Added additional options to Abyss

docs/CHANGELOG.rst

@@ -26,3 +26,4 @@ Added
 * Import expressions from tranSMART.
 * Limma differential expression (tranSMART)
 * Added VC filtering tool (Chemical mutagenesis)
+* Added aditional analysis options to Abyss assembler

resolwe_bio/processes/assembly/abyss.yml

@@ -4,25 +4,39 @@
 ---
 
 - name: assembler:abyss
-  version: 1.0.1
+  version: 1.0.2
   label: Assembler ABySS (1.9.0)
   type: data:abyss
   category: analyses
   persistence: CACHED
   description: >
     ABySS assembler
   input:
-    - name: reads
-      label: Reads
+    - name: paired_end
+      label: Paired-end reads
       type: data:reads:fastq:paired
+      required: false
       description: >
         Paired-end library
     - name: se
-      label: Reads without mates
+      label: Single-end reads
       type: data:reads:fastq:single
       required: false
       description: >
         Reads without mates should be placed in a file specified by the parameter se (single-end). Reads without mates in the paired-end files will slow down the paired-end assembler considerably during the abyss-fixmate stage.
+    - name: use_unmapped
+      label: Use unmapped reads
+      type: basic:boolean
+      default: false
+      description: >
+        Use unmapped reads from the reads alignment job (compatible with Bowtie and BWA output files). This selection will override the selection of single-end reads on the input.
+    - name: unmapped
+      label: Unmapped Reads
+      type: data:alignment:bam
+      required: false
+      description: >
+        Use unmapped reads from the reads alignment job (compatible with Bowtie and BWA output files). This selection will override the selection of single-end reads on the input.
+      hidden: "use_unmapped === false"
     - name: options
       label: Options
       group:
@@ -43,6 +57,12 @@
               The seed length should be at least twice the value of k. If more
               sequence  is  assembled  than  the  expected  genome  size,  try
               increasing s.
+        - name: n
+          label: Minimum number of pairs
+          type: basic:integer
+          default: 10
+          description: >
+            Minimum number of pairs required for building contigs.
   output:
     - name: contigs
       label: Contigs
@@ -54,7 +74,7 @@
     - name: name
       label: Name
       type: basic:string
-      default: "ABySS assembly ({{ reads.fastq.file|basename|default:'?' }})"
+      default: "ABySS assembly ({{ options.name }})"
     - name: alias
       label: Alias
       type: basic:string
@@ -83,18 +103,35 @@
       re-require common
       re-require abyss-1.9.0
 
-      NAME_1=`basename '{{reads.fastq.file}}' .fastq.gz`
-      NAME_2=`basename '{{reads.fastq2.file}}' .fastq.gz`
-      cp '{{reads.fastq.file}}' ${NAME_1}_1.fastq.gz
-      cp '{{reads.fastq2.file}}' ${NAME_2}_2.fastq.gz
+      {% if not paired_end and not se and not unmapped %}
+        re-error "No input files provided. Please use either Paired-end or Single-end input files to run Abyss."
+      {% endif %}
+
+      {% if paired_end %}
+        ln -s '{{paired_end.fastq.file}}' fw_1.fastq.gz
+        ln -s '{{paired_end.fastq2.file}}' rw_2.fastq.gz
+      {% endif %}
 
+      {% if use_unmapped %}
+        {% if use_unmapped and not unmapped %}
+          re-error "Use unmapped reads option is selected but the input file is not provided."
+        {% else %}
+          SE='se={{ unmapped.unmapped.file }}'
+        {% endif %}
+      {% elif se and not use_unmapped %}
+        SE='se={{ se.fastq.file }}'
+      {% endif %}
+      
       re-progress 0.1
 
-      abyss-pe name='{{options.name}}' k='{{options.k}}' s='{{options.s}}' {% if se %} se='{{se.fastq.file}}' {% endif %} in=''${NAME_1}'_1.fastq.gz '${NAME_2}'_2.fastq.gz'
+      # remove whitespace from a sample name
+      NAME="$(echo -e "{{options.name}}" | tr -d '[[:space:]]')"
+
+      abyss-pe name=${NAME} k='{{options.k}}' s='{{options.s}}' n='{{options.n}}' {% if paired_end %} in='fw_1.fastq.gz rw_2.fastq.gz' {% endif %} ${SE}
       re-checkrc
       re-progress 0.9
 
-      zip '{{options.name}}'_contigs *.fa
+      zip ${NAME}_contigs *.fa
       
-      re-save-file contigs '{{options.name}}'_contigs.zip
-      re-save-file stats '{{options.name}}'-stats.tab
+      re-save-file contigs ${NAME}_contigs.zip
+      re-save-file stats ${NAME}-stats.tab

resolwe_bio/tests/test_assembler.py

@@ -9,10 +9,17 @@ def test_abyss(self):
         inputs = {'src1': 'reads_paired_abyss_1.fastq.gz', 'src2': 'reads_paired_abyss_2.fastq.gz'}
         reads = self.run_processor('import:upload:reads-fastq-paired-end', inputs)
 
-        inputs = {'reads': reads.pk,
+        inputs = {'paired_end': reads.pk,
                   'se': se_reads.pk,
                   'options': {'k': 25,
                               'name': 'ecoli'}}
 
         self.run_processor('assembler:abyss', inputs)
-        # self.assertFiles(abyss, 'contigs', 'contigs.zip', compression='zip')
+
+        inputs = {'paired_end': reads.pk,
+                  'se': se_reads.pk,
+                  'use_unmapped': True,
+                  'options': {'k': 25,
+                              'name': 'ecoli'}}
+
+        self.run_processor('assembler:abyss', inputs, 'error')