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Changelog

(unreleased)

Changes

  • Captus readme.

Other

  • Merge pull request #3 from TomHarrop/no_moar_wildcards.

    Trying to reduce the number of checkpionts, because they cause trouble

0.7.1 (2024-10-24)

Other

  • Allow for empty trimal outputs.

0.7.0 (2024-10-11)

Fix

  • Remove as much temp() output from captus as possible, so it doesn't re run all the time.

  • Remove as much temp() output from captus as possible, so it doesn't re run all the time.

0.6.5 (2024-10-10)

Changes

  • Captus: make cluster_leftovers optional.

0.6.4 (2024-09-20)

Fix

  • Try not to use job time to copy file.

0.6.3 (2024-09-19)

Fix

  • Trimal - create fewer tempfiles.

0.6.2 (2024-09-16)

Fix

  • More time to tidy up trimal oiutput.

0.6.1 (2024-09-12)

New

  • Add a wscore filter to captus.

  • Add a wscore filter to captus.

Other

  • Run captus with cutoffs.

  • Run captus with cutoffs.

  • Run captus with cutoffs.

  • Run captus with cutoffs.

0.5.2 (2024-08-21)

Fix

  • Don't run trimal twice on the same alignments.

0.5.1 (2024-08-21)

New

  • Run trimal on a folder of alignments.

0.4.6 (2024-08-15)

New

  • Generate sample stats from Captus extractions.

0.4.5 (2024-08-13)

Fix

  • Bugfix in decruft.

0.4.4 (2024-08-12)

New

  • Include miscellaneous markers for captus extract.

0.4.3 (2024-08-09)

New

  • Add external reference sequence to captus extract.

0.4.02 (2024-08-08)

New

  • Aggressively decruft paragone input.

0.4.01 (2024-08-08)

New

  • Add outgroups for Captus align.

0.3.04 (2024-08-07)

Other

  • Detect files with two or fewer sequences.

  • Changelog.

0.3.03 (2024-08-05)

Fix

  • Check for empty files in orient_sequences.

Other

  • Changelog.

0.3.02 (2024-07-27)

Fix

  • Find cluster file inside temporary path script.

  • Find cluster file inside temporary path script.

Other

  • Update changelog.

  • Changelog.

0.3.01 (2024-07-25)

New

  • Recover plastid markers with Captus.

0.2.18 (2024-07-25)

Other

  • Log what happened during orientation.

0.2.17 (2024-07-24)

Other

  • Multiprocess fasta files.

0.2.13 (2024-07-24)

Other

  • Tags.

  • It's impossible to run modules on separate namelists without a checkpoint inthe modules.

  • Remove checkpoints from captus and demonstrate how to find output.

  • Checkpoints removed from iqtree.

  • Initial commit.

0.2.12 (2024-07-21)

Other

  • Mark tempfile as ancient.

0.2.11 (2024-07-19)

Other

  • Switch paragone to clustalo.

0.2.10 (2024-07-16)

Other

  • Paragone version bump.

0.2.09 (2024-07-15)

Other

  • Update iqtree nt flag.

0.2.08 (2024-07-14)

Other

  • Avoid temporary input directory.

0.2.07 (2024-07-14)

Other

  • Use ancient to prevent reruns.

  • Debug.

0.2.06 (2024-07-12)

Other

  • Refactor paragone to use archives for out and input.

  • Petrichor is making recursive symlinks.

0.2.05 (2024-07-10)

Other

  • Handle archives.

0.2.04 (2024-07-10)

Other

  • Revert captus changes.

  • Workaround lack of tmpdir for hybpiper tar.

0.2.03 (2024-07-09)

Other

  • Retrieve captus clusters.

  • Merge pull request #2 from TomHarrop/expand_captus_wildcards.

    Expand captus wildcards

0.2.02 (2024-07-09)

Other

  • Expand workaround.

0.2.01 (2024-07-09)

Other

  • Workaround for expand???

  • Update test workflows.

0.2.0 (2024-07-09)

Other

  • Refactor captus.

  • Attempt to use tmpdir.

  • Attempt to use tmpdir.

  • Attempt to use tmpdir.

  • Attempt to use tmpdir.

  • Attempt to use tmpdir.

  • Attempt to use tmpdir.

  • Attempt to use tmpdir.

  • Attempt to use tmpdir.

  • Attempt to use tmpdir.

  • Attempt to use tmpdir.

  • Attempt to use tmpdir.

  • Attempt to use tmpdir.

  • Use shadow rather than tmpdir.

  • Use shadow rather than tmpdir.

  • Use shadow rather than tmpdir.

  • Use shadow rather than tmpdir.

  • Attempt to use tmpdir.

  • Use shadow rather than tmpdir.

  • Use shadow rather than tmpdir.

  • Use shadow rather than tmpdir.

  • Attempt to use tmpdir.

  • Attempt to use tmpdir.

  • Attempt to fix tmp issues in modules.

0.1.07 (2024-07-04)

Other

  • Iqtree update.

  • Update iqtree container.

0.1.06 (2024-06-28)

Other

  • Update captus target.

0.1.05 (2024-06-27)

Other

  • Update captus target.

  • Merge remote-tracking branch 'origin'

0.1.03 (2024-06-27)

Other

  • Update captus target.

0.1.04 (2024-06-25)

Other

  • Typo in path.

  • Use a shadow directory for fasterq-dump.

0.1.02 (2024-06-20)

Other

  • Iqtree.

  • Iqtree.

0.1.01 (2024-06-20)

Other

  • Something wrong with wildcards.

0.1.00 (2024-06-19)

Other

  • Exclude groups with <3 seqs from tree.

  • Note on problematic alignments.

  • Use checkpoints to resolve alignments.

0.0.59 (2024-06-19)

Other

  • Format params in iqtree.

0.0.58 (2024-06-13)

Other

  • Make directory an input.

0.0.57 (2024-06-13)

Other

  • Use wildcards in iqtree.

0.0.56 (2024-06-13)

Other

  • Add iqtree.

0.0.55 (2024-04-19)

Other

  • Catch extract stats.

0.0.54 (2024-04-12)

Other

  • Mark captus directories temp.

0.0.53 (2024-04-12)

Other

  • Catch more captus output.

0.0.52 (2024-04-05)

Other

  • Captus typo:

0.0.51 (2024-04-05)

Other

  • Working captus v1.

  • Assemble works but extract fails.

0.0.50 (2024-03-28)

Other

  • Shadow for purge.

0.0.49 (2024-03-27)

Other

  • Use shadow directories to avoid CD.

0.0.48 (2024-03-21)

Other

  • Constrict sample names.

0.0.47 (2024-03-15)

Other

  • Tag.

  • Basic purge haplotigs function.

0.0.46 (2024-03-08)

Other

  • Rm typo.

0.0.45 (2024-03-08)

Other

  • Clean up RM.

0.0.44 (2024-03-01)

Other

  • Use module.

  • Module to get reads from hybpiper output.

  • Use read_usage_target to extract the reads used in assembly.

0.0.43 (2024-02-29)

Other

  • Hybpiper now reads samples from a namelist.

0.0.42 (2024-02-23)

Other

  • Bpdownload: cache csv and xml file to avoid repeated parsing.

  • Skip SE SRR files.

  • Test bpdownload module.

  • Cache csv files in bpdownload.

0.0.41 (2024-02-07)

Other

  • Braker3 pick up gtf and gff.

0.0.40 (2024-02-01)

Other

  • Add header length parameter.

0.0.39 (2024-02-01)

Other

  • Tag.

0.0.38 (2024-02-01)

Other

  • Split bamfiles.

  • Fa readme.

0.0.37 (2024-02-01)

Other

  • Tag.

  • Add optional parameters.

  • Update readme.

0.0.36 (2024-01-31)

Other

  • Tag.

  • Remove comments.

  • Conditional interproscan.

  • Add note about interproscan'

  • Tidy up env vars.

  • Move build script to container recipe repo.

0.0.35 (2024-01-24)

Other

  • Braker version bump.

  • Wrong path.

0.0.34 (2024-01-19)

Other

  • Tag.

  • Merge pull request #1 from TomHarrop/funannotate.

    Funannotate

  • Merge branch 'main' into funannotate.

  • Merge but add interproscan warning.

  • Update vars in singularity build script.

  • Add SLURM build.

  • Working annotation but without interproscan.

  • Download ipr database.

  • Working up to interproscan"

  • Draft interproscan rule.

  • Gitignlore.

  • Running predict and emapper.

  • Working up to train.

  • Funannotate db test.

  • Work out db extraction / download.

0.0.33 (2024-01-11)

Other

  • Turn off strandedness.

0.0.32 (2024-01-11)

Other

  • Hisat2.

0.0.31 (2023-12-29)

Other

  • Wrong flag in samtools.

0.0.30 (2023-12-27)

Other

  • Write index to outdir.

0.0.29 (2023-12-21)

Other

  • Relax sample names.

0.0.28 (2023-12-21)

Other

  • Allow running without annothation.

0.0.27 (2023-12-21)

Other

  • Removed drafts.

  • Draft files.

  • Imports.

  • Forgot container.

0.0.26 (2023-12-14)

Other

  • Forgot container.

0.0.25 (2023-12-14)

Other

  • No need to combine samples in bbmap.

0.0.24 (2023-12-14)

Other

  • Add bbmap.

  • Star pipeline.

0.0.23 (2023-12-12)

Other

  • Check the bamfile before running braker3.

0.0.22 (2023-12-01)

Other

  • Biocontainer.

0.0.21 (2023-12-01)

Other

  • Add resources for paragone.

0.0.20 (2023-11-30)

Other

  • Merge branch 'paragone'

  • Use module.

  • Simplify paragone module.

  • Too complicated, simplify.

  • Make internal and external outgroups optional.

  • Targetfile note.

  • Working tutorial.

  • Qc_trees_and_extract_fasta.

  • Initial paragone step.

0.0.19 (2023-11-30)

Other

  • Exponent time for repair.

0.0.18 (2023-10-27)

Other

  • Add some logging info for URLs.

  • Add logging info for URL checking.

  • Don't need to configure.

  • Configure ncbi.

  • Initial download working from accession alone.

0.0.17 (2023-09-28)

Other

  • Be stricter on targetfiles.

0.0.16 (2023-09-28)

Other

  • Collect targetfile in hybpiper.

0.0.15 (2023-09-27)

Other

  • Less ram usage for HP.

0.0.14 (2023-09-21)

Other

  • Deal with whitespace in proteins and genome.

0.0.13 (2023-09-21)

Other

  • Don't try to reformat proteins.

0.0.12 (2023-09-21)

Other

  • Simplify output.

0.0.11 (2023-09-21)

Other

  • Wrong arg.

0.0.10 (2023-09-21)

Other

  • Wrong arg.

0.0.9 (2023-09-21)

Other

  • Logger.

0.0.8 (2023-09-21)

Other

  • Make braker evidence optional.

  • Specify braker output.

0.0.7 (2023-09-19)

Other

  • Why re.

  • Add braker.

  • Remove bamfile.

  • Test commit.

  • Add braker.

0.0.6 (2023-09-18)

Other

  • Remote module.

  • Repeatmaskter.

0.0.5 (2023-09-14)

Other

  • Retrieve paralogs.

  • Add paralogs.

0.0.4 (2023-09-14)

Other

  • Don't search for files, name them appropriately.

0.0.3 (2023-09-14)

Other

  • Tag.

  • Hook into snakemake logger.

  • Handle missing files.

0.0.2 (2023-09-13)

Other

  • Add targetfile check to hybpiper.

  • Check steps.

  • Add check targetfile.

0.0.1 (2023-09-13)

Other

  • Try from GH.

  • Working hybpiper module.

  • Working hybpiper?

  • Initial commit.

  • Initial commit.