Merge branch 'CW-3334_jaffa_mem' into 'dev'

JAFFAL resources

Closes CW-3334

See merge request epi2melabs/workflows/wf-transcriptomes!155

.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"

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]

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')

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: