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Module/igv/1.0#303

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mannycruz wants to merge 137 commits intomasterLCR-BCCRC/lcr-modules:masterfrom module/igv/1.0LCR-BCCRC/lcr-modules:module/igv/1.0Copy head branch name to clipboard

+1,833

Commits

Commits on Jan 31, 2023

• initial IGV module, specify regions using MAF

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  bcf9916

Commits on Feb 2, 2023

• Add rules to reformat input regions files

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  f2091a4

• Add script to perform regions reformatting

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  f6980b9

• Add script to filter maf based on BED or MAF

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  e54b85c

• Modify liftover script to accomodate BED regions

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  f46ff3f

• Update config for changes made to module

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  d0693a6

• Remove commented out text

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  8fa8bab

Commits on Feb 4, 2023

• Add function to reformat hotmaps MAF results

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  d3b8e1c

Commits on Feb 7, 2023

• Add function to format mutation_id regions file

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  3791dd1

• Move constraint on n snaps/variant to filter step

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  e0c184d

Commits on Feb 11, 2023

• Remove metadata file option, fix pairing config

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  07bea16

• Grammar

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  ed501fb

• Convert from snakemake shell to script directive

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  2bb98e7

• Add sample_id tracking, metadata = CFG["samples"]

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  ff248e6

Commits on Feb 26, 2023

• Overhaul to sample_id-dependent workflow

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  e389982

• Add capability for VCF files as regions

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  31cba38

Commits on Feb 28, 2023

• Allow filtered MAF files to be temp

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  77f9d76

Commits on Mar 2, 2023

• Track what snapshots will be created (draft)

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  0bf93ad

Commits on Mar 8, 2023

• Workflow changed to run per sample-variant combo

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  f0047d5

Commits on Mar 9, 2023

• Merge variant batch scripts to prevent IGV crash

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  a9a27fe

Commits on Mar 13, 2023

• Remove conda environment in filter_maf rule

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  28c54f1

• Add symlinked snapshots to workflow targets

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  4318b8d

• Clean up comment lines

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  7805531

• Remove "exit" line from position batch scripts

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  0f4c924

• Fix variable referenced before assignment error

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  383ff17

Commits on Mar 14, 2023

• Add log outputs to igv run

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  13d6992

• Add dependency to regions files to checkpoint rule

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  c9a8abc

• Set thread limits on batch creation and IGV run

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  6bb0861

• Clean up format_regions script

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  351019f

Commits on Mar 15, 2023

• Clean up subdirectories

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  9764101

• Add log outputs to script rules

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  874d594

Commits on Mar 17, 2023

• Add descriptions to rules, remove redundant header statements from merged batch

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  4c34334

• Skip IGV run if empty batch script

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  901ab8d

• Clean up input functions

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  c229e74

• Rename tumour_sample_id wildcard to tumour_id

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  a5e04c4

• Fix typos

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  bf0154e

• Remove bam and index file reformatting

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  b151070

Commits on Mar 20, 2023

• Fix typo in subset of runs table

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  0e9e62c

Commits on Mar 22, 2023

• Add timeout proportional to batch lines

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  80dcd76

• Make dispatched batch file names cleaner

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  774ed17

• Improve test run output and functionality

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  cae1f6e

Commits on Mar 23, 2023

• Increase sleep interval to prevent cut-off snaps

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  a376b4b

• Prevent multiple exit statements added to batches

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  9490642

• Add ability to take snapshots in pair orientation

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  63ca909

Commits on Mar 24, 2023

• Increase sleep interval even more

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  58529cc

Commits on Mar 27, 2023

• Add ability to handle empty MAF files

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  5da0a49

• Fix issues with pairs version file suffix

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  95900fd

Commits on Apr 5, 2023

• Remove outdated lines

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  7a9b0f3

• Add sleep timer + igv options to batch scripts + change how suffix is added to filename

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  2054e41

• Add option for time limit on IGV run based on lines in batch script in case it errors and never exists

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  aa2d167

• Fix typos causing list errors

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  b5ff4f9

• Add example IGV options to default config

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  6717cd7

• Fix typos

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  60b84e8

• Move padding value from filename to file extension

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  c5f443f

Commits on May 2, 2023

• Fix stderr logging, remove outdated fxn

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  c5444f6

• Fix stderr logging

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  bf68f6c

• Fix stderr logging, move sleep interval to header

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  1f305bc

• Add log to batch script rule

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  d4d163d

• Track changelog

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  00ff6dd

Commits on May 9, 2023

• Merge remote-tracking branch 'origin/master' into module/igv/1.0

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  7686bf6

Commits on May 10, 2023

• Merge remote tracking branch with module/igv/1.0

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  2ac9e62

Commits on Jun 8, 2023

• Organize config for clarity

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  2a5462b

• Match values to new config structure

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  0491dc0

• Access genome map from new config structure

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  c4c1290

• Set server number and xvfb arguments in igv rule

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  dba7383

• Add check for IGV exit status to handle if xvfb-run error occurs but all snapshots have been taken succesfully

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  94f20a8

• Add QC to catch truncated/wrong dimensions snapshots

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  41c5eff

• Add thread limits to bam/bai symlinking rules

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  636dc7b

Commits on Jun 13, 2023

• Fix input error using input function

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  1f4ecfa

Commits on Jun 19, 2023

• Add resource limits to config

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  f2a5fe3

• Add resource limits, handle missing MAFs, fix server assignment typo

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  1af181b

Commits on Jul 12, 2023

• Improve quality control log descriptions, add thresholds to check for blank snaps, add while loop for multiple attempts, make symlink rule depend on successful completion of quality control step

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  838efdf

• Use rule wildcards to set additional columns in MAF instead of extracting values from metadata matches for cases where sample id matches more than one seq_type

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  28ad3c2

• Fix typo in HotMAPS formatting function

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  e6a1c3c

Commits on Jul 13, 2023

• Remove quality control thread config value

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  6f71a23

Commits on Aug 10, 2023

• Handle corrupt snapshots and minimize sleep interval + tries

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  c06b404

• Clean up commented out lines

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  1b9facb

Commits on Aug 14, 2023

• Rename snapshot estimate parameter for clarity

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  6a2a468

• Add function to estimate snapshots

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  fe60b94

Commits on Aug 16, 2023

• Add functions for estimating snapshots and finding failed snaps

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  e76c9f6

Commits on Sep 1, 2023

• Use filter maf rule outputs to estimate snapshots (faster)

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  801f308

Commits on Sep 7, 2023

• Add ability to load multiple bam files and image presets into batch scripts

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  5f971b7

• Update directory syntax for tumour normal pairs and igv preferences presets

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  d35faaa

• Add ability to define igv presets of different IGV parameters

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  91c0355

• Add preset and pair directory wildcards to batch scripts to track which variant/present combos have been run through IGV

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  1665b7f

Commits on Sep 12, 2023

• Create one merged batch per IGV preset, add quality control input function to fix error where not all snapshots were being checked, clean up quality control params

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  8b3c520

• Update snapshot estimate for igv presets

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  91df3cf

Commits on Sep 13, 2023

• Update failed snap estimate for presets

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  d7c8444

Commits on Sep 14, 2023

• Clean up rule _igv_touch_summary

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  97ff367

• Add function to variant batch generator script to handle samples with no variants to snapshot

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  9573e59

• Add ability to track failed snaps while snapshots are being taken

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  ad03a99

• Clean up preset wildcard

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  8d0af4e

• Clean up rule _igv_touch_failed

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  f02f0fb

Commits on Sep 15, 2023

• Add ability to provide multiple regions files in config

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  870068a

• Add rule to merge regions file of same tool + build combo

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  4ac8628

• Reformat regions for each tool and build combo

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  c447af1

• Touch snakemake output if no regions files provided for tool+build combo

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  ba82c64

• Fix typo

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  b04e6ce

• Add function to convert MAFs to BED format

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  9aee267

• Run liftover on each tool+build combo... for each required genome build in CFG["runs"]["tumour_genome_build"]

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  5971917

• Merge ALL tool+build combo files that are the same target build into one file

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  57e96e0

• Filter MAFs based using merged regions file of same build

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  d6eabda

• Update metadata argument position

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  a7f33e7

• Remove regions dependency in rule _igv_create_batch_script_per_variant

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  ff04705

Commits on Sep 18, 2023

• Skip liftover step if input regions file is empty

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  e62ce63

Commits on Dec 22, 2023

• Added more flexibility in setting qc thresholds, because trying to stack normal and tumor bams were producing many more truncated and blank snaps with a variety of heights

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  064ac93

Commits on Dec 30, 2023

• Move quality control process into a script

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  d8fa50c

Commits on Jan 24, 2024

• Overhaul to take snaps of N and T if applicable

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  f565b30

Commits on Jan 25, 2024

• Polishing

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  95f8f27

• Update config

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  0a5efd7

Commits on Feb 10, 2024

• Merge branch 'module/igv/1.0' of github.com:LCR-BCCRC/lcr-modules into module/igv/1.0

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  406f253

• Add local rules, add threads limit to merging batches script to prevent duplicates, remove typo in rule _igv_track_failed, edit how snapshot estimates are written

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  f3e3183

• Reorder config values to make it more understandable (i hope)

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  fea42ec

• Group variants by position so that snapshot instructions for multiple alleles in one position are incorporated into the batch scripts

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  b0a69bf

Commits on Mar 1, 2024

• Update local rules

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  50bfa6c

Commits on Mar 9, 2024

• Update oncodriveclustl results reformatting using new module outputs (expanded genomic coordinate output)

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  746b073

Commits on Mar 15, 2024

• Add blank line to the end of scripts

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  7c536f1

• Update CHANGELOG

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  27363e9

• Add slms 3 pairing config so that slms_3 can be set in the config["tool_names"]

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  24ea395

Commits on Mar 19, 2024

• Add more info to default config

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  0ee08cb

Commits on Mar 26, 2024

• Merge branch 'master' of github.com:LCR-BCCRC/lcr-modules into module/igv/1.0

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  f2f6807

Commits on Mar 27, 2024

• Fix typo

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  e044266

• Merge branch 'master' of github.com:LCR-BCCRC/lcr-modules into module/igv/1.0

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  c1f3806

• Remove outdated commented

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  0a7b028

• Add more descriptions to config, reduce timelimit of IGV run

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  0f21edc

• Update changelog, add empty line to end of script

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  4e01bac

Commits on Apr 4, 2024

• Switch to using liftover and add resources option to symlink rule

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  a821032

Commits on Apr 5, 2024

• Merge branch 'master' of github.com:LCR-BCCRC/lcr-modules into module/igv/1.0

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  e48e65e

Commits on Aug 8, 2024

• Fix typo in config

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  7d462f7

• Add more information for mutation_id file format

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  931a8b5

Commits on Aug 26, 2024

• Clean up conda envs

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  e922df5

• Remove scripy that runs crossmap since switched to liftover

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  2cdf675

• Remove unnecessary REGIONS_FORMAT dict

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  7290191

Commits on Sep 1, 2024

• Allow ability to specify version of IGV to download

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  5b9551c

Commits on Sep 4, 2024

• Fix typo in list of config wildcards so tumour_id matches wildcard in snakefile

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  f864881

Commits on Sep 15, 2024

• Add ability to specify bam path in config

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  7df9f19

Commits on Nov 28, 2024

• Fix string indexing for mutation_id formatted files

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  ef47a17