kb: first draft of main.nf

src/nf_modules/kb/main.nf

+version = "0.26.0"
+container_url = "lbmc/kb:${version}"
+
+params.kb_protocol = "10x_v3"
+
+params.index_fasta = ""
+params.index_fasta_out = ""
+process index_fasta {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  if (params.index_fasta_out != "") {
+    publishDir "results/${params.index_fasta_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(fasta)
+    tuple val(gtf_id), path(gtf)
+    tuple val(t2g_id), path(transcript_to_gene)
+
+  output:
+    tuple val(file_id), path("*.idx"), emit: index
+    tuple val(t2g_id), path("${transcript_to_gene}"), emit: t2g
+    tuple val(file_id), path("*_report.txt"), emit: report
+
+  script:
+"""
+kb ref \
+  -i ${fasta.simpleName}.idx \
+  -g ${transcript_to_gene} \
+  ${params.index_fasta} \
+  -f1 ${fasta} ${gtf} > ${fasta.simpleName}_kb_index_report.txt
+"""
+}
+
+params.count = ""
+params.count_out = ""
+workflow count {
+  take:
+    index
+    fastq
+    transcript_to_gene
+    whitelist
+
+  main:
+  whitelist
+    .ifEmpty(["NO WHITELIST", 0])
+    .set{ whitelist_optional }
+  switch(params.kb_protocol) {
+    case "marsseq":
+      kb_marseq(index, fastq, transcript_to_gene, whitelist_optional)
+      kb_marseq.out.counts.set{res_counts}
+      kb_marseq.out.report.set{res_report}
+    break;
+    default:
+      kb_default(index, fastq, transcript_to_gene, whitelist_optional)
+      kb_default.out.counts.set{res_counts}
+      kb_default.out.report.set{res_report}
+    break;
+  }
+  emit:
+    counts = res_counts
+    report = res_report
+}
+
+process kb_default {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_prefix"
+  if (params.kb_out != "") {
+    publishDir "results/${params.kb_out}", mode: 'copy'
+  }
+
+  input:
+  tuple val(index_id), path(index)
+  tuple val(file_id), path(reads)
+  tuple val(t2g_id), path(transcript_to_gene)
+  tuple val(whitelist_id), path(whitelist)
+
+  output:
+  tuple val(file_id), path("${file_prefix}"), emit: counts
+  tuple val(file_id), path("*_report.txt"), emit: report
+
+  script:
+  if (file_id instanceof List){
+    file_prefix = file_id[0]
+  } else {
+    file_prefix = file_id
+  }
+  def whitelist_param = ""
+  if (whitelist_id != "NO WHITELIST"){
+    whitelist_param = "-w ${white_list}"
+  }
+
+  if (reads.size() == 2)
+  """
+  mkdir ${file_prefix}
+  kb count  -t ${task.cpus} \
+    -m ${task.memory} \
+    -i ${index} \
+    -g ${transcript_to_gene} \
+    ${whitelist_param} \
+    -x 10XV3
+    ${params.mapping_fastq} \
+    -o ${file_prefix} \
+    ${reads[0]} ${reads[1]} &> ${file_prefix}_kb_mapping_report.txt
+  """
+}
+
+process kb_marseq {
+  // With the MARS-Seq protocol, we have:
+  // on the read 1: 4 nt of bc plate
+  // on the read 2: 6 nt of bc cell, and 8 nt of UMI
+  // this process expect that the bc plate is removed from the read 1
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_prefix"
+  if (params.kb_out != "") {
+    publishDir "results/${params.kb_out}", mode: 'copy'
+  }
+
+  input:
+  tuple val(index_id), path(index)
+  tuple val(file_id), path(reads)
+  tuple val(t2g_id), path(transcript_to_gene)
+  tuple val(whitelist_id), path(whitelist)
+
+  output:
+  tuple val(file_id), path("${file_prefix}"), emit: counts
+  tuple val(file_id), path("*_report.txt"), emit: report
+
+  script:
+  if (file_id instanceof List){
+    file_prefix = file_id[0]
+  } else {
+    file_prefix = file_id
+  }
+  def whitelist_param = ""
+  if (whitelist_id != "NO WHITELIST"){
+    whitelist_param = "-w ${white_list}"
+  }
+
+  if (reads.size() == 2)
+  """
+  mkdir ${file_prefix}
+  kb count  -t ${task.cpus} \
+    -m ${task.memory} \
+    -i ${index} \
+    -g ${transcript_to_gene} \
+    ${whitelist_param} \
+    -x 1,0,6:1,6,14:1,14,0
+    ${params.mapping_fastq} \
+    -o ${file_prefix} \
+    ${reads[0]} ${reads[1]} &> ${file_prefix}_kb_mapping_report.txt
+  """
+}
\ No newline at end of file