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FIX: Make output quant file an optional argument #151

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Sep 13, 2024
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FIX: Make output quant file an optional argument #151

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6 changes: 3 additions & 3 deletions src/salmon/salmon_quant/config.vsh.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ argument_groups:
description: |
Format string describing the library.
The library type string consists of three parts:
1. Relative orientation of the reads: This part is only provided if the library is paired-end, THe possible options are
1. Relative orientation of the reads: This part is only provided if the library is paired-end, The possible options are
I = inward
O = outward
M = matching
Expand Down Expand Up @@ -118,7 +118,7 @@ argument_groups:
direction: output
description: |
Salmon quantification file.
required: true
required: false
example: quant.sf

- name: Basic options
Expand Down Expand Up @@ -327,7 +327,7 @@ argument_groups:
If this option is provided, then the selective-alignment results will be written out in SAM-compatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead.
- name: --mapping_sam
type: file
description: Path to file that should output the selective-alignment results in SAM-compatible format. THis option must be provided while using --write_mappings
description: Path to file that should output the selective-alignment results in SAM-compatible format. This option must be provided while using --write_mappings
required: false
direction: output
example: mappings.sam
Expand Down