From 0d79273c27e9dd1d529ac2fcf94b459c560fbe26 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 24 Sep 2021 14:54:41 +0200
Subject: [PATCH] emase: add diploid_genome process
---
src/nf_modules/emase/main.nf | 22 ++++++++++------------
1 file changed, 10 insertions(+), 12 deletions(-)
diff --git a/src/nf_modules/emase/main.nf b/src/nf_modules/emase/main.nf
index 73ace1e8..850abe83 100644
--- a/src/nf_modules/emase/main.nf
+++ b/src/nf_modules/emase/main.nf
@@ -1,27 +1,25 @@
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}
"""
}
\ No newline at end of file
--
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