ARDaP reworks v1.5 for Nextflow

card.nf

@@ -0,0 +1,94 @@
+#!/usr/bin/env nextflow
+
+/*
+ *
+ *  Pipeline            ARDaP - CARD support pipeline
+ *  Version             1.4
+ *  Description         Download and index CARD DB
+ *  Notes               This is a support script for updating indices
+ *                      of the CARD DB for ARDaP.
+ *
+ */
+
+
+//Overwrites data in resources/card/latest, can be changed here or on CLI:
+
+params.outdir = "$baseDir/resources/card/latest"
+params.window = 10000
+
+process Download {
+
+  executor 'local'
+  publishDir "${params.outdir}", pattern: "*.txt", mode: "copy"
+  publishDir "${params.outdir}", pattern: "card.fasta", mode: "copy"
+
+
+  output:
+  file('date.txt')
+  file("card.fasta") into (card_bwa, card_sam, card_bed)
+
+  shell:
+
+  """
+  wget https://card.mcmaster.ca/latest/data -O card-data.tar.bz2
+  tar xvjf card-data.tar.bz2
+  wget https://card.mcmaster.ca/latest/ontology -O card-ontology.tar.bz2
+  tar xvjf card-ontology.tar.bz2
+  mv nucleotide_fasta_protein_homolog_model.fasta card.fasta
+  date > date.txt
+  """
+
+}
+
+process BWAIndex {
+
+   label "index"
+   publishDir "${params.outdir}", mode: "copy"
+
+   input:
+   file(ref) from card_bwa
+
+   output:
+   file("card.*")
+
+   """
+   bwa index -a is $ref
+   """
+
+}
+
+process SAMtoolsIndex {
+
+   label "index"
+   publishDir "${params.outdir}", mode: "copy"
+
+   input:
+   file(ref) from card_sam
+
+   output:
+   file("${ref}.fai") into card_bed_fai
+
+   """
+   samtools faidx $ref
+   """
+
+}
+
+process BEDtoolsIndex {
+
+   label "card"
+   publishDir "${params.outdir}", mode: "copy"
+
+   input:
+   file(ref) from card_bed
+   file(ref_index) from card_bed_fai
+
+   output:
+   file("${ref.baseName}.bed")
+   file("${ref.baseName}.coverage.bed")
+
+   """
+   bedtools makewindows -g $ref_index -w $params.window > ${ref.baseName}.bed && bedtools makewindows -g $ref_index -w 90000000 > ${ref.baseName}.coverage.bed
+   """
+
+}

configs/gatk.config

@@ -0,0 +1,21 @@
+params {
+
+  CLUSTER_SNP = 3
+  CLUSTER_WINDOW_SNP = 10
+  MLEAF_SNP = 0.95
+  QD_SNP = 10.0
+  MQ_SNP = 30.0
+  FS_SNP = 60.0
+  QUAL_SNP = 30.0
+  LOW_DEPTH = 2
+  HIGH_DEPTH = 3
+
+  MLEAF_INDEL = 0.95
+  QD_INDEL = 10.0
+  MQ_INDEL = 30.0
+  FS_INDEL = 200.0
+  QUAL_INDEL = 30.0
+  LOW_DEPTH_INDEL = 2
+  HIGH_DEPTH_INDEL = 3
+
+}

nextflow.config

@@ -0,0 +1,73 @@
+params {
+
+    fastq               =   "test/*_{1,2}.fastq.gz"
+    reference           =   "test/K96243.fasta"
+    gwas                =   true
+    matrix              =   true
+    annotate            =   true
+    mixtures            =   true
+    phylogeny           =   false
+    antibiotic_res      =   true
+    strain              =   "all"
+    tech                =   "Illumina"
+    pairing             =   "PE"
+    window              =   10000
+    indel_merge         =   true
+    tri_tetra_allelic   =   false
+    size                =   6000000
+    snpeff              =   "Burkholderia_pseudomallei_k96243"
+    phred               =   "-phred33"
+    org                 =   "haploid"
+}
+
+includeConfig 'configs/gatk.config'
+
+process {
+
+    errorStrategy = "ignore"
+
+    conda = "/home/esteinig/miniconda3/envs/ardap"
+
+    withLabel: card {
+        cpus = 1
+        memory = "4G"
+        time = "2h"
+    }
+
+    withLabel: index {
+        cpus = 1
+        memory = "4G"
+        time = "2h"
+    }
+
+    withLabel: spandx_default {
+        cpus = 2
+        memory = "4G"
+        time = "2h"
+    }
+
+    withLabel: spandx_alignment {
+        cpus = 8
+        memory = "8G"
+        time = "2h"
+    }
+
+    withLabel: spandx_gatk {
+        cpus = 8
+        memory = "8G"
+        time = "2h"
+    }
+
+    withLabel: spandx_snpeff {
+        cpus = 4
+        memory = "4G"
+        time = "2h"
+    }
+
+    withLabel: spandx_pindel {
+        cpus = 8
+        memory = "8G"
+        time = "2h"
+    }
+
+}

resources/trimmomatic/all_adapters.fa

@@ -0,0 +1,54 @@
+>PrefixNX/1
+AGATGTGTATAAGAGACAG
+>PrefixNX/2
+AGATGTGTATAAGAGACAG
+>Trans1
+TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
+>Trans1_rc
+CTGTCTCTTATACACATCTGACGCTGCCGACGA
+>Trans2
+GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
+>Trans2_rc
+CTGTCTCTTATACACATCTCCGAGCCCACGAGAC
+>PrefixPE/1
+AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>PrefixPE/2
+CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+>PCR_Primer1
+AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>PCR_Primer1_rc
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
+>PCR_Primer2
+CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+>PCR_Primer2_rc
+AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG
+>FlowCell1
+TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC
+>FlowCell2
+TTTTTTTTTTCAAGCAGAAGACGGCATACGA
+>TruSeq2_SE
+AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
+>TruSeq2_PE_f
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
+>TruSeq2_PE_r
+AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
+>PrefixPE/1
+TACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>PrefixPE/2
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+>PE1
+TACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>PE1_rc
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
+>PE2
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+>PE2_rc
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
+>PrefixPE/1
+TACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>PrefixPE/2
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+>TruSeq3_IndexedAdapter
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
+>TruSeq3_UniversalAdapter
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA