emase: add diploid_genome process

src/nf_modules/emase/main.nf

 version = "0.10.16"
 container_url = "lbmc/emase:${version}"
 
-params.personalised_transcriptome = ""
-
-process personalised_transcriptome {
+params.diploid_genome = "-x"
+params.diploid_genome_out = "-x"
+process diploid_genome {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$file_id"
+  if (params.diploid_genome_out != "") {
+    publishDir "results/${params.diploid_genome_out}", mode: 'copy'
+  }
 
   input:
-    tuple val(file_id), path(fasta)
-    tuple val(gtf_id), path(gtf)
+    tuple val(genome_a), path(fasta_a)
+    tuple val(genome_b), path(fasta_b)
 
   output:
-    tuple val(file_id), path("${fasta.simpleName}.*"), emit: index
-    tuple val(file_id), path("*_bwa_report.txt"), emit: report
+    tuple val(file_id), path(".fa"), emit: index
 
   script:
 """
-prepare-emase ${personalised_transcriptome} -G ${REF_FASTA} -g ${REF_GTF} -o ${REF_DIR} -m --no-bowtie-index
-// ${REF_DIR}/emase.transcriptome.fa
-// ${REF_DIR}/emase.transcriptome.info
-// ${REF_DIR}/emase.gene2transcripts.tsv
-prepare-emase -G ${SAMPLE_DIR}/L.fa,${SAMPLE_DIR}/R.fa -s L,R -o ${SAMPLE_DIR}
+prepare-emase -G ${fasta_a},${fasta_b} -s ${genome_a},${genome_b} ${params.diploid_genome} 
 """
 }
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