Rubicon #123
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Rubicon #123
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- coreutil on non-linux platforms (realpath, sha<nnn>sum, etc.) - optional inputs (dehuman, fasta checksums, etc.)
- allow user to tailor the script to their needs e.g. uploading to an SFTP server, etc.
- comment in indented rule block inside condition
- reuse rejects from bwa/bowtie/ngshmmalign - option to redo a (bwa) align to rejects, WITHOUT forcing to reprocess everything else
- "local" option in dehuman.smk (was using wrong config property) - "results" and "samples" are separate in common.smk
- keep the linter happy - runs tests on upload.smk, too - lint Docker
- ref_{xxx} fasta files now follows "consensus" property,
like consensus.bcftools.fasta
- RegEx expanded to cover more corner cases to convert
Illumina index "1:N:0:..." into SAM comment "BC:Z:..."
- support dual index: ATCG+CGAT
- support single index: GATTA
- support numerical indicator: 180
- compressing unfiltered raw read into cram - use dehuman ressource for larger alignements (host, etc.) - options to exec in demo upload script - typos - unfiltered cram in tests
- use temp_prefix-ed temporary files for sorting - keep only aligned raw reads in host_aln.cram
MegaLinter status: ✅ SUCCESS
See errors details in artifact MegaLinter reports on CI Job page |
- it is mandatory for some targets like GISAID
- When _NOT_ in catchup mode, re-use the extracted_data/R?.fastq that is produced as part of the normal processing. (Note: unlike prinseq, the sorting isn't required for BWA) - Change text to "host" instead of "human" or "H. Sapiens"
- Can use an URL for host genome (Homo Sapiens) - re-organising bwa indexing code to support this - can still crash in various circumstance, considered unstable
- small cosmetic fixes (mostly uppercase and final dot) - sync HTML manual
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I think that's about how much polishing we'll do on that upload feature for now.
Care to have a look at how it is organized?