From de84e6d5f8b6458da20641f61932c1009dd30c5b Mon Sep 17 00:00:00 2001 From: kerstenbreuer Date: Tue, 26 Nov 2019 17:43:41 +0100 Subject: [PATCH] fix formating of doc --- CWL/tools/deeptools_bamCoverage.cwl | 4 +- .../bed_to_coverage_track.cwl | 4 +- CWL/workflows/ATACseq.cwl | 80 ++++++++++--------- CWL/workflows/ATACseq_aligned.cwl | 24 +++--- 4 files changed, 60 insertions(+), 52 deletions(-) diff --git a/CWL/tools/deeptools_bamCoverage.cwl b/CWL/tools/deeptools_bamCoverage.cwl index b42ceb1..fd67f3f 100644 --- a/CWL/tools/deeptools_bamCoverage.cwl +++ b/CWL/tools/deeptools_bamCoverage.cwl @@ -55,8 +55,10 @@ inputs: position: 10 ignoreForNormalization: doc: | - List of space-delimited chromosome names that shall be ignored + List of space-delimited chromosome names that shall be ignored when calculating the scaling factor. + Specify as space-delimited string. + Default: "chrX chrY chrM" type: string? default: "chrX chrY chrM" inputBinding: diff --git a/CWL/workflow_modules/bed_to_coverage_track.cwl b/CWL/workflow_modules/bed_to_coverage_track.cwl index 7ab2c0c..b22383a 100644 --- a/CWL/workflow_modules/bed_to_coverage_track.cwl +++ b/CWL/workflow_modules/bed_to_coverage_track.cwl @@ -14,8 +14,10 @@ inputs: type: int ignoreForNormalization: doc: | - List of space-delimited chromosome names that shall be ignored + List of space-delimited chromosome names that shall be ignored when calculating the scaling factor. + Specify as space-delimited string. + Default: "chrX chrY chrM" type: string? default: "chrX chrY chrM" diff --git a/CWL/workflows/ATACseq.cwl b/CWL/workflows/ATACseq.cwl index a8db051..680e4a0 100644 --- a/CWL/workflows/ATACseq.cwl +++ b/CWL/workflows/ATACseq.cwl @@ -15,51 +15,51 @@ inputs: type: string fastq1: doc: | - List of fastq files containing the first mate of raw reads. - Muliple files are provided if multiplexing of the same library has been done - on multiple lanes. The reads comming from different fastq files are pooled - after alignment. Also see parameter "fastq2". + List of fastq files containing the first mate of raw reads. + Muliple files are provided if multiplexing of the same library has been done + on multiple lanes. The reads comming from different fastq files are pooled + after alignment. Also see parameter "fastq2". type: type: array items: File fastq2: doc: | - List of fastq files containing the second mate of raw reads. + List of fastq files containing the second mate of raw reads. Important: this list has to be of same length as parameter "fastq1". type: type: array items: File adapter1: doc: | - Adapter sequence for first reads. - If not specified (set to "null"), trim_galore will try to autodetect whether ... - - Illumina universal adapter (AGATCGGAAGAGC) - - Nextera adapter (CTGTCTCTTATA) - - Illumina Small RNA 3-prime Adapter (TGGAATTCTCGG) - ... was used. - You can directly choose one of the above configurations - by setting the string to "illumina", "nextera", or "small_rna". + Adapter sequence for first reads. + If not specified (set to "null"), trim_galore will try to autodetect whether ...\n + - Illumina universal adapter (AGATCGGAAGAGC)\n + - Nextera adapter (CTGTCTCTTATA)\n + - Illumina Small RNA 3-prime Adapter (TGGAATTCTCGG)\n + ... was used.\n + You can directly choose one of the above configurations + by setting the string to "illumina", "nextera", or "small_rna". Or you specify the adaptor string manually (e.g. "AGATCGGAAGAGC"). type: string? adapter2: doc: | - Adapter sequence for second reads. - If it is not specified (set to "null"), trim_galore will try to autodetect whether ... - - Illumina universal adapter (AGATCGGAAGAGC) - - Nextera adapter (CTGTCTCTTATA) - - Illumina Small RNA 3-prime Adapter (TGGAATTCTCGG) - ... was used. - You can directly choose one of the above configurations - by setting the string to "illumina", "nextera", or "small_rna". + Adapter sequence for second reads. + If not specified (set to "null"), trim_galore will try to autodetect whether ...\n + - Illumina universal adapter (AGATCGGAAGAGC)\n + - Nextera adapter (CTGTCTCTTATA)\n + - Illumina Small RNA 3-prime Adapter (TGGAATTCTCGG)\n + ... was used.\n + You can directly choose one of the above configurations + by setting the string to "illumina", "nextera", or "small_rna". Or you specify the adaptor string manually (e.g. "AGATCGGAAGAGC"). type: string? genome: doc: | - Path to reference genome in fasta format. - Bowtie2 index files (".1.bt2", ".2.bt2", ...) as well as a samtools index (".fai") - has to be located in the same directory. - All of these files can be downloaded for the most common genome builds at - https://support.illumina.com/sequencing/sequencing_software/igenome.html. + Path to reference genome in fasta format. + Bowtie2 index files (".1.bt2", ".2.bt2", ...) as well as a samtools index (".fai") + has to be located in the same directory.\n + All of these files can be downloaded for the most common genome builds at + https://support.illumina.com/sequencing/sequencing_software/igenome.html. Alternatively, you can use "bowtie2-build" or "samtools index" to create them yourself. type: File secondaryFiles: @@ -72,27 +72,27 @@ inputs: - ^.rev.2.bt2 genome_info: doc: | - Path to a tab-delimited file listing chromosome sizes in following fashion: - "chromosome_nametotal_number_of_bp". - For the most common UCSC genome build, you can find corresponding files at: - https://github.com/CompEpigen/ATACseq_workflows/tree/master/chrom_sizes. + Path to a tab-delimited file listing chromosome sizes in following fashion:\n + "chromosome_nametotal_number_of_bp".\n + For the most common UCSC genome build, you can find corresponding files at: + https://github.com/CompEpigen/ATACseq_workflows/tree/master/chrom_sizes. Or you can generate them yourself using UCSC script fetchChromSizes - (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes) in following fashion: - "fetchChromSizes hg38 > hg38.chrom.sizes". - If you are dealing with a non-UCSC build, you can generate such a file from a samtools index using: + (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes) in following fashion:\n + "fetchChromSizes hg38 > hg38.chrom.sizes".\n + If you are dealing with a non-UCSC build, you can generate such a file from a samtools index using:\n "awk -v OFS='\t' {'print $1,$2'} hg38.fa.fai > hg38.chrom.sizes". type: File max_mapping_insert_length: doc: | - Maximum insert length between two reads of a pair. In case of ATACseq, - very long insert sizes are possible. So it is recommended to use at least + Maximum insert length between two reads of a pair. In case of ATACseq, + very long insert sizes are possible. So it is recommended to use at least a value of 1500. However, please note that alignment will take significantly longer for higher insert sizes. The default is 2500. type: long default: 2500 macs2_qvalue: doc: | - Q-value cutoff used for peak calling by MACS2. + Q-value cutoff used for peak calling by MACS2. The default is 0.05. type: float default: 0.05 @@ -103,15 +103,17 @@ inputs: type: long bin_size: doc: | - Bin size used for generation of coverage tracks. - The larger the bin size the smaller are the coverage tracks, however, + Bin size used for generation of coverage tracks. + The larger the bin size the smaller are the coverage tracks, however, the less precise is the signal. For single bp resolution set to 1. type: int default: 10 ignoreForNormalization: doc: | - List of space-delimited chromosome names that shall be ignored + List of space-delimited chromosome names that shall be ignored when calculating the scaling factor. + Specify as space-delimited string. + Default: "chrX chrY chrM" type: string? default: "chrX chrY chrM" diff --git a/CWL/workflows/ATACseq_aligned.cwl b/CWL/workflows/ATACseq_aligned.cwl index a7ac7d7..37c8d5e 100644 --- a/CWL/workflows/ATACseq_aligned.cwl +++ b/CWL/workflows/ATACseq_aligned.cwl @@ -18,19 +18,19 @@ inputs: type: File genome_info: doc: | - Path to a tab-delimited file listing chromosome sizes in following fashion: - "chromosome_nametotal_number_of_bp". - For the most common UCSC genome build, you can find corresponding files at: - https://github.com/CompEpigen/ATACseq_workflows/tree/master/chrom_sizes. + Path to a tab-delimited file listing chromosome sizes in following fashion:\n + "chromosome_nametotal_number_of_bp".\n + For the most common UCSC genome build, you can find corresponding files at: + https://github.com/CompEpigen/ATACseq_workflows/tree/master/chrom_sizes. Or you can generate them yourself using UCSC script fetchChromSizes - (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes) in following fashion: - "fetchChromSizes hg38 > hg38.chrom.sizes". - If you are dealing with a non-UCSC build, you can generate such a file from a samtools index using: + (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes) in following fashion:\n + "fetchChromSizes hg38 > hg38.chrom.sizes".\n + If you are dealing with a non-UCSC build, you can generate such a file from a samtools index using:\n "awk -v OFS='\t' {'print $1,$2'} hg38.fa.fai > hg38.chrom.sizes". type: File macs2_qvalue: doc: | - Q-value cutoff used for peak calling by MACS2. + Q-value cutoff used for peak calling by MACS2. The default is 0.05. type: float default: 0.05 @@ -41,15 +41,17 @@ inputs: type: long bin_size: doc: | - Bin size used for generation of coverage tracks. - The larger the bin size the smaller are the coverage tracks, however, + Bin size used for generation of coverage tracks. + The larger the bin size the smaller are the coverage tracks, however, the less precise is the signal. For single bp resolution set to 1. type: int default: 10 ignoreForNormalization: doc: | - List of space-delimited chromosome names that shall be ignored + List of space-delimited chromosome names that shall be ignored when calculating the scaling factor. + Specify as space-delimited string. + Default: "chrX chrY chrM" type: string? default: "chrX chrY chrM"