recursively map

template2/recursive_map.jinja2

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+### run
+
+reference={{reference}}
+
+{% for i in range(iterations) %}
+    {% if i <= (iterations / 2) %}{% set aln_param=param_strict %}
+    {% else %}{% set aln_param=param_loose %}
+    {% endif %}
+    echo "Iteration {{i}} ---"
+    echo "With reference: ${reference}"
+    if [[ ! -f "db.{{i}}.ann" ]]
+    then
+        echo "create bwa database {{i}}"
+        bwa index -p db.{{i}} ${reference}
+    fi
+
+    echo "start aligning $i"
+    bamfiles=""
+    {% for ffq in fq_forward %}
+       {% set rfq =  fq_reverse[loop.index0] %}
+       base=`basename {{ ffq }} .fq`
+       [[ -f "${base}__{{i}}.f.sai" ]] || \
+           bwa aln {{ aln_param }} -t {{ threads }} \
+               -f ${base}__{{i}}.f.sai db.{{i}} {{ ffq }}
+       [[ -f "${base}__{{i}}.r.sai" ]] || \
+           bwa aln {{ aln_param }} -t {{ threads }} \
+               -f ${base}__{{i}}.r.sai db.{{i}} {{ rfq }} 
+       [[ -f ${base}__{{i}}.bam ]] || \
+           bwa sampe db.{{i}} ${base}__{{i}}.f.sai ${base}__{{i}}.r.sai \
+           {{ ffq }} {{ rfq }} \
+           | samtools view -Sb -f 2 - \
+           | samtools sort - ${base}__{{i}}
+       bamfiles="${bamfiles} ${base}__{{i}}.bam"
+    {% endfor %}
+
+    echo "bamfiles collected: ${bamfiles}"
+    if [[ ! -f variants.{{i}}.vcf ]]
+    then
+        samtools mpileup -uf $reference \
+            ${bamfiles} \
+            | bcftools view -bvcg - \
+            > variants.raw.{{i}}.bcf
+        bcftools view variants.raw.{{i}}.bcf \
+            | vcfutils.pl varFilter -D100 \
+            > variants.{{i}}.vcf
+    fi
+
+    if [[ ! -f consensus.{{i}}.fasta ]]
+    then
+        vcf_applicator ${reference} variants.{{i}}.vcf \
+            consensus.{{i}}.fasta
+    fi
+
+    reference=consensus.{{i}}.fasta
+    #false
+{% endfor %}

template2/recursive_map.moa

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+author: Mark Fiers
+backend: ruff
+commands:
+  run:
+    help: 'recusive map'
+    mode: reduce
+creation_date: Fri, 08 Jun 2012 13:32:30 +1200
+title: Recursively map a genome to the reference
+description: Recursively map a resequence dataset against a reference genome
+modification_date: Fri, 08 Jun 2012 13:43:19 +1200
+moa_id: recursive_map
+name: recursive_map
+filesets:
+  reference:
+    category: prerequisite
+    type: single
+    optional: false
+    pattern: '*/*'
+  fq_forward:
+    category: input
+    help: fastq input files directory - forward
+    optional: false
+    pattern: '*/*_1.fq'
+    type: set
+  fq_reverse:
+    category: input
+    help: fastq input files directory - reverse
+    optional: true
+    pattern: '*/*_2.fq'
+    source: fq_forward
+    type: map
+  output:
+    category: output
+    help: 'base output filename'  
+    optional: true
+    pattern: output
+    type: single
+parameters:
+  iterations:
+    help: 'no of iterations to run'
+    optional: true
+    type: integer
+    default: 3
+  threads:
+    help: 'Number of threads to use'
+    optional: true
+    type: integer
+    default: 4
+  param_strict:
+    help: 'Strict parameters for the first half of alignment runs'
+    optional: true
+    type: string
+    default: ''
+  param_loose:
+    help: 'Looser parameters for the second half of alignment runs'
+    optional: true
+    type: string
+    default: '-e 1 -E 3 -k 3 -O 10'