Add ExpansionHunter, glnexus_cli, lofreq

bio.txt

@@ -1,6 +1,7 @@
 Bifrost
 CrossMap.py
 DAS_Tool
+ExpansionHunter
 GUESSmyLT
 Genrich
 GraphAligner
@@ -261,6 +262,7 @@ gfatools
 gff3-to-ddbj
 gffread
 gffutils-cli
+glnexus_cli
 graphlan.py
 gridss
 gt
@@ -322,6 +324,7 @@ krakenuniq-download
 load-graph.py
 load-into-counting.py
 loadPromoters.pl
+lofreq
 long_fastx
 lumpy
 lumpyexpress

bio/json/ExpansionHunter.json

@@ -0,0 +1 @@
+{"name":"ExpansionHunter","description":"A suite of tools for detecting expansions of short tandem repeats","usage":"","options":[{"names":["-h","--help"],"argument":"","description":"Print help message"},{"names":["-v","--version"],"argument":"","description":"Print version number"},{"names":["--reads"],"argument":"arg","description":"BAM/CRAM file with aligned reads"},{"names":["--reference"],"argument":"arg","description":"FASTA file with reference genome"},{"names":["--variant-catalog"],"argument":"arg","description":"JSON file with variants to genotype"},{"names":["--output-prefix"],"argument":"arg","description":"Prefix for the output files"},{"names":["--region-extension-length"],"argument":"arg (=1000)","description":"How far from on/off-target regions to search for informative reads"},{"names":["--sex"],"argument":"arg (=female)","description":"Sex of the sample; must be either male or female"},{"names":["--log-level"],"argument":"arg (=info)","description":"trace, debug, info, warn, or error"},{"names":["-a","--aligner"],"argument":"arg (=dag-aligner)","description":"Specify which aligner to use (dag-aligner or path-aligner)"},{"names":["-m","--analysis-mode"],"argument":"arg (=seeking)","description":"Specify which analysis workflow to use (seeking or streaming)"},{"names":["-n","--threads"],"argument":"arg (=1)","description":"Number of threads to use"}],"version":"ExpansionHunter v5.0.0"}

bio/json/glnexus_cli.json

@@ -0,0 +1 @@
+{"name":"glnexus_cli","description":"Merge and joint-call input gVCF files, emitting multi-sample BCF on standard output","usage":"glnexus_cli [options] /vcf/file/1 .. /vcf/file/N","options":[{"names":["--dir","-d"],"argument":"DIR","description":"scratch directory path (mustn't already exist; default: ./GLnexus.DB)"},{"names":["--config","-c"],"argument":"X","description":"configuration preset name or .yml filename (default: gatk)"},{"names":["--bed","-b"],"argument":"FILE","description":"three-column BED file with ranges to analyze (if neither --range nor --bed: use full length of all contigs)"},{"names":["--list","-l"],"argument":"","description":"expect given files to contain lists of gVCF filenames, one per line"},{"names":["--more-PL","-P"],"argument":"","description":"include PL from reference bands and other cases omitted by default"},{"names":["--squeeze","-S"],"argument":"","description":"reduce pVCF size by suppressing detail in cells derived from reference bands"},{"names":["--trim-uncalled-alleles","-a"],"argument":"","description":"remove alleles with no output GT calls in postprocessing"},{"names":["--mem-gbytes","-m"],"argument":"X","description":"memory budget, in gbytes (default: most of system memory)"},{"names":["--threads","-t"],"argument":"X","description":"thread budget (default: all hardware threads)"},{"names":["--help","-h"],"argument":"","description":"print this help message"}],"version":"v1.4.1-0-g68e25e5"}

bio/yaml/ExpansionHunter.yaml

@@ -0,0 +1,58 @@
+name: ExpansionHunter
+description: A suite of tools for detecting expansions of short tandem repeats
+usage: ""
+options:
+  - names:
+      - -h
+      - --help
+    argument: ""
+    description: Print help message
+  - names:
+      - -v
+      - --version
+    argument: ""
+    description: Print version number
+  - names:
+      - --reads
+    argument: arg
+    description: BAM/CRAM file with aligned reads
+  - names:
+      - --reference
+    argument: arg
+    description: FASTA file with reference genome
+  - names:
+      - --variant-catalog
+    argument: arg
+    description: JSON file with variants to genotype
+  - names:
+      - --output-prefix
+    argument: arg
+    description: Prefix for the output files
+  - names:
+      - --region-extension-length
+    argument: arg (=1000)
+    description: How far from on/off-target regions to search for informative reads
+  - names:
+      - --sex
+    argument: arg (=female)
+    description: Sex of the sample; must be either male or female
+  - names:
+      - --log-level
+    argument: arg (=info)
+    description: trace, debug, info, warn, or error
+  - names:
+      - -a
+      - --aligner
+    argument: arg (=dag-aligner)
+    description: Specify which aligner to use (dag-aligner or path-aligner)
+  - names:
+      - -m
+      - --analysis-mode
+    argument: arg (=seeking)
+    description: Specify which analysis workflow to use (seeking or streaming)
+  - names:
+      - -n
+      - --threads
+    argument: arg (=1)
+    description: Number of threads to use
+version: ExpansionHunter v5.0.0

bio/yaml/bio.yaml

@@ -59,7 +59,7 @@ subcommands:
         description: fields
   - name: fetch
     description: download GenBank/ENSEMBL data
-    usage: bio download [-h] [-d ''] [-t ''] [-f ''] [-l None] [acc ...]
+    usage: bio download [-h] [-d ''] [-t ''] [-f ''] [-l 100] [-o ''] [acc ...]
     options:
       - names:
           - -h
@@ -84,8 +84,13 @@ subcommands:
       - names:
           - -l
           - --limit
-        argument: None
+        argument: "100"
         description: limit results
+      - names:
+          - -o
+          - --out
+        argument: ''''''
+        description: output file (used as prefix in for FASTQ)
   - name: fasta
     description: convert to FASTA
     usage: bio fasta [-h] [-s 1] [-e ''] [-t ''] [-i ''] [-m ''] [-g ''] [-r ''] [-p] [-T] [-R] [-G] [-A ''] [-o ''] [-F 1] [fnames ...]
@@ -697,7 +702,7 @@ subcommands:
           - --tab
         argument: ""
         description: tab delimited (default is csv)
-version: '1.5.9'
+version: '1.6.0'
 tldr: |
   >  bio is a bioinformatics toy to play with.
   >  More information: <https://github.com/ialbert/bio>.

bio/yaml/glnexus_cli.yaml

@@ -0,0 +1,55 @@
+name: glnexus_cli
+description: Merge and joint-call input gVCF files, emitting multi-sample BCF on standard output
+usage: glnexus_cli [options] /vcf/file/1 .. /vcf/file/N
+options:
+  - names:
+      - --dir
+      - -d
+    argument: DIR
+    description: 'scratch directory path (mustn''t already exist; default: ./GLnexus.DB)'
+  - names:
+      - --config
+      - -c
+    argument: X
+    description: 'configuration preset name or .yml filename (default: gatk)'
+  - names:
+      - --bed
+      - -b
+    argument: FILE
+    description: 'three-column BED file with ranges to analyze (if neither --range nor --bed: use full length of all contigs)'
+  - names:
+      - --list
+      - -l
+    argument: ""
+    description: expect given files to contain lists of gVCF filenames, one per line
+  - names:
+      - --more-PL
+      - -P
+    argument: ""
+    description: include PL from reference bands and other cases omitted by default
+  - names:
+      - --squeeze
+      - -S
+    argument: ""
+    description: reduce pVCF size by suppressing detail in cells derived from reference bands
+  - names:
+      - --trim-uncalled-alleles
+      - -a
+    argument: ""
+    description: remove alleles with no output GT calls in postprocessing
+  - names:
+      - --mem-gbytes
+      - -m
+    argument: X
+    description: 'memory budget, in gbytes (default: most of system memory)'
+  - names:
+      - --threads
+      - -t
+    argument: X
+    description: 'thread budget (default: all hardware threads)'
+  - names:
+      - --help
+      - -h
+    argument: ""
+    description: print this help message
+version: v1.4.1-0-g68e25e5