Markdown formatting changes in configs

emmarousseau · Jul 5, 2024 · 20bc1fe · 20bc1fe
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commit 20bc1fe
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Showing 2 changed files with 35 additions and 30 deletions.
diff --git a/src/samtools/samtools_fasta/config.vsh.yaml b/src/samtools/samtools_fasta/config.vsh.yaml
@@ -56,7 +56,7 @@ argument_groups:
         type: string
         description: |
           Specify a comma-separated list of tags to copy to the FASTA header line, if they exist. 
-          TAGLIST can be blank or * to indicate all tags should be copied to the output. If using *, 
+          TAGLIST can be blank or `*` to indicate all tags should be copied to the output. If using `*`, 
           be careful to quote it to avoid unwanted shell expansion.
       - name: --read1
         alternatives: -1
@@ -91,34 +91,34 @@ argument_groups:
         type: integer
         description: |
           Only output alignments with all bits set in INT present in the FLAG field. INT can be specified 
-          in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' 
-          (i.e. /^0[0-7]+/). [0]
+          in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with '0' 
+          (i.e. /^0[0-7]+/). Default: `0`.
         example: 0
       - name: --excl_flags
         alternatives: -F
         type: string
         description: |
           Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified 
-          in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' 
+          in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with '0'
           (i.e. /^0[0-7]+/). This defaults to 0x900 representing filtering of secondary and 
-          supplementary alignments. [0x900]
+          supplementary alignments. Default: `0x900`.
         example: "0x900"
       - name: --incl_flags
         alternatives: --rf
         type: string
         description: |
           Only output alignments with any bits set in INT present in the FLAG field. INT can be specified 
-          in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0' 
+          in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with '0'
           (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a comma-separated list of 
-          flag names. [0]
+          flag names. Default: `0`.
         example: 0
       - name: --excl_flags_all
         alternatives: -G
         type: integer
         description: |
           Only EXCLUDE reads with all of the bits set in INT present in the FLAG field. INT can be specified 
-          in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' 
-          (i.e. /^0[0-7]+/). [0]
+          in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with '0' (i.e. /^0[0-7]+/).
+          Default: `0`.
         example: 0
       - name: --aux_tag
         alternatives: -d
@@ -153,20 +153,22 @@ argument_groups:
         description: write second index reads to FILE.
       - name: --barcode_tag
         type: string
-        description: Auxiliary tag to find index reads in. [BC]
+        description: |
+          Auxiliary tag to find index reads in. Default: `BC`.
         example: "BC"
       - name: --quality_tag
         type: string
-        description: Auxiliary tag to find index quality in. [QT]
+        description: |
+          Auxiliary tag to find index quality in. Default: `QT`.
         example: "QT"
       - name: --index_format
         type: string
         description: |
           string to describe how to parse the barcode and quality tags. For example:
-          [i14i8]: the first 14 characters are index 1, the next 8 characters are index 2.
-          [n8i14]: ignore the first 8 characters, and use the next 14 characters for index 1.
-          If the tag contains a separator, then the numeric part can be replaced with '*' to mean 
-          'read until the separator or end of tag', for example: [n*i*].
+          * `i14i8`: the first 14 characters are index 1, the next 8 characters are index 2.
+          * `n8i14`: ignore the first 8 characters, and use the next 14 characters for index 1.
+          If the tag contains a separator, then the numeric part can be replaced with`*` to mean 
+          'read until the separator or end of tag', for example: `n*i*`.
 
 resources:
   - type: bash_script

diff --git a/src/samtools/samtools_fastq/config.vsh.yaml b/src/samtools/samtools_fastq/config.vsh.yaml
@@ -56,7 +56,7 @@ argument_groups:
         type: string
         description: |
           Specify a comma-separated list of tags to copy to the FASTQ header line, if they exist. 
-          TAGLIST can be blank or * to indicate all tags should be copied to the output. If using *, 
+          TAGLIST can be blank or `*` to indicate all tags should be copied to the output. If using `*`, 
           be careful to quote it to avoid unwanted shell expansion.
       - name: --read1
         alternatives: -1
@@ -91,34 +91,34 @@ argument_groups:
         type: integer
         description: |
           Only output alignments with all bits set in INT present in the FLAG field. INT can be specified 
-          in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' 
-          (i.e. /^0[0-7]+/). [0]
+          in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with '0'
+          (i.e. /^0[0-7]+/). Default: `0`.
         example: 0
       - name: --excl_flags
         alternatives: -F
         type: string
         description: |
           Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified 
-          in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' 
+          in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with '0' 
           (i.e. /^0[0-7]+/). This defaults to 0x900 representing filtering of secondary and 
-          supplementary alignments. [0x900]
+          supplementary alignments. Default: `0x900`.
         example: "0x900"
       - name: --incl_flags
         alternatives: --rf
         type: string
         description: |
           Only output alignments with any bits set in INT present in the FLAG field. INT can be specified 
-          in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0' 
+          in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with '0'
           (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a comma-separated list of 
-          flag names. [0]
+          flag names. Default: `0`.
         example: 0
       - name: --excl_flags_all
         alternatives: -G
         type: integer
         description: |
           Only EXCLUDE reads with all of the bits set in INT present in the FLAG field. INT can be specified 
-          in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' 
-          (i.e. /^0[0-7]+/). [0]
+          in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with '0' (i.e. /^0[0-7]+/).
+          Default: `0`.
         example: 0
       - name: --aux_tag
         alternatives: -d
@@ -137,7 +137,8 @@ argument_groups:
       - name: --casava
         alternatives: -i
         type: boolean_true
-        description: add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)
+        description: |
+          Add Illumina Casava 1.8 format entry to header, for example: `1:N:0:ATCACG`.
       - name: --compression
         alternatives: -c
         type: integer
@@ -153,20 +154,22 @@ argument_groups:
         description: write second index reads to FILE.
       - name: --barcode_tag
         type: string
-        description: Auxiliary tag to find index reads in. [BC]
+        description: |
+          Auxiliary tag to find index reads in. Default: `BC`.
         example: "BC"
       - name: --quality_tag
         type: string
-        description: Auxiliary tag to find index quality in. [QT]
+        description: |
+          Auxiliary tag to find index quality in. Default: `QT`.
         example: QT
       - name: --index_format
         type: string
         description: |
           string to describe how to parse the barcode and quality tags. For example:
-          [i14i8]: the first 14 characters are index 1, the next 8 characters are index 2.
-          [n8i14]: ignore the first 8 characters, and use the next 14 characters for index 1.
+          * `i14i8`: the first 14 characters are index 1, the next 8 characters are index 2.
+          * `n8i14`: ignore the first 8 characters, and use the next 14 characters for index 1.
           If the tag contains a separator, then the numeric part can be replaced with '*' to mean 
-          'read until the separator or end of tag', for example: [n*i*].
+          'read until the separator or end of tag', for example: `n*i*`.
 
 resources:
   - type: bash_script