#36 draft of annotation pipeline created; testing and editing phase

annotation-config.conf

@@ -0,0 +1,14 @@
+/*
+ * -------------------------------------------------
+ *  UIUC RefGraph Annotation Nextflow config file
+ * -------------------------------------------------
+ */
+
+params {
+    genome1 = "./GRCh38/GRCh38_full_analysis_set_plus_decoy_hla.fa"
+    genome2 = "./GRCh38.p0/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"
+    genome3 = "./CHM13.v1.1_GRCh38.p13.chrY/CHM13.v1.1_GRCh38.p13.chrY.fna"
+    samplePath = "./results/filter/Final-Filtered/masurca/*_filter.final.fasta"
+    myQueue = "normal"
+    clusterAcct = " -A h3abionet "
+}

annotation.nf

@@ -0,0 +1,170 @@
+#!/usr/bin/env nextflow
+
+/*
+  LIST OF TOOLS USED IN THIS PIPLINE:
+  1. repeatmasker  -->  RepeatMasker/4.1.2
+  2. quast         -->  quast/5.0.0
+  3. cd-hit        -->  CD-HIT/4.8.1
+*/
+
+/*Parameters that are specified at the command line or via config file*/
+params.genome1                = false          /*genome fasta file GRCh38, must specify complete path. Required parameter*/
+params.genome2                = false          /*genome fasta file GRCh38.p0, must specify complete path. Required parameter*/
+params.genome3                = false          /*genome fasta file, CHM13, must specify complete path. Required parameter*/
+params.samplePath             = false          /*input folder, must specify complete path. Required parameter*/
+
+/*Parameters to be used inside the pipeline */
+params.outputDir              = "./results"    /*output folder, must specify path from current directory. Required parameter*/
+params.assembler              = 'masurca'      /*options: megahit|masurca. Default is masurca*/
+
+/*Parameters for cdhit */
+params.cdhit_identity         = '0.9'          /*proportion of idenitity for clustering using cdhit. Default is 0.9*/
+params.cdhit_wordsize         = '7'            /*word size for cdhit. Default is 7*/
+
+/*Stage*/
+stage = "annotation"
+
+/*Results path*/
+resultsPath = "${params.outputDir}/${stage}"
+
+/*Cluster parameters */
+myExecutor                   = 'slurm'
+params.myQueue               = 'hpcbio'
+defaultCPU                   = '9'
+defaultMemory                = '120'
+params.clusterAcct           = " -A h3bionet "
+
+/*Prepare input*/
+genome_file1                 = file(params.genome1)
+genome_file2                 = file(params.genome2)
+genome_file3                 = file(params.genome3)
+genomeStore1                 = genome_file1.getParent()
+genomeStore2                 = genome_file2.getParent()
+genomeStore3                 = genome_file3.getParent()
+
+// Sanity checks
+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: ${params.assembler}"
+
+/* Create channcel for input files */
+filtered_fasta_Ch = Channel.fromFilePairs("${params.samplePath}", size: 1)
+filtered_fasta_Ch2 = Channel.fromFilePairs("${params.samplePath}", size: 1)
+filtered_fasta_Ch3 = Channel.fromFilePairs("${params.samplePath}", size: 1)
+
+/*
+  STEP 1: RUN REPEAT MASKER ON FILTERED READS
+*/
+process repeatmasker {
+    tag                    { id }
+    executor               myExecutor
+    clusterOptions         params.clusterAcct 
+    cpus                   defaultCPU
+    queue                  params.myQueue
+    memory                 "$defaultMemory GB"
+    module                 "RepeatMasker/4.1.2-p1-IGB-gcc-8.2.0-Perl-5.28.1"
+    publishDir             "${resultsPath}/RepeatMasker/${params.assembler}/",mode:"copy"
+
+    input:
+    tuple val(id), file(fasta) from filtered_fasta_Ch 
+
+    output:
+    tuple val(id), file('*.fasta.cat')
+    tuple val(id), file('*.fasta.masked') 
+    tuple val(id), file('*.fasta.out') 
+    tuple val(id), file('*.fasta.tbl')
+
+    script:
+    """
+    # Run Repeat Masker ------
+    RepeatMasker -species human ${fasta} -nolow
+
+    """
+}
+
+/*
+  STEP 2: RUN QUAST ON FILTERED READS
+*/
+process quast {
+    tag                    { id }
+    executor               myExecutor
+    clusterOptions         params.clusterAcct 
+    cpus                   defaultCPU
+    queue                  params.myQueue
+    memory                 "$defaultMemory GB"
+    module                 "quast/5.0.0-IGB-gcc-4.9.4-Python-3.6.1"
+    publishDir             "${resultsPath}/QUAST/${id}/",mode:"copy"
+
+    input:
+    tuple val(id), file(fasta2) from filtered_fasta_Ch2
+
+    output:
+    file '*'
+
+    script:
+    """
+    # Run QUAST ------
+    quast.py ${fasta2} \
+    --threads ${task.cpus}
+
+    """
+}
+
+/*
+  STEP 3: MERGE ALL SEQUENCES FROM ALL SAMPLES
+*/
+process merge_reads {
+    tag                    { id }
+    executor               myExecutor
+    clusterOptions         params.clusterAcct 
+    cpus                   defaultCPU
+    queue                  params.myQueue
+    memory                 "$defaultMemory GB"
+    publishDir             "${resultsPath}/Merged_Reads/${params.assembler}/",mode:"copy"
+
+    input:
+    tuple val(id), file(fasta3) from filtered_fasta_Ch3
+
+    output:
+    file('merged_sequences.fasta') into merged_seqs
+
+    script:
+    """
+    # Combine all sequences ------
+    cat ${fasta3} >> merged_sequences.fasta
+
+    """
+}
+
+/*
+  STEP 4: RUN CD-HIT ON FILTERED READS
+*/
+process cdhit {
+    tag                    { id }
+    executor               myExecutor
+    clusterOptions         params.clusterAcct 
+    cpus                   defaultCPU
+    queue                  params.myQueue
+    memory                 "$defaultMemory GB"
+    module                 "CD-HIT/4.8.1-IGB-gcc-8.2.0"
+    publishDir             "${resultsPath}/Cluster_CDHIT/${params.assembler}/",mode:"copy"
+
+    input:
+    tuple val(id), file(merged) from merged_seqs
+
+    output:
+    tuple val(id), file('*_clustered.fasta') into clustered
+
+    script:
+    """
+    # Use cd-hit to cluster and remove redundancy ------
+    cd-hit-est \
+    -i ${merged} \
+    -o ${id}_clustered.fasta \
+    -c ${params.cdhit_identity} \
+    -n ${params.cdhit_wordsize} \
+    -T ${task.cpus}
+
+    """
+}