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Long RNA-seq analysis workflow

License: GNU General Public License v3.0

Python 47.56% R 4.12% AngelScript 0.14% Shell 3.89% Perl 41.56% Awk 0.08% Raku 2.64%

bioinformatics snakemake-workflow cls rnaseq pacbio-iso-seq transcriptomics gencode

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razielar jacobwindsor diekhans

lyric's Issues

Update shell prefix command in master.smk

I think the shell.prefix definition in master.smk would need to be updated:

loading .bashrc is not needed most of the times
deactivating the active conda environment can give problems (e.g. missing binaries)

Something like:

shell.prefix('set -euo pipefail; export PATH="$PWD/LyRic/utils/:$PATH";')

should probably be fine.

Rule makeHtmlSummaryDashboard fails complaining about missing columns

This is the error message:

Error: Can't subset columns that don't exist.✖ Column `intron.x` doesn't exist.Backtrace:     █  1. ├─dplyr::relocate(ntCoverageStats, intron.x, .after = exonOfPseudo.y)  2. ├─dplyr:::relocate.data.frame(ntCoverageStats, intron.x, .after = exonOfPseudo.y)  3. │ ├─base::unname(tidyselect::eval_select(expr(c(...)), .data))  4. │ └─tidyselect::eval_select(expr(c(...)), .data)  5. │   └─tidyselect:::eval_select_impl(...)  6. │     ├─tidyselect:::with_subscript_errors(...)  7. │     │ ├─base::tryCatch(...)  8. │     │ │ └─base:::tryCatchList(expr, classes, parentenv, handlers)  9. │     │ │   └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10. │     │ │     └─base:::doTryCatch(return(expr), name, parentenv, handler)
 11. │     │ └─tidyselect:::instrument_base_errors(expr)
 12. │     │   └─base::withCallingHandlers(...)
 13. │     └─tidyselect:::vars_select_eval(...)
 14
Execution halted
Error: Can't subset columns that don't exist.
✖ Column `intron.x` doesn't exist.
Backtrace:
     █
  1. ├─dplyr::relocate(ntCoverageStats, intron.x, .after = exonOfPseudo.y)
  2. ├─dplyr:::relocate.data.frame(ntCoverageStats, intron.x, .after = exonOfPseudo.y)
  3. │ ├─base::unname(tidyselect::eval_select(expr(c(...)), .data))
  4. │ └─tidyselect::eval_select(expr(c(...)), .data)
  5. │   └─tidyselect:::eval_select_impl(...)
  6. │     ├─tidyselect:::with_subscript_errors(...)
  7. │     │ ├─base::tryCatch(...)
  8. │     │ │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
  9. │     │ │   └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10. │     │ │     └─base:::doTryCatch(return(expr), name, parentenv, handler)
 11. │     │ └─tidyselect:::instrument_base_errors(expr)
 12. │     │   └─base::withCallingHandlers(...)
 13. │     └─tidyselect:::vars_select_eval(...)
 14
Execution halted
[Thu Jul 28 18:08:30 2022]
Error in rule makeHtmlSummaryDashboard

Usee POSIX atomic file install instead of copying from TMPDIR

LyRic would be faster and more robust if it used POSIX atomic file creation instead of writing to TMPDIR and then
copying in place.

TMPDIR is usually on a separate file system, so

mv {TMPDIR}/$uuidTmpOut {output.bam}

Would usually be a copy. If there is an error, such as out of disk space, an incomplete output file
out exist.

If the file is created on the same file system as the output file, so the mv is an atomic rename.
In bash I would do:

tmpout=${outbam}.tmp
do_something  > ${tmpout}
mv -f ${tmpout} ${outbam}

Assuming bash is run with -e, the completed file doesn't exist under
the final name until it is successfully completed, and there is no copy overhead.

[Feature request] Configurable genome assembly name for UCSC track hubs

Currently the genome assembly variable for the track hub config is taken from the {genome} wildcard, which is linked to the basename of the fasta file in the local filesystem. The two should be decoupled

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