From 275c5d8db87c6c5f1680d4ec10cb47ad8de4636b Mon Sep 17 00:00:00 2001 From: Andrew Thrasher Date: Mon, 28 Oct 2024 10:49:59 -0400 Subject: [PATCH] chore: apply PR feedback --- tools/samtools.wdl | 2 +- workflows/hic/hicpro-core.wdl | 2 +- workflows/reference/make-hic-reference.wdl | 18 +++++++++--------- 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/tools/samtools.wdl b/tools/samtools.wdl index d1e5b02d..563d9d94 100755 --- a/tools/samtools.wdl +++ b/tools/samtools.wdl @@ -1343,7 +1343,7 @@ task sort { bam: "Input BAM format file to sort" tag_sort: { description: "Sort by the value of the alignment tag specified in `tag_sort`. When specified, samtools sorts by the value of the alignment tag and then by either position or read name.", - external_help: "https://www.htslib.org/doc/samtools-sort.html" + external_help: "https://www.htslib.org/doc/samtools-sort.html", } prefix: "Prefix for the output file. The extension `.bam` will be added." uncompressed: "Output uncompressed BAM?" diff --git a/workflows/hic/hicpro-core.wdl b/workflows/hic/hicpro-core.wdl index 18fe5f96..028ea2e4 100644 --- a/workflows/hic/hicpro-core.wdl +++ b/workflows/hic/hicpro-core.wdl @@ -49,7 +49,7 @@ workflow hicpro_core { hicpro_field: "MAX_ITER", } bin_sizes: { - description: "Resolution of contact maps to generate ", + description: "Resolution of contact maps to generate", hicpro_field: "BIN_SIZE", } matrix_format: { diff --git a/workflows/reference/make-hic-reference.wdl b/workflows/reference/make-hic-reference.wdl index b9fce2f7..ed1af9bb 100644 --- a/workflows/reference/make-hic-reference.wdl +++ b/workflows/reference/make-hic-reference.wdl @@ -8,13 +8,13 @@ workflow make_hic_reference { meta { description: "Downloads and creates all reference files needed to run the `hic` workflow" outputs: { - reference_fasta: "FASTA format reference file used to generate `bowtie2_db_tar_gz`" - reference_fasta_index: "FASTA index file for `reference_fasta`" - reference_chromsizes: "Chromosome sizes file for `reference_fasta`" - genome_fragment: "BED file(s) with restriction fragments" - exclude_list: "BED file with regions to exclude from analysis" - bowtie2_db_tar_gz: "Gzipped tar archive of the Bowtie2 reference files. Files are at the root of the archive." - bowtie2_index_files: "Bowtie2 index files" + reference_fasta: "FASTA format reference file used to generate `bowtie2_db_tar_gz`", + reference_fasta_index: "FASTA index file for `reference_fasta`", + reference_chromsizes: "Chromosome sizes file for `reference_fasta`", + genome_fragment: "BED file(s) with restriction fragments", + exclude_list: "BED file with regions to exclude from analysis", + bowtie2_db_tar_gz: "Gzipped tar archive of the Bowtie2 reference files. Files are at the root of the archive.", + bowtie2_index_files: "Bowtie2 index files", } allowNestedInputs: true } @@ -26,8 +26,8 @@ workflow make_hic_reference { exclude_list_name: "Name of output exclude list file" restriction_sites: { description: "List of restriction sites for which to extract restriction fragments" - help: "This uses HiC-Pro's `digest_genome.py` script to generate restriction fragments. Each site should be specified as a string of nucleotides. A carat (`^`) marks the cut site." - external_help: "https://github.com/nservant/HiC-Pro/blob/master/doc/UTILS.md#digest_genomepy-or-how-can-i-generate-the-list-of-restriction-fragments-after-genome-digestion-" + help: "This uses HiC-Pro's `digest_genome.py` script to generate restriction fragments. Each site should be specified as a string of nucleotides. A carat (`^`) marks the cut site.", + external_help: "https://github.com/nservant/HiC-Pro/blob/master/doc/UTILS.md#digest_genomepy-or-how-can-i-generate-the-list-of-restriction-fragments-after-genome-digestion-", } restriction_sites_names: "Names for the restriction sites to use in output files" }