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sbslee · Mar 1, 2022 · c6b5e8f · c6b5e8f
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,8 +1,8 @@
 Changelog
 *********
 
-0.31.0 (in development)
------------------------
+0.31.0 (2022-03-01)
+-------------------
 
 * Fix bug in :meth:`pykallisto.KallistoFrame.compute_fold_change` method.
 * Add new method :meth:`pyvcf.call` and new command :command:`vcf-call`.

diff --git a/README.rst b/README.rst
@@ -46,10 +46,10 @@ Currently, fuc can be used to analyze, summarize, visualize, and manipulate the
 
 Additionally, fuc can be used to parse output data from the following programs:
 
-- Ensembl Variant Effect Predictor (VEP)
-- SnpEff
-- bcl2fastq and bcl2fastq2
-- Kallisto
+- `Ensembl Variant Effect Predictor (VEP) <https://asia.ensembl.org/info/docs/tools/vep/index.html>`__
+- `SnpEff <http://pcingola.github.io/SnpEff/>`__
+- `bcl2fastq and bcl2fastq2 <https://sapac.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html>`__
+- `Kallisto <https://pachterlab.github.io/kallisto/>`__
 
 Your contributions (e.g. feature ideas, pull requests) are most welcome.
 
@@ -112,38 +112,38 @@ For getting help on the fuc CLI:
    
    positional arguments:
      COMMAND
-       bam-aldepth  Compute allelic depth from a SAM/BAM/CRAM file.
+       bam-aldepth  Compute allelic depth from a BAM file.
        bam-depth    Compute per-base read depth from BAM files.
-       bam-head     Print the header of a SAM/BAM/CRAM file.
-       bam-index    Index a SAM/BAM/CRAM file.
-       bam-rename   Rename the sample in a SAM/BAM/CRAM file.
-       bam-slice    Slice a SAM/BAM/CRAM file.
+       bam-head     Print the header of a BAM file.
+       bam-index    Index a BAM file.
+       bam-rename   Rename the sample in a BAM file.
+       bam-slice    Slice a BAM file.
        bed-intxn    Find the intersection of BED files.
        bed-sum      Summarize a BED file.
        cov-concat   Concatenate depth of coverage files.
        cov-rename   Rename the samples in a depth of coverage file.
-       fa-filter    Filter sequence records in a FASTA file
+       fa-filter    Filter sequence records in a FASTA file.
        fq-count     Count sequence reads in FASTQ files.
        fq-sum       Summarize a FASTQ file.
        fuc-bgzip    Write a BGZF compressed file.
        fuc-compf    Compare the contents of two files.
        fuc-demux    Parse the Reports directory from bcl2fastq.
        fuc-exist    Check whether certain files exist.
-       fuc-find     Retrieve absolute paths of files whose name matches a 
+       fuc-find     Retrieve absolute paths of files whose name matches a
                     specified pattern, optionally recursively.
-       fuc-undetm   Compute top unknown barcodes using undertermined FASTQ from 
+       fuc-undetm   Compute top unknown barcodes using undertermined FASTQ from
                     bcl2fastq.
        maf-maf2vcf  Convert a MAF file to a VCF file.
        maf-oncoplt  Create an oncoplot with a MAF file.
        maf-sumplt   Create a summary plot with a MAF file.
        maf-vcf2maf  Convert a VCF file to a MAF file.
        ngs-bam2fq   Pipeline for converting BAM files to FASTQ files.
-       ngs-fq2bam   Pipeline for converting FASTQ files to analysis-ready BAM 
+       ngs-fq2bam   Pipeline for converting FASTQ files to analysis-ready BAM
                     files.
        ngs-hc       Pipeline for germline short variant discovery.
        ngs-m2       Pipeline for somatic short variant discovery.
        ngs-pon      Pipeline for constructing a panel of normals (PoN).
-       ngs-quant    Pipeline for running RNAseq quantification from FASTQ files 
+       ngs-quant    Pipeline for running RNAseq quantification from FASTQ files
                     with Kallisto.
        ngs-trim     Pipeline for trimming adapters from FASTQ files.
        tabix-index  Index a GFF/BED/SAM/VCF file with Tabix.