bio/sra-tools/fasterq-dump (#1355) (d1118bd)

• autobump bio/tabix/index (#1336) (dfab9c6)

• autobump bio/vembrane/table (#1337) (953c0dc)

• autobump bio/vep/plugins (#1346) (887ba11)

• autobump bio/vg/sim (#1332) (91574fd)

1.29.0 (2023-05-04)

Features

• Add seqkit subseq (#1318) (262d9bb)

• Deeptools Alignement seive (#1320) (b7cb7ab)

• fix threads and new IO options in Bowtie2 (#1324) (a9c7117)

• gatk CallCopyRatioSegments (#1323) (528c91a)

• gatk collectalleliccount wrapper (#1316) (158c328)

• gatk collectreadcount wrapper (#1315) (ee55de4)

• gatk DenoisedReadCounts wrapper (#1319) (0288ace)

• gatk modelsegments wrapper (#1321) (dfecc26)

• Pyroe make-spliced+unspliced (#1290) (96a2cbb)

Bug Fixes

• Lofreq indelqual (#1325) (dabecf0)

Performance Improvements

• Updated version of datavzrd to 2.19.1 (#1328) (fd89645)

1.28.0 (2023-04-28)

Features

• Pyroe make-spliced+intronic (#1288) (352d6f3)

Performance Improvements

• autobump bio/bbtools/loglog (#1304) (9316253)

• autobump bio/bismark/bismark (#1303) (fa68ba8)

• autobump bio/fgbio/annotatebamwithumis (#1312) (13cb583)

• autobump bio/gatk/intervallisttobed (#1305) (d895b8f)

• autobump bio/minimap2/index (#1308) (a578d2f)

• autobump bio/paladin/prepare (#1299) (1e27b4c)

• autobump bio/picard/mergevcfs (#1307) (7a8a8aa)

• autobump bio/qualimap/rnaseq (#1306) (0ba2d3e)

• autobump bio/samtools/merge (#1300) (69332cd)

• autobump bio/samtools/mpileup (#1310) (f72ccf0)

• autobump bio/seqkit/grep (#1301) (dfa1f4d)

• autobump bio/snpsift/dbnsfp (#1309) (007437e)

• autobump bio/vembrane/filter (#1311) (15dc129)

• update datavzrd to 2.18.5 (#1313) (0089e88)

1.27.0 (2023-04-26)

Features

• Update datavzrd to 2.18.4 and add extra params (#1292) (fa11c1c)

1.26.0 (2023-04-21)

Features

• added vsearch wrapper (#1149) (79342b7)

• also define overhang on params.extra (#1173) (7e63821)

• automate inference of index name (#1169) (0d2c92a)

• Enhance deeptools compute matrix (#1236) (a44bef5)

• Lofreq indelqual wrapper (#1166) (e2215f2)

• update datavzrd 2.18.1 (#1171) (00b9b1c)

Bug Fixes

• allow for arbitrary filename prefixes in the optitype wrapper (#500) (0bf7175)

Performance Improvements

• autobump bio/bazam (#1187) (df7d90e)

• autobump bio/bbtools/bbduk (#1269) (86c7a0a)

• autobump bio/bcftools/call (#1181) (7fbc611)

• autobump bio/bcftools/concat (#1183) (93d7103)

• autobump bio/bcftools/index (#1279) (3affe33)

• autobump bio/bcftools/merge (#1266) (b0a2c88)

• autobump bio/bcftools/norm (#1192) (9e06c59)

• autobump bio/bcftools/norm (#1212) (3667c6b)

• autobump bio/bcftools/sort (#1257) (dd478d2)

• autobump bio/bcftools/stats (#1197) (c844da5)

• autobump bio/bellerophon (#1199) (a2fe593)

• autobump bio/bellerophon (#1286) (2a21d19)

• autobump bio/bismark/bismark_genome_preparation (#1276) (5074972)

• autobump bio/bismark/bismark_methylation_extractor (#1220) (05964de)

• autobump bio/bismark/bismark2bedGraph (#1258) (3eb60c2)

• autobump bio/bismark/bismark2summary (#1235) (74a9de2)

• autobump bio/bowtie2/align (#1206) (d3544b0)

• autobump bio/busco (#1255) (402aaaa)

• autobump bio/bwa-mem2/mem (#1202) (90e1d60)

• autobump bio/bwa-meme/index (#1180) (1f0378c)

• autobump bio/bwa-meme/mem (#1163) (5236667)

• autobump bio/bwa-meme/mem (#1231) (1ad2b8d)

• autobump bio/bwa-memx/index (#1207) (59be498)

• autobump bio/bwa-memx/mem (#1268) (a2fe8b9)

• autobump bio/bwa/sampe (#1225) (d759781)

• autobump bio/cutadapt/pe (#1219) (44f346e)

• autobump bio/cutadapt/se (#1253) (95c8278)

• autobump bio/delly (#1267) (75a0d1a)

• autobump bio/diamond/blastp (#1161) (1f89877)

• autobump bio/diamond/blastx (#1221) (480fc20)

• autobump bio/diamond/makedb (#1223) (49d1484)

• autobump bio/fgbio/collectduplexseqmetrics (#1201) (04e4ec7)

• autobump bio/gatk/applybqsrspark (#1194) (65f53d8)

• autobump bio/gatk/applybqsrspark (#1250) (56efdd1)

• autobump bio/gatk/applyvqsr (#1274) (8b8d890)

• autobump bio/gatk/baserecalibrator (#1249) (788ed8f)

• autobump bio/gatk/baserecalibratorspark (#1185) (f5a5f47)

• autobump bio/gatk/combinegvcfs (#1261) (bd3066a)

• autobump bio/gatk/estimatelibrarycomplexity (#1252) (12f5440)

• autobump bio/gatk/filtermutectcalls (#1155) (0071533)

• autobump bio/gatk/filtermutectcalls (#1195) (7f05ddf)

• autobump bio/gatk/genomicsdbimport (#1215) (300dbe8)

• autobump bio/gatk/genotypegvcfs (#1179) (85758b7)

• autobump bio/gatk/getpileupsummaries (#1277) (2239049)

• autobump bio/gatk/haplotypecaller (#1256) (5caa178)

• autobump bio/gatk/learnreadorientationmodel (#1158) (97cd747)

• autobump bio/gatk/leftalignandtrimvariants (#1205) (377f253)

• autobump bio/gatk/markduplicatesspark (#1224) (0893b4e)

• autobump bio/gatk/mutect (#1262) (a01e719)

• autobump bio/gatk/splitintervals (#1188) (2d610dd)

• autobump bio/gatk/variantannotator (#1160) (f7001e2)

• autobump bio/gatk/variantannotator (#1282) (a158262)

• autobump bio/gatk3/baserecalibrator (#1273) (63e7ae2)

• autobump bio/gatk3/printreads (#1174) (22f8e69)

• autobump bio/gatk3/printreads (#1217) (5d05b88)

• autobump bio/gdc-api/bam-slicing (#1159) (96a1a42)

• autobump bio/hisat2/align (#1281) (a9edff7)

• autobump bio/homer/makeTagDirectory (#1246) (44847e2)

• autobump bio/last/lastal (#1165) (ca0d13f)

• autobump bio/last/lastdb (#1254) (2f11b1e)

• autobump bio/lofreq/call (#1156) (c750bbf)

• autobump bio/lofreq/call (#1275) (e2c4dc2)

• autobump bio/lofreq/indelqual (#1283) (9730460)

• autobump bio/mashmap (#1244) (fad0092)

• autobump bio/microphaser/filter (#1164) (8932d38)

• autobump bio/minimap2/aligner (#1177) (07f4e02)

• autobump bio/open-cravat/module (#1232) (be62998)

• autobump bio/paladin/align (#1234) (df3c213)

• autobump bio/picard/collectalignmentsummarymetrics (#1175) (856224a)

• autobump bio/picard/collectgcbiasmetrics (#1247) (202ab81)

• autobump bio/picard/collecthsmetrics (#1198) (874fc3f)

• autobump bio/picard/collectinsertsizemetrics (#1190) (543540a)

• autobump bio/picard/collectmultiplemetrics (#1284) (1e90009)

• autobump bio/picard/collecttargetedpcrmetrics (#1203) (7e55cfc)

• autobump bio/picard/markduplicates (#1233) (1708e12)

• autobump bio/picard/mergesamfiles (#1176) (554f501)

• autobump bio/picard/samtofastq (#1218) (da9e010)

• autobump bio/picard/sortsam (#1248) (4cf9fdd)

• autobump bio/pretext/map (#1227) (fafa6ee)

• autobump bio/qualimap/bamqc (#1251) (4dc2495)

• autobump bio/rbt/csvreport (#1243) (25acb2f)

• autobump bio/reference/ensembl-variation (#1265) (ede45c7)

• autobump bio/samtools/faidx (#1182) (c223f0c)

• autobump bio/samtools/faidx (#1287) (511d539)

• autobump bio/samtools/fixmate (#1264) (f42a717)

• autobump bio/samtools/flagstat (#1184) (4f5349c)

• autobump bio/samtools/flagstat (#1280) (5fbbbbf)

• autobump bio/samtools/idxstats (#1193) (f930f9e)

• autobump bio/samtools/idxstats (#1259) (c6b3b40)

• autobump bio/samtools/index (#1214) (a1ca2a1)

• autobump bio/samtools/stats (#1222) (0eb7652)

• autobump bio/seqkit/rmdup (#1162) (88f74d4)

• autobump bio/seqkit/stats (#1213) (523b69b)

• autobump bio/snpeff/annotate (#1189) (d873ee8)

• autobump bio/snpsift/annotate (#1204) (8c069ff)

• autobump bio/snpsift/genesets (#1245) (a2649a7)

• autobump bio/snpsift/gwascat (#1191) (0c3c051)

• autobump bio/snpsift/gwascat (#1211) (53d82b9)

• autobump bio/snpsift/varType (#1196) (75bd430)

• autobump bio/snpsift/varType (#1196) (eaee058)

• autobump bio/strling/call (#1216) (fa539be)

• autobump bio/strling/extract (#1272) (128d8b9)

• autobump bio/strling/index (#1228) (6cc0059)

• autobump bio/tximport (#1278) (f309cb9)

• autobump bio/umis/bamtag (#1260) (1334743)

• autobump bio/varscan/mpileup2indel (#1186) (72816c8)

• autobump bio/varscan/mpileup2snp (#1230) (0266507)

• autobump bio/varscan/somatic (#1178) (1882608)

• autobump bio/vembrane/filter (#1229) (1a30d43)

• autobump bio/vep/plugins (#1200) (a7909be)

• autobump bio/vg/construct (#1226) (4b2745f)

• autobump bio/vg/ids (#1285) (8ffb3ea)

• autobump bio/vg/prune (#1263) (8a36dec)

• bump Salmon to v1.10.1 (#1168) (a718777)

1.25.0 (2023-03-23)

Features

• added several Seqkit wrappers (#1128) (9c4e667)

• added wrapper for loglog (#1154) (08917f9)

• added wrapper for tadpole (#1152) (cb1372b)

• Merqury (#540) (f7914c4)

• Mutect2 additional parameters (#516) (f2b70ca)

Bug Fixes

• use new java memory overhead utils (#1150) (d15d5f5)

Performance Improvements

• autobump bio/bcftools/filter (#646) (b7b98fd)

• autobump bio/bismark/deduplicate_bismark (#1141) (45cd1a6)

• autobump bio/cooltools/dots (#702) (7ac6569)

• autobump bio/fgbio/collectduplexseqmetrics (#1100) (ae2a295)

• autobump bio/gatk/markduplicatesspark (#1142) (190dd18)

• autobump bio/gridss/preprocess (#800) (71463ad)

• autobump bio/gridss/setupreference (#848) (c2f9766)

• autobump bio/hisat2/align (#1079) (dea181a)

• autobump bio/liftoff (#953) (0928808)

• autobump bio/lofreq/call (#1120) (a327d86)

• autobump bio/muscle (#612) (659d106)

• autobump bio/snpeff/annotate (#1038) (5628ccd)

• autobump bio/subread/featurecounts (#1044) (b7d7ed4)

• autobump bio/trinity (#634) (d084304)

• autobump bio/vep/cache (#1132) (d8c3faa)

1.24.0 (2023-03-17)

Features

• allowed strelka germline using multiple bam (#1092) (422e849)

• BWA-MEME Version 1.0.6 update (#1123) (7422b0b)

• update arriba to 2.4.0 (#1148) (eda64d8)

Bug Fixes

• Add tests to Sickle and fixed typo (#1126) (02518ff)

Performance Improvements

• autobump bio/bgzip (#1140) (f0e1aa4)

• autobump bio/bismark/bam2nuc (#1099) (fd24a3d)

• autobump bio/bismark/bismark2summary (#1105) (e8ec077)

• autobump bio/bustools/text (#1107) (c280d8b)

• autobump bio/bwa-mem2/mem (#1130) (25a44a5)

• autobump bio/bwa-memx/mem (#1108) (75964c1)

• autobump bio/bwa-memx/mem (#1145) (2bf0fee)

• autobump bio/bwa/samse (#1119) (c591284)

• autobump bio/cooltools/expected_cis (#1098) (a642717)

• autobump bio/cooltools/saddle (#1138) (0108e6d)

• autobump bio/cutadapt/pe (#1006) (ab85e5d)

• autobump bio/diamond/blastp (#1114) (0aeb9b2)

• autobump bio/diamond/blastx (#1122) (1638662)

• autobump bio/diamond/makedb (#1111) (b17ff0a)

• autobump bio/fastqc (#1147) (e0efb68)

• autobump bio/fgbio/callmolecularconsensusreads (#1101) (2a0a77d)

• autobump bio/genomepy (#1137) (ab85927)

• autobump bio/kallisto/index (#1005) (17613e6)

• autobump bio/last/lastal (#1143) (c0443b1)

• autobump bio/last/lastdb (#1110) (905a6e6)

• autobump bio/last/lastdb (#1121) (394942a)

• autobump bio/mlst (#1117) (c97bae1)

• autobump bio/multiqc (#1104) (2a4894e)

• autobump bio/picard/addorreplacereadgroups (#1115) (7748621)

• autobump bio/picard/collectalignmentsummarymetrics (#1131) (a9af1d2)

• autobump bio/picard/collectgcbiasmetrics (#1096) (c6896b8)

• autobump bio/picard/collectinsertsizemetrics (#1097) (cb3f91d)

• autobump bio/picard/collectrnaseqmetrics (#1103) (6f53085)

• autobump bio/picard/collecttargetedpcrmetrics (#1102) (b8615ed)

• autobump bio/picard/markduplicateswithmatecigar (#1135) (2f6a0de)

• autobump bio/picard/mergesamfiles (#1109) (155484c)

• autobump bio/picard/mergevcfs (#1095) (7abf5cc)

• autobump bio/picard/samtofastq (#1146) (a670bc5)

• autobump bio/reference/ensembl-variation (#1144) (0a9cdfc)

• autobump bio/salmon/index (#1139) (fdd9619)

• autobump bio/sambamba/sort (#1106) (3f06b9f)

• autobump bio/tabix/query (#1134) (c3249e0)

• autobump bio/trim_galore/pe (#1136) (b10b38f)

• autobump bio/ucsc/gtfToGenePred (#1093) (d145388)

• autobump bio/ucsc/twoBitInfo (#1112) (407f8b3)

• autobump bio/umis/bamtag (#1133) (d58e25c)

• autobump bio/vep/annotate (#1116) (20b9a8d)

• autobump bio/vg/construct (#1118) (622e244)

1.23.5 (2023-02-24)

Bug Fixes

• fixed bug in obtaining paired_end parameter for RSEM calculate-expression (#1075) (8bf224b)

Performance Improvements

• autobump bio/dada2/dereplicate-fastq (#1084) (437f6a8)

• autobump bio/diamond/blastp (#1083) (7a33605)

• autobump bio/fgbio/filterconsensusreads (#1088) (39c3c37)

• autobump bio/fgbio/setmateinformation (#1089) (c50c845)

• autobump bio/jellyfish/dump (#1077) (260ba99)

• autobump bio/last/lastal (#1087) (03401fa)

• autobump bio/last/lastdb (#1091) (8bf8271)

• autobump bio/pbmm2/align (#1086) (3cc3e23)

• autobump bio/picard/collectrnaseqmetrics (#1082) (812a58a)

• autobump bio/picard/collecttargetedpcrmetrics (#1003) (43682ed)

• autobump bio/picard/sortsam (#1081) (176f729)

• autobump bio/star/index (#1090) (9e654cb)

• autobump bio/transdecoder/longorfs (#1080) (d8c37ce)

• autobump bio/transdecoder/predict (#1085) (2ef8d50)

• autobump bio/unicycler (#1078) (3c1770c)

1.23.4 (2023-02-17)

Performance Improvements

• autobump bio/bismark/bismark2bedGraph (#1073) (2766554)

• autobump bio/bismark/bismark2report (#1063) (599ae52)

• autobump bio/bustools/count (#1067) (19154c6)

• autobump bio/cooltools/eigs_cis (#1007) (2742fb7)

• autobump bio/cooltools/pileup (#1058) (127917f)

• autobump bio/dada2/filter-trim (#1065) (677627f)

• autobump bio/fastq_screen (#1060) (14dc0ab)

• autobump bio/fgbio/annotatebamwithumis (#1064) (9ed4c70)

• autobump bio/fgbio/groupreadsbyumi (#1070) (b93045c)

• autobump bio/freebayes (#1055) (7b21acc)

• autobump bio/gdc-api/bam-slicing (#1004) (eae8d4d)

• autobump bio/hifiasm (#1069) (da38102)

• autobump bio/microphaser/normal (#1051) (70cbcc5)

• autobump bio/picard/collecthsmetrics (#1057) (dd3b642)

• autobump bio/picard/collectmultiplemetrics (#1054) (c1c1d02)

• autobump bio/picard/revertsam (#1061) (6b7abe4)

• autobump bio/picard/samtofastq (#1066) (3b269b1)

• autobump bio/sambamba/flagstat (#1068) (8f038a0)

• autobump bio/sambamba/view (#1056) (13ebb41)

• autobump bio/sourmash/compute (#1059) (58d1b56)

• autobump bio/star/align (#1009) (61b9c99)

• autobump bio/umis/bamtag (#1053) (1056357)

• autobump bio/vg/ids (#1052) (f0c864c)

• autobump bio/vg/kmers (#1062) (3c65ce9)

• autobump bio/vg/prune (#1050) (9c0b28d)

• autobump utils/cairosvg (#1072) (b978339)

• autobump utils/datavzrd (#1071) (341cd67)

1.23.3 (2023-02-12)

Performance Improvements

• update datavzrd wrapper to 2.16.2 (a3784ec)

1.23.2 (2023-02-10)

Performance Improvements

• autobump bio/bismark/bismark (#1046) (4c692f6)

• autobump bio/bustools/sort (#1039) (915ff3d)

• autobump bio/bwa-mem2/mem-samblaster (#1035) (68d0b8e)

• autobump bio/cooltools/insulation (#1032) (3ccb3c1)

• autobump bio/dada2/add-species (#1031) (1e84d85)

• autobump bio/dada2/assign-species (#1040) (939fb25)

• autobump bio/dada2/sample-inference (#1043) (8d40576)

• autobump bio/igv-reports (#1029) (a9765ed)

• autobump bio/last/lastal (#1041) (1854b53)

• autobump bio/mapdamage2 (#1045) (dae7008)

• autobump bio/minimap2/aligner (#1033) (c1bbdd8)

• autobump bio/paladin/index (#1036) (0ce4cee)

• autobump bio/picard/markduplicateswithmatecigar (#1042) (19a404b)

• autobump bio/sra-tools/fasterq-dump (#1047) (c74a7c3)

• autobump bio/trim_galore/se (#1034) (daeb43d)

• autobump bio/vg/ids (#1037) (d89576e)

1.23.1 (2023-02-07)

Performance Improvements

• update to datavzrd 2.16.0 (4a988ce)

1.23.0 (2023-02-06)

Features

• Add GATK LeftAlignAndTrimVariants (#993) (4ec0c91)

Performance Improvements

• autobump bio/bismark/bismark_methylation_extractor (#1024) (e6f7f0a)

• autobump bio/bowtie2/build (#1025) (f242c1c)

• autobump bio/bwa/mem-samblaster (#1015) (2ff4af3)

• autobump bio/cooltools/eigs_trans (#1026) (01eb73c)

• autobump bio/cooltools/expected_trans (#995) (080b51d)

• autobump bio/cutadapt/se (#1010) (8cf09dc)

• autobump bio/dada2/quality-profile (#1022) (f077b94)

• autobump bio/deeptools/plotprofile (#1018) (d9d2a69)

• autobump bio/delly (#1000) (f499f25)

• autobump bio/dragmap/build (#1002) (f0e0334)

• autobump bio/gatk/varianteval (#997) (1690ac6)

• autobump bio/gatk3/baserecalibrator (#1016) (3e2bef3)

• autobump bio/gridss/assemble (#998) (fa9002e)

• autobump bio/hmmer/hmmbuild (#1021) (492a0c5)

• autobump bio/microphaser/somatic (#1012) (95854e8)

• autobump bio/paladin/align (#1027) (7ebca79)

• autobump bio/pbmm2/index (#1011) (d170c59)

• autobump bio/picard/addorreplacereadgroups (#1008) (094c52e)

• autobump bio/picard/bedtointervallist (#1019) (284c3ba)

• autobump bio/picard/mergesamfiles (#1014) (ea653db)

• autobump bio/pyfastaq/replace_bases (#1020) (46f165f)

• autobump bio/sambamba/slice (#996) (a3daa64)

• autobump bio/snpsift/gwascat (#1023) (c797edb)

• autobump bio/tximport (#1017) (b4005d1)

• autobump bio/ucsc/gtfToGenePred (#999) (aeb6bd0)

• autobump bio/vg/merge (#1001) (158c387)

• autobump bio/vg/sim (#1013) (94ecd75)

1.22.0 (2023-02-01)

Features

• Add GATK VariantsToTable (#989) (e3654ce)

Bug Fixes

• do not download fasta file in VEP cache wrapper (#992) (612933e)

Performance Improvements

• Sambamba version update 0.8.2->1.0 (#988) (6525373)

1.21.6 (2023-01-30)

Bug Fixes

• properly handle proxy setting in vep cache wrapper (#986) (3a5379b)

1.21.5 (2023-01-30)

Performance Improvements

• autobump bio/sambamba/merge (#982) (701abe0)

• update datavzrd to version 2.14.1 (#985) (07fc839)

1.21.4 (2023-01-20)

Bug Fixes

• channel definitions for cooltools (and update version to 0.5.2), genefuse, genomescope, qualimap and meryl (#980) (26271ac)

• RSEM-calculate-expression wrapper with FASTQ-files as input + Integration of test case (#970) (ea9c897)

1.21.3 (2023-01-20)

Bug Fixes

• consensus meta wrapper (#977) (a320aa5)

• snakemake and mamba deployment (#978) (4c64b96)

1.21.2 (2023-01-10)

Bug Fixes

• make ‘params: extra=’ optional for rbt collapse_reads_to_fragments-bam wrapper (#968) (03463da)

Performance Improvements

• update datavzrd wrapper to 2.12.0 (#973) (8523e73)

1.21.1 (2022-12-21)

Performance Improvements

• update datavzrd wrapper to 2.11.1 (12b3076)

1.21.0 (2022-12-12)

Features

• tmpdir in Sambamba wrappers (#960) (a8333a3)

• update arriba and star_arriba meta-wrapper (#963) (f75d997)

Bug Fixes

• updated parsing of bcftools opts (#959) (0af69c9)

Performance Improvements

• autobump bio/bwa-memx/index (#955) (f51c0d6)

• autobump bio/cooltools/pileup (#948) (bf28d88)

• autobump bio/dada2/assign-taxonomy (#946) (ed9ebfb)

• autobump bio/diamond/makedb (#944) (a95b5db)

• autobump bio/gatk/genotypegvcfs (#951) (5fb96d8)

• autobump bio/gatk/selectvariants (#947) (5f697b8)

• autobump bio/homer/annotatePeaks (#952) (8f1270d)

• autobump bio/homer/mergePeaks (#957) (0330a43)

• autobump bio/jellyfish/count (#950) (0a6f68d)

• autobump bio/last/lastal (#942) (8e5ef69)

• autobump bio/microphaser/build_reference (#943) (1e7ece5)

• autobump bio/picard/collecttargetedpcrmetrics (#949) (5239da9)

• autobump bio/transdecoder/longorfs (#956) (54c2b74)

• autobump bio/tximport (#954) (4942f36)

• autobump bio/varscan/somatic (#958) (28df43c)

1.20.0 (2022-12-01)

Features

• Add threads to cooltools insulation (#919) (fdf035e)

• GATK SplitIntervals wrapper (#836) (986fa3a)

• samtools view allow region specification (#940) (c1fdb5e)

Bug Fixes

• Correct referencing of Snakemake input variables (release: 1.19.2) (#937) (b828ac3)

Performance Improvements

• autobump bio/bowtie2/build (#932) (26bcc0b)

• autobump bio/dada2/learn-errors (#929) (32e9f5c)

• autobump bio/gatk/baserecalibratorspark (#935) (ff15e44)

• autobump bio/gatk/cleansam (#792) (6055e79)

• autobump bio/gatk/estimatelibrarycomplexity (#926) (c366755)

• autobump bio/infernal/cmscan (#924) (36634d9)

• autobump bio/microphaser/somatic (#925) (cb44ee0)

• autobump bio/picard/collectinsertsizemetrics (#934) (fd8fecd)

• autobump bio/picard/collectrnaseqmetrics (#920) (40eccd5)

• autobump bio/pretext/graph (#930) (2a1fb56)

• autobump bio/purge_dups/get_seqs (#922) (ad5fba2)

• autobump bio/samtools/sort (#921) (4dde2ae)

• autobump bio/samtools/view (#936) (24254fd)

• autobump bio/vembrane/filter (#927) (510b06a)

• autobump bio/vep/annotate (#928) (bb30b19)

• autobump bio/vg/kmers (#931) (067b6a8)

• autobump bio/vg/merge (#933) (5ac344d)

• update to latest datavzrd (d08bc08)

1.19.2 (2022-11-18)

Bug Fixes

• Removed unnecessary openjdk references (#835) (0353285)

Performance Improvements

• autobump bio/bismark/bismark (#907) (2c8dc87)

• autobump bio/bwa-meme/mem (#897) (d377cce)

• autobump bio/bwa-memx/mem (#909) (31974b1)

• autobump bio/deeptools/computematrix (#895) (b0b1943)

• autobump bio/deeptools/plotfingerprint (#887) (5157780)

• autobump bio/fastq_screen (#916) (6c62488)

• autobump bio/fgbio/groupreadsbyumi (#908) (caa4b85)

• autobump bio/gatk/depthofcoverage (#905) (8043b30)

• autobump bio/gatk/mutect (#892) (6fcabfa)

• autobump bio/gatk/variantfiltration (#911) (b9cc5d4)

• autobump bio/homer/getDifferentialPeaks (#894) (fba57fa)

• autobump bio/homer/makeTagDirectory (#899) (762aa81)

• autobump bio/last/lastdb (#889) (f3ffc52)

• autobump bio/meryl/count (#896) (c1dea53)

• autobump bio/paladin/prepare (#900) (f06905d)

• autobump bio/pbmm2/index (#893) (7b84d5b)

• autobump bio/picard/mergesamfiles (#906) (c89123b)

• autobump bio/pindel/pindel2vcf (#904) (7582c86)

• autobump bio/qualimap/bamqc (#912) (d73c713)

• autobump bio/qualimap/rnaseq (#914) (43ec0e7)

• autobump bio/rsem/calculate-expression (#915) (4a02028)

• autobump bio/salmon/index (#917) (9a7dd71)

• autobump bio/salmon/quant (#901) (1abf483)

• autobump bio/sambamba/index (#903) (e15388c)

• autobump bio/sambamba/slice (#890) (7d90b49)

• autobump bio/seqtk/mergepe (#910) (374d337)

• autobump bio/snpsift/annotate (#898) (6aabee4)

• autobump bio/snpsift/varType (#902) (c200777)

• autobump bio/vep/plugins (#913) (298ab04)

• autobump bio/vg/kmers (#888) (5570e67)

• autobump bio/vg/sim (#886) (83c3189)

• autobump utils/datavzrd (#891) (4a4e4ce)

1.19.1 (2022-11-11)

Performance Improvements

• autobump bio/bismark/bismark_genome_preparation (#819) (1da1afc)

• autobump bio/bismark/bismark2report (#812) (8ce5b1a)

• autobump bio/bismark/deduplicate_bismark (#816) (7f539c4)

• autobump bio/bowtie2/align (#798) (6fa3cc7)

• autobump bio/bwa-meme/index (#862) (68f9c48)

• autobump bio/bwa-memx/index (#780) (9937924)

• autobump bio/cooltools/eigs_cis (#853) (3973951)

• autobump bio/cooltools/eigs_trans (#777) (348c67d)

• autobump bio/dada2/collapse-nomismatch (#852) (2ab7b64)

• autobump bio/dada2/dereplicate-fastq (#808) (c0692ff)

• autobump bio/dada2/make-table (#796) (a42557f)

• autobump bio/dada2/merge-pairs (#847) (67a8ee6)

• autobump bio/dada2/remove-chimeras (#776) (2da85cc)

• autobump bio/deeptools/plotheatmap (#864) (1eea5f0)

• autobump bio/diamond/blastx (#875) (a503669)

• autobump bio/epic/peaks (#781) (400c8ce)

• autobump bio/fgbio/callmolecularconsensusreads (#826) (194056e)

• autobump bio/fgbio/filterconsensusreads (#801) (491eed9)

• autobump bio/gatk/applybqsr (#803) (d27cc85)

• autobump bio/gatk/applyvqsr (#858) (202ab9f)

• autobump bio/gatk/baserecalibrator (#820) (20e258c)

• autobump bio/gatk/combinegvcfs (#811) (6b27084)

• autobump bio/gatk/filtermutectcalls (#845) (15de736)

• autobump bio/gatk/getpileupsummaries (#866) (ae118d0)

• autobump bio/gatk/learnreadorientationmodel (#854) (82d03d5)

• autobump bio/gatk/splitncigarreads (#790) (a7a890b)

• autobump bio/gatk3/indelrealigner (#827) (a0793af)

• autobump bio/gatk3/printreads (#806) (998852c)

• autobump bio/gatk3/realignertargetcreator (#865) (b76bd75)

• autobump bio/gridss/call (#846) (01b3056)

• autobump bio/hisat2/index (#815) (3c13af5)

• autobump bio/hmmer/hmmpress (#779) (d08c5fd)

• autobump bio/jellyfish/histo (#818) (0dd35bc)

• autobump bio/jellyfish/merge (#861) (278a80e)

• autobump bio/kallisto/quant (#821) (af4128c)

• autobump bio/lofreq/call (#872) (000eb6e)

• autobump bio/macs2/callpeak (#810) (9fe846b)

• autobump bio/meryl/sets (#783) (f8bec12)

• autobump bio/meryl/stats (#785) (bfae5c5)

• autobump bio/microphaser/build_reference (#823) (7a79754)

• autobump bio/msisensor/msi (#850) (7d605a0)

• autobump bio/msisensor/scan (#842) (1db9fe6)

• autobump bio/open-cravat/module (#782) (996fe01)

• autobump bio/open-cravat/run (#807) (70c6500)

• autobump bio/pandora/index (#805) (8c9ea62)

• autobump bio/picard/collecthsmetrics (#788) (0220a41)

• autobump bio/picard/revertsam (#874) (c811ef5)

• autobump bio/picard/sortsam (#822) (30f468d)

• autobump bio/preseq/lc_extrap (#840) (d0ec0bb)

• autobump bio/pretext/map (#841) (0a0193c)

• autobump bio/pretext/snapshot (#843) (4d3a224)

• autobump bio/prosolo/single-cell-bulk (#870) (da52ad6)

• autobump bio/purge_dups/calcuts (#793) (95f421c)

• autobump bio/purge_dups/ngscstat (#791) (a7d6ef9)

• autobump bio/purge_dups/pbcstat (#787) (3775e6a)

• autobump bio/rbt/collapse_reads_to_fragments-bam (#794) (2eb9983)

• autobump bio/rbt/csvreport (#838) (eea403e)

• autobump bio/rsem/generate-data-matrix (#828) (e16d591)

• autobump bio/sambamba/markdup (#814) (0cd1c99)

• autobump bio/sambamba/merge (#839) (b81e778)

• autobump bio/sambamba/sort (#784) (6252efd)

• autobump bio/samtools/faidx (#859) (cbdae53)

• autobump bio/samtools/fastx (#855) (509c570)

• autobump bio/samtools/fixmate (#774) (bb28da9)

• autobump bio/samtools/merge (#844) (5905d2e)

• autobump bio/samtools/mpileup (#829) (d5120cb)

• autobump bio/samtools/stats (#797) (524db3e)

• autobump bio/sickle/se (#786) (ef4a4ad)

• autobump bio/snpeff/download (#851) (3bc7aa5)

• autobump bio/snpsift/dbnsfp (#856) (67ed70a)

• autobump bio/snpsift/genesets (#799) (251fd82)

• autobump bio/sourmash/compute (#795) (e063ce8)

• autobump bio/spades/metaspades (#860) (983754f)

• autobump bio/sra-tools/fasterq-dump (#873) (5914529)

• autobump bio/strelka/somatic (#813) (d52a2ad)

• autobump bio/strling/call (#789) (9fa5f86)

• autobump bio/strling/extract (#876) (45152e6)

• autobump bio/strling/index (#809) (9472934)

• autobump bio/strling/merge (#824) (82cc5a7)

• autobump bio/tabix/index (#863) (9de5e3c)

• autobump bio/tabix/query (#868) (088f3db)

• autobump bio/ucsc/bedGraphToBigWig (#825) (c72f046)

• autobump bio/ucsc/gtfToGenePred (#802) (b306b81)

• autobump bio/varscan/mpileup2snp (#849) (300738b)

• autobump bio/vcftools/filter (#804) (a18db0a)

• autobump bio/vep/annotate (#857) (84bd8bd)

• autobump bio/vep/cache (#741) (ef12aed)

• autobump bio/vg/ids (#871) (10a1c0d)

• autobump bio/vg/merge (#867) (064ca8c)

• autobump bio/vg/prune (#817) (104775a)

1.19.0 (2022-11-08)

Features

• add wrapper for coolpuppy (#554) (60f1fc1)

Bug Fixes

• fixed GATK3 conda channel priorities and code reformat (#534) (43e5a16)

Performance Improvements

• autobump bio/bismark/deduplicate_bismark (#672) (c4ee12f)

• autobump bio/gatk/variantrecalibrator (#773) (8de1652)

• autobump bio/hmmer/hmmscan (#830) (727b385)

• autobump bio/picard/bedtointervallist (#833) (f1faa62)

• autobump bio/picard/collectalignmentsummarymetrics (#831) (c264c15)

• autobump bio/picard/collectinsertsizemetrics (#834) (8381cd8)

• autobump bio/seqtk/seq (#832) (754c4df)

• update datavzrd wrapper to version 2.7.2 (12e47fd)

1.18.3 (2022-10-30)

Performance Improvements

• autobump bio/bwa-memx/mem (#729) (eb4ceba)

• autobump bio/cooltools/expected_cis (#754) (3507020)

• autobump bio/cooltools/expected_trans (#728) (b2b6598)

• autobump bio/cooltools/pileup (#710) (8f675a7)

• autobump bio/cooltools/saddle (#719) (77b7765)

• autobump bio/dada2/filter-trim (#722) (2784d7d)

• autobump bio/dada2/learn-errors (#727) (2df75ab)

• autobump bio/dada2/quality-profile (#753) (2d541c7)

• autobump bio/diamond/blastp (#756) (a4d1a2c)

• autobump bio/fgbio/annotatebamwithumis (#740) (2405be7)

• autobump bio/fgbio/setmateinformation (#751) (3f335df)

• autobump bio/gatk/applybqsrspark (#757) (5afaf86)

• autobump bio/gatk/estimatelibrarycomplexity (#717) (1ec8a34)

• autobump bio/gatk/intervallisttobed (#721) (d7a2d2a)

• autobump bio/gatk/printreadsspark (#749) (42f55d3)

• autobump bio/gatk/scatterintervalsbyns (#712) (fd1d5a3)

• autobump bio/gatk3/printreads (#737) (6a595c3)

• autobump bio/gdc-api/bam-slicing (#747) (b7c4734)

• autobump bio/gdc-client/download (#720) (7245dab)

• autobump bio/hmmer/hmmsearch (#752) (57b7f73)

• autobump bio/homer/findPeaks (#746) (396d6ba)

• autobump bio/igv-reports (#603) (b2c306a)

• autobump bio/infernal/cmpress (#750) (4c9dbc0)

• autobump bio/liftoff (#605) (a963375)

• autobump bio/manta (#606) (186bad3)

• autobump bio/mapdamage2 (#607) (8c20ad2)

• autobump bio/microphaser/normal (#755) (a1d3025)

• autobump bio/picard/collectgcbiasmetrics (#725) (35af564)

• autobump bio/picard/createsequencedictionary (#714) (d12cf4f)

• autobump bio/picard/markduplicates (#733) (4fabb76)

• autobump bio/picard/markduplicateswithmatecigar (#744) (0981aab)

• autobump bio/prosolo/control-fdr (#723) (b71e470)

• autobump bio/purge_dups/purge_dups (#748) (e277e97)

• autobump bio/purge_dups/split_fa (#726) (5cd0255)

• autobump bio/sambamba/flagstat (#711) (4c1322d)

• autobump bio/samtools/depth (#715) (e2973ae)

• autobump bio/samtools/idxstats (#738) (3da64d0)

• autobump bio/samtools/index (#743) (a4aa08f)

• autobump bio/strelka/germline (#716) (10d123f)

• autobump bio/subread/featurecounts (#724) (3984c2b)

• autobump bio/transdecoder/predict (#742) (61c3552)

• autobump bio/ucsc/faToTwoBit (#718) (234a306)

• autobump bio/ucsc/twoBitToFa (#745) (bea275e)

• autobump bio/varscan/mpileup2indel (#759) (96d3944)

1.18.2 (2022-10-29)

Bug Fixes

• bwa-meme and bwa-memx documentation (#765) (43fc0b7)

1.18.1 (2022-10-28)

Performance Improvements

• autobump bio/gatk/haplotypecaller (#758) (ec87a20)

• autobump bio/mashmap (#608) (7168282)

• autobump bio/microphaser/filter (#734) (3e1f7d3)

• autobump bio/pbmm2/align (#761) (14dd875)

• autobump bio/picard/mergevcfs (#760) (286d041)

• autobump bio/rsem/prepare-reference (#732) (2a146ac)

• autobump bio/samtools/calmd (#735) (df4c61e)

• autobump bio/samtools/flagstat (#736) (a189006)

• autobump bio/sickle/pe (#731) (866bfb5)

• autobump bio/verifybamid/verifybamid2 (#730) (8e0f3d7)

1.18.0 (2022-10-28)

Features

• bwa memx (#691) (f281336)

Performance Improvements

• autobump bio/art/profiler_illumina (#640) (9c91417)

• autobump bio/bamtools/filter (#641) (ad679b8)

• autobump bio/bamtools/filter_json (#642) (41ac02f)

• autobump bio/bamtools/split (#643) (ca4cd00)

• autobump bio/bamtools/stats (#644) (7967763)

• autobump bio/bazam (#600) (1dc1cde)

• autobump bio/bbtools/bbduk (#645) (40c20a9)

• autobump bio/bcftools/mpileup (#648) (547922e)

• autobump bio/bcftools/norm (#649) (46c6686)

• autobump bio/bcftools/reheader (#650) (e1f3303)

• autobump bio/bcftools/sort (#651) (897bdab)

• autobump bio/bcftools/stats (#652) (6aa4a38)

• autobump bio/bcftools/view (#653) (7e67f97)

• autobump bio/bedtools/bamtobed (#654) (a84d5d4)

• autobump bio/bedtools/complement (#655) (8c69237)

• autobump bio/bedtools/coveragebed (#656) (12e7f9f)

• autobump bio/bedtools/genomecov (#657) (db7b0df)

• autobump bio/bedtools/intersect (#658) (5be4783)

• autobump bio/bedtools/merge (#659) (23e0c2f)

• autobump bio/bedtools/slop (#660) (1dc9593)

• autobump bio/bedtools/sort (#661) (c19f269)

• autobump bio/benchmark/chm-eval (#663) (a192bfc)

• autobump bio/benchmark/chm-eval-sample (#662) (4c21a14)

• autobump bio/biobambam2/bamsormadup (#664) (32fa98c)

• autobump bio/bismark/bam2nuc (#665) (5b29dc2)

• autobump bio/bismark/bismark_genome_preparation (#670) (4099d65)

• autobump bio/bismark/bismark_methylation_extractor (#671) (48993a9)

• autobump bio/bismark/bismark2report (#668) (fc9277f)

• autobump bio/blast/blastn (#673) (c9cbd1a)

• autobump bio/blast/makeblastdb (#674) (0e76eab)

• autobump bio/bowtie2/align (#675) (ba0ea38)

• autobump bio/bowtie2/build (#676) (3c4915f)

• autobump bio/bustools/count (#677) (d60a41e)

• autobump bio/bustools/sort (#678) (9380cc6)

• autobump bio/bustools/text (#679) (e423131)

• autobump bio/bwa-mem2/mem-samblaster (#681) (8871969)

• autobump bio/dada2/add-species (#703) (3296efd)

• autobump bio/dada2/assign-taxonomy (#705) (cf0b49e)

• autobump bio/dada2/collapse-nomismatch (#706) (e314e90)

• autobump bio/gatk/variantannotator (#762) (4b11881)

• autobump bio/hap.py/hap.py (#713) (a901d87)

• autobump bio/hifiasm (#602) (24cc310)

• autobump bio/jannovar (#604) (dece141)

• autobump bio/mlst (#609) (a949c78)

• autobump bio/mosdepth (#610) (1a25a6f)

• autobump bio/multiqc (#611) (7fabb68)

• autobump bio/nanosim-h (#613) (b046dd6)

• autobump bio/ngs-disambiguate (#614) (1ff4b77)

• autobump bio/optitype (#615) (6c3d720)

• autobump bio/pear (#616) (c64a0f1)

• autobump bio/plass (#617) (19ffcc6)

• autobump bio/ptrimmer (#625) (93869a9)

• autobump bio/quast (#626) (4a948d3)

• autobump bio/rasusa (#627) (ae7393e)

• autobump bio/razers3 (#628) (71c4c16)

• autobump bio/rebaler (#629) (7822769)

• autobump bio/refgenie (#630) (caf7da7)

• autobump bio/shovill (#632) (62bac99)

• autobump bio/snp-mutator (#633) (444237a)

• autobump bio/star/index (#739) (a2723ec)

• autobump bio/tximport (#635) (4dede59)

• autobump bio/unicycler (#636) (8d8c8d7)

• autobump bio/vardict (#637) (1494755)

• autobump bio/vembrane/table (#763) (a5eded7)

• autobump bio/wgsim (#638) (77dd163)

• autobump utils/cairosvg (#639) (cbb1239)

1.17.5 (2022-10-27)

Performance Improvements

• autobump bio/bcftools/merge (#647) (56e4237)

• autobump bio/bismark/bismark (#666) (94f83e8)

• autobump bio/bismark/bismark2bedGraph (#667) (bccafa5)

• autobump bio/bismark/bismark2summary (#669) (1343842)

• autobump bio/bwa-mem2/index (#680) (9644bd9)

• autobump bio/bwa-mem2/mem (#682) (50f2ba7)

• autobump bio/bwa-meme/index (#683) (39041dd)

• autobump bio/bwa-meme/mem (#684) (595b2d8)

• autobump bio/bwa/aln (#685) (8867513)

• autobump bio/bwa/index (#686) (940b7a4)

• autobump bio/bwa/mem (#688) (b087056)

• autobump bio/bwa/mem-samblaster (#687) (b8ecfd0)

• autobump bio/bwa/sampe (#689) (007c6dd)

• autobump bio/bwa/samse (#690) (23c4d2a)

• autobump bio/bwa/samxe (#701) (fe75619)

• autobump bio/dada2/assign-species (#704) (c196baa)

1.17.4 (2022-10-25)

Performance Improvements

• update datavzrd wrapper to 2.6.1 (4fb483d)

1.17.3 (2022-10-24)

Performance Improvements

• update datavzrd wrapper to 2.5.2 (533c542)

1.17.2 (2022-10-19)

Bug Fixes

• allow for optional pindel bed files (#598) (123fd98)

1.17.1 (2022-10-18)

Performance Improvements

• update datavzrd wrapper to version 2.5.1 (#618) (6fff732)

1.17.0 (2022-10-13)

Features

• move pindel region bed files to input (#594) (8f52877)

1.16.0 (2022-10-13)

Features

• bazam wrapper (#580) (17e58e6)

Bug Fixes

• set RG tag (#593) (506a083)

Performance Improvements

• autobump bio/deepvariant (#583) (9b7c4fe)

1.15.2 (2022-10-12)

Performance Improvements

• update bio/adapterremoval/environment.yaml. (#573) (8cb0391)

• update bio/assembly-stats/environment.yaml. (#575) (2c12db0)

• update bio/bellerophon/environment.yaml. (#576) (fd06157)

• update bio/bgzip/environment.yaml. (#577) (36720ca)

• update bio/busco/environment.yaml. (#581) (9825a5f)

• update bio/clustalo/environment.yaml. (#582) (dc322c8)

• update bio/delly/environment.yaml. (#584) (0eb8ebc)

• update bio/fastp/environment.yaml. (#585) (a573035)

• update bio/fastq_screen/environment.yaml. (#586) (73a3d45)

• update bio/fastqc/environment.yaml. (#587) (9a0b30e)

• update bio/fasttree/environment.yaml. (#588) (b9b8a4e)

• update bio/filtlong/environment.yaml. (#589) (3394085)

• update bio/freebayes/environment.yaml. (#590) (17c9581)

• update bio/genefuse/environment.yaml. (#591) (63c620d)

• update bio/genomepy/environment.yaml. (#592) (4cfb29b)

1.15.1 (2022-10-11)

Performance Improvements

• autobump bio/bcftools/index/environment.yaml (#570) (bc77e03)

• update bio/bcftools/call/environment.yaml. (#567) (5c4356a)

• update bio/bcftools/concat/environment.yaml. (#568) (70685f1)

• update utils/datavzrd/environment.yaml. (#566) (a6f4ff8)

1.15.0 (2022-10-11)

Features

• add cram support to applybsqr (#563) (41bb50b)

• bwa-meme picard option (#558) (76174cf)

Bug Fixes

• improve bcftools norm example rule (#561) (ad41354)

1.14.1 (2022-09-27)

Bug Fixes

• fix regression in bcftools concat wrapper that made it use only the first input file. The bug was introduced in wrapper version v1.8.0. (#559) (80960db)

1.14.0 (2022-09-19)

Features

• Add wrapper for GATK DepthOfCoverage (#494) (636060a)

1.13.0 (2022-09-17)

Features

• Add wrapper for bwa-meme (#555) (92579c4)

Performance Improvements

• bwa mem2 version update and use wrapper utils (#553) (356ee4d)

1.12.2 (2022-09-02)

Performance Improvements

• update to datavzrd wrapper to datavzrd 2.0 (#551) (a0bb674)

1.12.1 (2022-09-01)

Bug Fixes

• remove debug code from vep wrapper (c58334b)

• tabix wrapper names (bf7627e)

1.12.0 (2022-08-30)

Features

• genefuse wrapper (#493) (9bcf282)

Bug Fixes

• upgrade vep wrappers to latest version, fixing issues with strict channel priorities. (#547) (c3b46e5)

1.11.0 (2022-08-29)

Features

• Wrapper and meta-wrapper for rbt consensus reads (#544) (6736211)

1.10.0 (2022-08-21)

Features

• Delly automated conversion of output file (#468) (67c11a3)

• support branches (e.g. plants) in ensembl wrappers for sequence, annotation, and variation download (#546) (94d7f8e)

1.9.0 (2022-08-18)

Features

• add datavzrd wrapper (#535) (8c05064)

• BWA mem2 index - remove prefix parameter and determine prefix from output (#515) (ab8d4ad)

Performance Improvements

• update bcftools norm versions (#543) (5313db6)

1.8.0 (2022-08-16)

Features

• add “qualimap bamqc” wrapper (#533) (3af38c8)

• added bamtobed wrapper (#531) (0486745)

• added Bellerophon wrapper (#529) (888f651)

• added gfatools wrapper (#512) (2c6b897)

• added purge_dups wrapper (#528) (17d87e2)

• added Salsa2 wrapper (#532) (8cb4137)

• added wrapper-utils, and tempdirs (#467) (48c49a9)

• added wrappers for pretext map, snapshot and graph (#530) (2eb3fdd)

• BUSCO auto lineage mode, tempdir, updated version (#526) (67cf8e1)

• Bustools count (#511) (bb050e4)

• Bustools sort (#513) (1415748)

• Bustools text (#509) (00f60b7)

• cooltools wrappers (#519) (d28de15)

• fixed minimap2 bioconda strict channels, updated version, and added test (#527) (8f95ddb)

• GATK FilterMutectCall enhancement (#521) (eea67d4)

• GATK Getpileupsummaries (#517) (4281982)

• gatk Learnreadorientationmodel (#523) (cd68aa5)

• hifiasm wrapper (#510) (5360346)

• Meryl wrapper (#506) (f5ddac1)

• output aln is saved from stdout, to reduce I/O (#502) (6695486)

• Quast wrapper (#525) (754dfc1)

Bug Fixes

• create tabix index sub-wrapper (#501) (6c47164)

Performance Improvements

• updated cutadapt version, formatted files, and improved docs. (#505) (3a20eb7)

1.7.2 (2022-08-15)

Bug Fixes

• give conda-forge highest priority to ensure proper semantic under strict channel priorities (#508) (6976c9a)

1.7.1 (2022-07-19)

Bug Fixes

• better error handling for ensembl sequence download (#524) (c289800)

• give conda-forge highest priority to ensure proper semantic under strict channel priorities (ce78f79)

• issue when picard does not create output files (#496) (aceab7e)

• remove misleading kmer size parameter for kallisto index (#518) (309b376)

• use strict channel priorities (#503) (6419dbf)

1.7.0 (2022-06-14)

Features

• Salmon decoy-aware gentrome (#490) (5bb3eab)

1.6.0 (2022-05-23)

Features

• make it possible to set input as files or dirs to multiqc (#488) (32fd0e0)

• Mashmap (#485) (c05006d)

• Salmon update (#482) (3684276)

1.5.0 (2022-05-13)

Features

• samtools stat bed params (#418) (28fa3a8)

• support cram output in picardtools markduplicates (#486) (218fd39)

1.4.0 (2022-05-05)

Features

• added ref as an optional input file (#473) (dd8c066)

• Added specific param for strandness (#474) (12b7978)

• added support for gzip output files in ensembl annotation download wrapper (#475) (42696c2)

• convert gtf to gene pred output (#477) (4672e5b)

• DragMap wrapper (#472) (6f54512)

• make it possible to set output type, vcf or gvcf. (#476) (e62744d)

Bug Fixes

• fixed issue when several output files are specified with gatk splitncigarreads wrapper (#471) (353bf0a)

• restrict bwa wrappers’ picard installation to picard-slim (e.g. removes r-base dependency) (#484) (bd3cdbc)

1.3.2 (2022-03-28)

Bug Fixes

• fixed some known bugs, added docs, and reformat (#469) (58247e3)

1.3.1 (2022-03-17)

Bug Fixes

• Nextflow profile (#456) (bd9af55)

1.3.0 (2022-03-16)

Features

• added GATK variantAnnotator wrapper (#462) (3ace5fa)

1.2.1 (2022-03-11)

Bug Fixes

• bcftools filter cannot run with mem options and this will prevent mem-max to be set. (#464) (d7a0de4)

• issue 339 (#461) (6734675)

• update multiqc version to 1.12 (#460) (330359d)

1.2.0 (2022-02-21)

Features

• added samtools wrapper utils (#454) (23c28bf)

• added STAR temp dir (#453) (86a6c11)

• added temp dir to featurecounts (#455) (d93866e)

• added tmpdir to all GATK wrappers, plus some doc changes (#449) (c17266b)

• explicitly specify bwa index in bwa samxe (#448) (ef5b36a)

1.1.0 (2022-02-07)

Features

• automatically set temp dir tempfile (#446) (5b0d26a)

• updated delly wrapper to version 0.9.1.

Bug Fixes

• added missing dependencies and improved docs (#450) (e99f2a1)

1.0.0 (2022-01-26)

⚠ BREAKING CHANGES

• added tempdir, updated version and metadata to all picard wrappers (#443)

Features

• added tempdir, updated version and metadata to all picard wrappers (#443) (55e672a)

0.87.0 (2022-01-26)

Features

• added wrapper for bcftools stats (#201) (2caecb9)

• added wrapper for bgzip (#195) (6d837f2)

• added wrapper for seqtk seq subcommand (#202) (599f370)

• added wrapper for using tabix to query an indexed file (#203) (2bb9131)

• explicitly specify bwa index in bwa wrappers (#232) (0e323b1)

• Implemented handling of memory constraints in fasterq-dump wrapper (#432) (7febbb0)

• parse mem for samtools sort (#442) (37c2d08)

• wrapper for Manta SV caller (#415) (6b4d6a1)

0.86.0 (2022-01-18)

Features

• add fasttree wrapper (#405) (ad99f9e)

• add MUSCLE wrapper (#404) (564ada7)

• added shards temp folder (#441) (dda1546)

• update multiqc wrapper to v1.11 (#422) (0fa22a3)

• updated versions and fixes for samtools wrappers. (#431) (cbba82d)

• added wrapper for verifybamid2 (#401)

Bug Fixes

• log file handling and other small improvements for bcftools wrappers (#429) (961edb8)

• proper tempfile handling for STAR and improved documentation (#430) (922cf87)

• correctly handle extra parameters in vardict wrapper (#437)

0.85.1 (2022-01-14)

Bug Fixes

• fix bug in pindel2vcf wrapper (#433) (f94b225)