Added hisat2 component

changelog.md

@@ -4,10 +4,11 @@
 
 ### New components
 
-- `Bwa`: align short paired-end sequencing reads to long reference sequences
+- `Bwa`: Align short paired-end sequencing reads to long reference sequences
 - `MarkDuplicates`: Identifies duplicate reads
 - `BaseRecalibrator`: Detects systematic errors in base quality scores
 - `Haplotypecaller`: Call germline SNPs and indels via local re-assembly of haplotypes
+- `HiSAT2`: Alignment program for mapping next-generation sequencing reads to a reference genome
 
 - `Seroba`: Serotyping of *Streptococcus pneumoniae* sequencing data (FastQ)
 - `Concoct`: Clustering metagenomic assembled comtigs with coverage and composition

flowcraft/generator/components/mapping.py

@@ -245,4 +245,64 @@ def __init__(self, **kwargs):
         self.status_channels = [
             "base_recalibrator",
             "apply_bqsr"
+        ]
+
+
+class Hisat2(Process):
+    """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome)
+        This process is set with:
+            - ``input_type``: fastq
+            - ``output_type``: bam
+            - ``ptype``: mapping
+        """
+
+    def __init__(self, **kwargs):
+
+        super().__init__(**kwargs)
+
+        self.input_type = "fastq"
+        self.output_type = "bam"
+
+        self.params = {
+            "reference": {
+                "default": "null",
+                "description": "Specifies the reference genome to be provided "
+                               "to HISAT2."
+            },
+            "hisat2_index": {
+                "default": "null",
+                "description": "Specifies the reference indexes to be provided "
+                               "to HISAT2."
+            },
+            "hisat2_index_name": {
+                "default": "null",
+                "description": "Specifies the reference indexes folder & basename to be provided "
+                               "to HISAT2, eg hisat2_index_folder/basename."
+            }
+        }
+
+        self.directives = {
+            "make_hisat2_index": {
+                "container": "makaho/hisat2-zstd",
+                "version": "latest",
+                "memory": "{5.Gb*task.attempt}",
+                "cpus": 1
+            },
+            "hisat2": {
+                "container": "makaho/hisat2-zstd",
+                "version": "latest",
+                "memory": "{5.Gb*task.attempt}",
+                "cpus": 4
+            },
+            "samtools_sort": {
+                "container": "lifebitai/samtools",
+                "version": "latest",
+                "memory": "{5.Gb*task.attempt}",
+                "cpus": 4
+            }
+        }
+
+        self.status_channels = [
+            "hisat2",
+            "samtools_sort"
         ]

flowcraft/generator/templates/hisat2.nf

@@ -0,0 +1,84 @@
+if (params.reference{{ param_id }}) {
+    Channel
+        .fromPath("${params.reference{{ param_id }}}.fasta")
+        .ifEmpty { exit 1, "FASTA annotation file not found: ${params.reference{{ param_id }}}" }
+        .set { hisat2Fasta_{{pid}} }
+} else if (params.hisat2_index{{ param_id }}) {
+    Channel
+        .fromPath(params.hisat2_index{{ param_id }})
+        .ifEmpty { exit 1, "Folder containing Hisat2 indexes for reference genome not found: ${params.hisat2_index{{ param_id }}}" }
+        .set { hisat2Index_{{pid}} }
+    hisat2IndexName_{{pid}} = Channel.value( "${params.hisat2_index_name{{ param_id }}}" )
+} else {
+    exit 1, "Please specify either `--reference /path/to/file_basename` OR `--hisat2_index /path/to/hisat2_index_folder` AND `--hisat2_index_name hisat2_index_folder/basename`"
+}
+
+if (!params.hisat2_index{{ param_id }}) {
+  process make_hisat2_index_{{ pid }} {
+
+    {% include "post.txt" ignore missing %}
+    tag "$fasta"
+
+    input:
+    each file(fasta) from hisat2Fasta_{{pid}}
+
+    output:
+    val "hisat2_index/${fasta.baseName}.hisat2_index" into hisat2IndexName_{{pid}}
+    file "hisat2_index" into hisat2Index_{{pid}}
+
+    """
+    mkdir hisat2_index
+    hisat2-build -p ${task.cpus} $fasta hisat2_index/${fasta.baseName}.hisat2_index
+    """
+  }
+}
+
+process hisat2_{{ pid }} {
+
+    {% include "post.txt" ignore missing %}
+    tag "$sample_id"
+
+    input:
+    set sample_id, file(fastq_pair) from {{ input_channel }}
+    each index_name from hisat2IndexName_{{pid}}
+    each file(index) from hisat2Index_{{pid}}
+
+    output:
+    set sample_id, file("${sample_id}.sam") into  hisat2Sam_{{pid}}
+    {% with task_name="hisat2" %}
+    {%- include "compiler_channels.txt" ignore missing -%}
+    {% endwith %}
+
+    """
+    hisat2 \
+    -p ${task.cpus} \
+    -x $index_name \
+    -1 ${fastq_pair[0]} \
+    -2 ${fastq_pair[1]} \
+    -S ${sample_id}.sam
+    """
+}
+
+process samtools_sort_{{ pid }} {
+
+    {% include "post.txt" ignore missing %}
+    publishDir "results/mapping/hisat2_{{ pid }}"
+    tag "$sample_id"
+
+    input:
+    set sample_id, file(sam) from hisat2Sam_{{pid}}
+
+    output: 
+    set sample_id, file("${sample_id}.sorted.bam"), file("${sample_id}.sorted.bam.bai") into {{ output_channel }}
+    {% with task_name="samtools_sort" %}
+    {%- include "compiler_channels.txt" ignore missing -%}
+    {% endwith %}
+
+    """
+    samtools view -Sb $sam > ${sample_id}.bam
+    samtools sort -T ${sample_id}.bam.tmp ${sample_id}.bam -o ${sample_id}.sorted.bam
+    samtools index ${sample_id}.sorted.bam
+    """
+}
+
+{{ forks }}