#36 Created Nextflow script for annotation seqkit process

filter.nf

@@ -14,6 +14,7 @@ params.min_read_length       = '500'          /*minimum length of read to be kep
 /*Stage*/
 stage = "annotation"
 
+/*Results path*/
 resultsPath = "${params.outputDir}/${stage}"
 
 
@@ -27,19 +28,61 @@ assemblerMemory              = '100'
 params.clusterAcct           = " -A h3bionet "
 
 /*Prepare input*/
-genome_file                  = file(params.genome)
-genomeStore                  = genome_file.getParent()
+genome_file1                 = file(params.genome1)
+genome_file2                  = file(params.genome2)
+genome_file3                  = file(params.genome2)
+genomeStore1                  = genome_file1.getParent()
+genomeStore2                  = genome_file2.getParent()
+genomeStore3                  = genome_file3.getParent()
 
 // Sanity checks
-if( !genome_file.exists() ) exit 1, "Missing reference genome file: ${genome_file}"
+if( !genome_file1.exists() ) exit 1, "Missing reference genome file: ${genome_file1}"
+if( !genome_file2.exists() ) exit 1, "Missing reference genome file: ${genome_file2}"
+if( !genome_file3.exists() ) exit 1, "Missing reference genome file: ${genome_file3}"
 //if( params.assembler != "megahit" || params.assembler != "masurca" ) exit 1, "Unknown assembler: ${params.assembler}"
 
-CRAM_Ch1 = Channel.fromFilePairs("${params.samplePath}", size: 1)
+
+/*
+  Introduce input files -----
+*/
+fasta_Ch1 = Channel.fromFilePairs("${params.samplePath}", size: 1)
+
+
+/*
+  Filter the assembly file -----
+*/
+process filter_seqkit {
+    tag                    { id }
+    executor               myExecutor
+    clusterOptions         params.clusterAcct 
+    cpus                   defaultCPU
+    queue                  params.myQueue
+    memory                 "$defaultMemory GB"
+    module                 "seqkit/0.12.1"
+    publishDir             "${resultsPath}/seqkit/masurca/test"
+
+    input:
+    tuple val(id), file(fasta) from fasta_Ch1
+
+    output:
+    tuple val(id), file('*.filtered.fasta') into filtered_file
+    file "${id}.filter-stats.txt"
+
+    script:
+    """
+    # Run seqkit to filter below 500 length ------
+    seqkit seq --min-len 500 --remove-gaps ${fasta} > ${id}.filtered.fasta
+  
+    # Create seqkit stats before and after filtering ------
+    seqkit stats ${fasta} > ${id}.filter-stats.txt
+    seqkit stats ${id}.filtered.fasta | sed -e '1d' >> ${id}.filter-stats.txt
+
+    """
+}
 
 /*
   prepare_genome 
   This process is executed only once
-*/
 
 process prepare_genome{
     tag                    { "PREP:${genome}" }
@@ -55,10 +98,11 @@ process prepare_genome{
     file genome from genome_file
 
     output:
-    file "*.fai" into genome_index_ch
+    file "*." into genome_index_ch
     
     script:
     """
     samtools faidx ${genome}
     """
-}
+}
+*/