23 Pull requests merged by 17 people

• [Upgrade] Normalize input of lofreq-viterbi to match other lofreq modules

  #5989 merged Jul 17, 2024

• RNAseq preprocessing: rrna sequences make more sense as a channel of FASTAs, port tests

  #5988 merged Jul 17, 2024

• Improve strandedness derivation in rnaseq preprocessing swf

  #5982 merged Jul 16, 2024

• Swap unzip to nf-test (continuation of 5357)

  #5897 merged Jul 16, 2024

• Using Seqera containers for Sentieon to avoid LD_LIBRARY errors

  #5823 merged Jul 16, 2024

• Rename preprocess rnaseq

  #5959 merged Jul 16, 2024

• Added agat/spmergeannotations

  #5772 merged Jul 15, 2024

• Fix gtffilter output definition

  #5977 merged Jul 15, 2024

• new module: custom_gtffilter

  #5965 merged Jul 15, 2024

• Handle empty files

  #5720 merged Jul 15, 2024

• chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.5.2

  #5975 merged Jul 15, 2024

• by remove the 2>&1 to avoid the warning message.

  #5974 merged Jul 15, 2024

• port gridss/gridss to nf-test

  #5933 merged Jul 12, 2024

• Add new input to multiqc module for use with --rename_samples

  #5973 merged Jul 12, 2024

• stubs and test for rnaseq modules - part IV

  #5939 merged Jul 12, 2024

• Update Glimpse2 phase

  #5944 merged Jul 11, 2024

• Update dupradar test snapshot

  #5966 merged Jul 11, 2024

• Update the module: nanoq

  #5964 merged Jul 11, 2024

• Update dupradar.r according to new MultiQC (>=v1.22) config values

  #5943 merged Jul 11, 2024

• Update lofreq somatic and callparallel

  #5931 merged Jul 11, 2024

• LAST alignment statistics for MultiQC

  #5902 merged Jul 11, 2024

• chore(deps): update actions/setup-python digest to 39cd149

  #5961 merged Jul 11, 2024

• Add prefix to output file for barrnap

  #5919 merged Jul 11, 2024

6 Pull requests opened by 3 people

• ltrharvest: Added test to verify graceful handling of no ltr input

  #5978 opened Jul 16, 2024

• ltrfinder: Added test to verify graceful handling of no ltr input

  #5979 opened Jul 16, 2024

• ltrretriever/ltrretriever: Added test to verify graceful handling of …

  #5980 opened Jul 16, 2024

• liftoff: Re-added conda environment

  #5981 opened Jul 16, 2024

• Updated mkfastq module

  #5984 opened Jul 16, 2024

• Split deepvariant 2

  #5990 opened Jul 17, 2024

6 Issues closed by 5 people

• new module: pbtk/pbindex

  #5900 closed Jul 16, 2024

• new module: agat/spmergeannotations

  #5418 closed Jul 15, 2024

• new module: custom/gtffilter

  #5963 closed Jul 15, 2024

• new File breaks cloud execution in bcl_demultiplex

  #5612 closed Jul 15, 2024

• `--assembly` flag of gridss module leads to empty bam files

  #5949 closed Jul 12, 2024

• Update lofreq somatic & lofreq call-parallel

  #5930 closed Jul 11, 2024

12 Issues opened by 4 people

• new module: pypgx/runngspipeline

  #5987 opened Jul 17, 2024

• new module: pypgx/computecontrolstatistics

  #5986 opened Jul 17, 2024

• new module: pypgx/preparedepthofcoverage

  #5985 opened Jul 17, 2024

• Fix malt tests that are using a 739.0 MiB zip as input

  #5983 opened Jul 16, 2024

• new module: pypgx/createinputvcf

  #5976 opened Jul 15, 2024

• Investigate unknown issue for checkv/updatedatabase module

  #5972 opened Jul 12, 2024

• Investigate issue extracting data.tar.gz for rgi related modules

  #5971 opened Jul 12, 2024

• Investigate issue extracting minigut_cf.tar.gz for centrifuge

  #5970 opened Jul 12, 2024

• new module: mgikit/demultiplex

  #5969 opened Jul 12, 2024

• [FEATURE] Centralize all modules using ubuntu container into a single container

  #5968 opened Jul 11, 2024

• IGVREPORTS: wrong variable name

  #5967 opened Jul 11, 2024

• [FEATURE] Deprecate untarfiles

  #5962 opened Jul 11, 2024

13 Unresolved conversations

Sometimes conversations happen on old items that aren’t yet closed. Here is a list of all the Issues and Pull Requests with unresolved conversations.

• Add Seqfu/derep

  #5958 commented on Jul 16, 2024 • 17 new comments

• Refactor Sentieon

  #5945 commented on Jul 17, 2024 • 9 new comments

• New module: checkqc

  #4158 commented on Jul 17, 2024 • 3 new comments

• add usearch-unoise3

  #5955 commented on Jul 12, 2024 • 3 new comments

• Add module fgbio/collectduplexseqmetrics

  #5960 commented on Jul 17, 2024 • 2 new comments

• new module: fgbio/collectduplexseqmetrics

  #3257 commented on Jul 11, 2024 • 0 new comments

• new module: picard/samtofastq

  #4176 commented on Jul 15, 2024 • 0 new comments

• [FEATURE] Add `stub` support to every module

  #4570 commented on Jul 16, 2024 • 0 new comments

• Renovate Dashboard 🤖

  #4211 commented on Jul 17, 2024 • 0 new comments

• [FEATURE] Split DeepVariant process

  #5793 commented on Jul 17, 2024 • 0 new comments

• Add module `muse/sump`

  #5629 commented on Jul 15, 2024 • 0 new comments

• chore(deps): update pre-commit hook renovatebot/pre-commit-hooks to v37.432.0

  #5815 commented on Jul 16, 2024 • 0 new comments

• Add stub and test to lofreq/indelqual

  #5941 commented on Jul 17, 2024 • 0 new comments