🔧 Fix FASTQ Bug #58
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🔧 Fix FASTQ Bug #58
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🔨 added sam attrs input
📝 added guidance for mulitple RGs
migbro
added
bug
sickler-alex
approved these changes
Nov 7, 2024
dmiller15
requested changes
Nov 7, 2024
docs/10X_STAR_Solo_alignment.md
Outdated
| @@ -31,7 +31,8 @@ They can also be obtained from the following sources: | |||
| - `r2_max_len`: Set read2 to a fixed length. Useful for single cell experiments in which the number of cycles was improperly configured during sequencing. Recommend `91` for 10X v3 chemistry | |||
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| ### STAR Solo | |||
| - `outSAMattrRGline`: Set if outputting bam, with TABS SEPARATING THE TAGS, format is: ID:sample_name LB:aliquot_id PL:platform SM:BSID for example ID:7316-242 LB:750189 PL:ILLUMINA SM:BS_W72364MN | |||
| - `outSAMattrRGline`: Set if outputting bam, with TABS SEPARATING THE TAGS, format is: ID:sample_name LB:aliquot_id PL:platform SM:BSID for example `ID:HFWFVDMXX.L001 LB:750189 PL:ILLUMINA SM:BS_W72364MN`. If more than one fastq pair in input, it is recommended to have one read group per pair, separated by space-comma-space (` , `) | |||
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I think we should make this a list input since BixOps seems to prefer that approach.
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dmiller15
approved these changes
Nov 8, 2024
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Description
A recent update to add a scatter job of cutadapt to fix lengths of inputs introduced a bug in which if a user does not provide lengths to fix, the workflow does not pass the correct input to STAR causing failure. This replaces pickValue with a valueFrom to better asses a [null, null] evaluation. Als,o more for added functionality, is the read group name input in the rare event a user wants to keep the bam output
Fixes # https://d3b.atlassian.net/browse/BIXU-3795
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