From d5b0cc620325cbb9e3040fbc3aefb477b8c8f037 Mon Sep 17 00:00:00 2001
From: Neil Horner <neil.horner@nanoporetech.com>
Date: Mon, 12 Feb 2024 15:25:19 +0000
Subject: [PATCH] JAFFAL resources

---
 .gitlab-ci.yml                      | 2 +-
 CHANGELOG.md                        | 2 ++
 bin/workflow_glue/report.py         | 2 +-
 subworkflows/JAFFAL/gene_fusions.nf | 5 +++--
 4 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f358225..409ac83 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -78,7 +78,7 @@ docker-run:
         - if: $MATRIX_NAME == "fusions"
           variables:
               NF_BEFORE_SCRIPT: wget -O test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz && tar -xzvf  test_data.tar.gz &&  wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
-              NF_WORKFLOW_OPTS: "--fastq  ERR6053095_chr20.fastq --transcriptome-source reference-guided \
+              NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB --fastq  ERR6053095_chr20.fastq --transcriptome-source reference-guided \
                   --ref_genome chr20/hg38_chr20.fa --ref_annotation chr20/gencode.v22.annotation.chr20.gtf \
                   --jaffal_refBase chr20/ --jaffal_genome hg38_chr20 --jaffal_annotation genCode22 \
                   -c demo.nextflow.config"
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 48be511..d79b409 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,6 +18,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add gene name column to the de_analysis counts TSV files.
 ### Fixed
 - Mapping stage using a single thread only.
+### Changed
+- More memory assigned to the fusion detection process.
 - When no `--ref_annotation` is provided the workflow will still run but the output transcripts will not be annotated. However `--de_analysis` mode still requires a `--ref_annotation`.
 
 ## [v1.0.0]
diff --git a/bin/workflow_glue/report.py b/bin/workflow_glue/report.py
index 77c5f44..cdc7afc 100755
--- a/bin/workflow_glue/report.py
+++ b/bin/workflow_glue/report.py
@@ -834,7 +834,7 @@ def jaffal_table(report, result_csv):
         This section summarizes putative fusion transcripts identified
         by [JAFFAL](https://github.com/Oshlack/JAFFA/).
 
-        No fusion transcripts detected for current sample.
+        No fusion transcripts were detected for any of the samples.
         """)
     else:
         sid_col = df.pop('sample_id')
diff --git a/subworkflows/JAFFAL/gene_fusions.nf b/subworkflows/JAFFAL/gene_fusions.nf
index e2b5013..795106d 100644
--- a/subworkflows/JAFFAL/gene_fusions.nf
+++ b/subworkflows/JAFFAL/gene_fusions.nf
@@ -1,8 +1,8 @@
 
 process jaffal{
     label "isoforms"
-    cpus 4
-    memory "2 GB"
+    cpus params.threads
+    memory "31 GB"
     input:
         tuple val(sample_id), path(fastq)
         path refBase
@@ -47,6 +47,7 @@ process jaffal{
     """
 }
 
+
 // workflow module
 workflow gene_fusions {
     take: