update changelog, hep.txt, functional test, large test data

CHANGELOG.md

@@ -78,6 +78,9 @@
     - `bedtools_getfasta`: extract sequences from a FASTA file for each of the
                            intervals defined in a BED/GFF/VCF file (PR #59).
 
+* `bbmap`:
+    - `bbmap_bbsplit`: Split sequencing reads by mapping them to multiple references simultaneously (PR #138).
+
 ## MINOR CHANGES
 
 * Uniformize component metadata (PR #23).

src/bbmap_bbsplit/config.vsh.yaml

@@ -21,6 +21,7 @@ argument_groups:
     type: file
     multiple: true
     description: Input fastq files, either one or two (paired), separated by ";".
+    multiple_sep: ","
     example: reads.fastq
   - name: "--primary_ref"
     type: file
@@ -38,8 +39,8 @@ argument_groups:
     description: |
       Designate index to use. Corresponds to the number specified when building the index.
       If building the index, this will be the build's id. If multiple references are indexed
-      in the same directory, each needs a unique build ID. Default: 1.\
-    example: 1
+      in the same directory, each needs a unique build ID. Default: 1.
+    example: "1"
   - name: "--qin"
     type: string
     description: |
@@ -127,8 +128,6 @@ argument_groups:
     type: file
     description: |
       Directory with index files.
-    direction: output
-    example: bbsplit
   - name: "--sam2bam"
     alternatives: ["--bs"]
     type: file
@@ -175,7 +174,7 @@ engines:
         cp -r bbmap/* /usr/local/bin
     - type: docker
       run: |
-        echo "${meta_functionality_name}: bbmap: $(bbversion.sh | grep -v "Duplicate cpuset")" > /var/software_versions.txt
+        bbsplit.sh --version 2>&1 | awk '/BBMap version/{print "BBMAP:", $NF}' > /var/software_versions.txt
 runners:
   - type: executable
   - type: nextflow

src/bbmap_bbsplit/help.txt

@@ -0,0 +1,83 @@
+```
+bbsplit.sh
+```
+
+BBSplit
+Written by Brian Bushnell, from Dec. 2010 - present
+Last modified June 11, 2018
+
+Description:  Maps reads to multiple references simultaneously.
+Outputs reads to a file for the reference they best match, with multiple options for dealing with ambiguous mappings.
+
+To index:     bbsplit.sh build=<1> ref_x=<reference fasta> ref_y=<another reference fasta>
+To map:       bbsplit.sh build=<1> in=<reads> out_x=<output file> out_y=<another output file>
+
+To be concise, and do everything in one command:
+bbsplit.sh ref=x.fa,y.fa in=reads.fq basename=o%.fq
+
+that is equivalent to
+bbsplit.sh build=1 in=reads.fq ref_x=x.fa ref_y=y.fa out_x=ox.fq out_y=oy.fq
+
+By default paired reads will yield interleaved output, but you can use the # symbol to produce twin output files.
+For example, basename=o%_#.fq will produce ox_1.fq, ox_2.fq, oy_1.fq, and oy_2.fq.
+
+
+Indexing Parameters (required when building the index):
+ref=<file,file>     A list of references, or directories containing fasta files.
+ref_<name>=<ref.fa> Alternate, longer way to specify references. e.g., ref_ecoli=ecoli.fa
+                    These can also be comma-delimited lists of files; e.g., ref_a=a1.fa,a2.fa,a3.fa
+build=<1>           If multiple references are indexed in the same directory, each needs a unique build ID.
+path=<.>            Specify the location to write the index, if you don't want it in the current working directory.
+
+Input Parameters:
+build=<1>           Designate index to use.  Corresponds to the number specified when building the index.
+in=<reads.fq>       Primary reads input; required parameter.
+in2=<reads2.fq>     For paired reads in two files.
+qin=<auto>          Set to 33 or 64 to specify input quality value ASCII offset.
+interleaved=<auto>  True forces paired/interleaved input; false forces single-ended mapping.
+                    If not specified, interleaved status will be autodetected from read names.
+
+Mapping Parameters:
+maxindel=<20>       Don't look for indels longer than this.  Lower is faster.  Set to >=100k for RNA-seq.
+minratio=<0.56>     Fraction of max alignment score required to keep a site.  Higher is faster.
+minhits=<1>         Minimum number of seed hits required for candidate sites.  Higher is faster.
+ambiguous=<best>    Set behavior on ambiguously-mapped reads (with multiple top-scoring mapping locations).
+                       best   (use the first best site)
+                       toss   (consider unmapped)
+                       random   (select one top-scoring site randomly)
+                       all   (retain all top-scoring sites.  Does not work yet with SAM output)
+ambiguous2=<best>   Set behavior only for reads that map ambiguously to multiple different references.
+                    Normal 'ambiguous=' controls behavior on all ambiguous reads;
+                    Ambiguous2 excludes reads that map ambiguously within a single reference.
+                       best   (use the first best site)
+                       toss   (consider unmapped)
+                       all   (write a copy to the output for each reference to which it maps)
+                       split   (write a copy to the AMBIGUOUS_ output for each reference to which it maps)
+qtrim=<true>        Quality-trim ends to Q5 before mapping.  Options are 'l' (left), 'r' (right), and 'lr' (both).
+untrim=<true>       Undo trimming after mapping.  Untrimmed bases will be soft-clipped in cigar strings.
+
+Output Parameters:
+out_<name>=<file>   Output reads that map to the reference <name> to <file>.
+basename=prefix%suffix     Equivalent to multiple out_%=prefix%suffix expressions, in which each % is replaced by the name of a reference file.
+bs=<file>           Write a shell script to 'file' that will turn the sam output into a sorted, indexed bam file.
+scafstats=<file>    Write statistics on how many reads mapped to which scaffold to this file.
+refstats=<file>     Write statistics on how many reads were assigned to which reference to this file.
+                    Unmapped reads whose mate mapped to a reference are considered assigned and will be counted.
+nzo=t               Only print lines with nonzero coverage.
+
+***** Notes *****
+Almost all BBMap parameters can be used; run bbmap.sh for more details.
+Exceptions include the 'nodisk' flag, which BBSplit does not support.
+BBSplit is recommended for fastq and fasta output, not for sam/bam output.
+When the reference sequences are shorter than read length, use Seal instead of BBSplit.
+
+Java Parameters:
+-Xmx                This will set Java's memory usage, overriding autodetection.
+                    -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
+                    The max is typically 85% of physical memory.
+-eoom               This flag will cause the process to exit if an
+                    out-of-memory exception occurs.  Requires Java 8u92+.
+-da                 Disable assertions.
+
+This list is not complete.  For more information, please consult /readme.txt
+Please contact Brian Bushnell at [email protected] if you encounter any problems.