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Releases: wtsi-npg/p4

0.40.0

07 Aug 16:13
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  • change permissions of STAR working directory to allow deletion by standard pipeline tools
  • add Dockerfile to create container with appropriate tools for basic analyses
  • Updated image labels

0.39.0

12 Feb 18:02
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  • use "samtools index" instead of "cram_index to create cram indexes
  • for bam and cram index creation, use "samtools index -o <index_file>" to explicitly indicate the index file

0.38.0

04 Dec 13:29
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  • add additional autosome specific coverage threshold to final_output_prep.json

0.37.2

18 Sep 17:35
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  • change bambi i2b command in stage1 analysis to use new boolean version of --nocall-quality flag

0.37.1

15 Aug 13:49
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  • amend markdup command chain for duplexseq (nanoseq) analyses
  • updated to use samtools merge instead of bammerge for library merging

0.37.0

25 Jul 16:02
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  • add i2b_nocall_qual_switch to stage1 analysis to enable "--nocall-quality=2" to be set for bambi i2b

0.36.0

08 Jun 22:07
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  • add hs_bwa_executable parameter to allow different bwa executables for target and nchs alignments (e.g. bwa-mem2 and bwa0_6)
  • add optminpixeldif flag (optical distance for duplicates) to bamstreamingmarkduplicates command (biobambam markdup method)

0.35.0

03 Apr 11:40
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replace scramble with samtools in analysis pipeline templates

0.34.0

14 Feb 16:58
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  • add calmd to biobambam,samtools and duplexseq markdup methods

0.33.1

14 Dec 15:09
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  • update CI and tests