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JAFFAL resources

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This commit is contained in:
Neil Horner 2024-02-12 15:25:19 +00:00
parent f025538f17
commit d5b0cc6203
4 changed files with 7 additions and 4 deletions
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2
.gitlab-ci.yml
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@ -78,7 +78,7 @@ docker-run:
- if: $MATRIX_NAME == "fusions" - if: $MATRIX_NAME == "fusions"
variables: 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_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 \ --ref_genome chr20/hg38_chr20.fa --ref_annotation chr20/gencode.v22.annotation.chr20.gtf \
--jaffal_refBase chr20/ --jaffal_genome hg38_chr20 --jaffal_annotation genCode22 \ --jaffal_refBase chr20/ --jaffal_genome hg38_chr20 --jaffal_annotation genCode22 \
-c demo.nextflow.config" -c demo.nextflow.config"

2
CHANGELOG.md
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@ -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. - Add gene name column to the de_analysis counts TSV files.
### Fixed ### Fixed
- Mapping stage using a single thread only. - 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`. - 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] ## [v1.0.0]

2
bin/workflow_glue/report.py
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@ -834,7 +834,7 @@ def jaffal_table(report, result_csv):
This section summarizes putative fusion transcripts identified This section summarizes putative fusion transcripts identified
by [JAFFAL](https://github.com/Oshlack/JAFFA/). 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: else:
sid_col = df.pop('sample_id') sid_col = df.pop('sample_id')

5
subworkflows/JAFFAL/gene_fusions.nf
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@ -1,8 +1,8 @@
process jaffal{ process jaffal{
label "isoforms" label "isoforms"
cpus 4 cpus params.threads
memory "2 GB" memory "31 GB"
input: input:
tuple val(sample_id), path(fastq) tuple val(sample_id), path(fastq)
path refBase path refBase
@ -47,6 +47,7 @@ process jaffal{
""" """
} }
// workflow module // workflow module
workflow gene_fusions { workflow gene_fusions {
take: take: