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jdidion / atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)
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request: with --output-format sam , add @PG and @CO header lines to output #105

Closed plijnzaad closed 4 years ago

plijnzaad commented 4 years ago

The SAM header has a provision to annotate files going through pipelines with the processing steps they underwent. E.g. STAR add something like the following to the header:

@PG ID:STAR PN:STAR VN:STAR_2.6.1a_08-27    CL:STAR   --runThreadN 16   --genomeDir ...   --readFilesIn ...  --readFilesCommand zcat --outTmpDir ... --outStd BAM_Unsorted   --outSAMtype BAM   Unsorted      --outSAMunmapped Within      --alignSJoverhangMin 5   --alignEndsType Local   --alignSoftClipAtReferenceEnds yes   --twopassMode Basic
@CO user command line: STAR --genomeDir ... --runThreadN 16 --twopassMode Basic --alignEndsType Local --alignSoftClipAtReferenceEnds yes --outSAMunmapped Within --alignSJoverhangMin 5 --readFilesCommand zcat --outStd BAM_Unsorted --outSAMtype BAM Unsorted --readFilesIn ...  --outTmpDir ...

It would be nice to have something similar in atropos' sam output.

jdidion commented 4 years ago

good idea - will add this in the next release

jdidion commented 4 years ago

Added in develop. @PG header is now always the last header line written. Will be in in alpha6 release.