From 20bc1fe0b65b23b32306e4a51f66468b0f946164 Mon Sep 17 00:00:00 2001 From: emmarousseau Date: Fri, 5 Jul 2024 13:42:27 +0100 Subject: [PATCH] Markdown formatting changes in configs --- src/samtools/samtools_fasta/config.vsh.yaml | 32 ++++++++++---------- src/samtools/samtools_fastq/config.vsh.yaml | 33 +++++++++++---------- 2 files changed, 35 insertions(+), 30 deletions(-) diff --git a/src/samtools/samtools_fasta/config.vsh.yaml b/src/samtools/samtools_fasta/config.vsh.yaml index 9a85ab5f..23517f6c 100644 --- 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 index e6436067..cac7653b 100644 --- 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