Features
- add logs to refgenie rules (fce4bb0)
- 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)
- Allow for large assets in refgenie (1c99871)
- force string in reference_prefix (fe7b05a)
- formatting refgenie (ee3bad5)
- handle refgenconf write lock error (4d3758c)
- read-only conf acces for concurrent rules dl (d0dcc61)
- remove input string from rsem wrapper (73e3a02)
- reorder to prioritize bioconda (8eb7a1d)
- switch to Path in order to resolve basename more robustly (0d10e6a)
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/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/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/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/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/gatk3/printreads (#1174) (22f8e69)
- autobump bio/gatk3/printreads (#1217) (5d05b88)
- autobump bio/gdc-api/bam-slicing (#1159) (96a1a42)
- 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/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/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/fixmate (#1264) (f42a717)
- autobump bio/samtools/flagstat (#1184) (4f5349c)
- 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/index (#1228) (6cc0059)
- 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/prune (#1263) (8a36dec)
- bump Salmon to v1.10.1 (61758c3)
- bump Salmon to v1.10.1 (#1168) (a718777)
- reorganize inputs and add back input_string (a3b02b8)