From b2ac1edbb9b67a217f135357a099176b6d5c085e Mon Sep 17 00:00:00 2001 From: Neil Horner Date: Fri, 16 May 2025 08:38:28 +0000 Subject: [PATCH] Container update CW-5998 --- CHANGELOG.md | 4 ++-- bin/workflow_glue/parse_gffcompare.py | 2 ++ main.nf | 4 ++-- nextflow.config | 4 ++-- 4 files changed, 8 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9a0f992..107ae05 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,14 +4,14 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). - ## [Unreleased] ### Changed - Updated to wf-template v5.6.1, changing: - Reduce verbosity of debug logging from fastcat which can occasionally occlude errors found in FASTQ files during ingress. - Log banner art to say "EPI2ME" instead of "EPI2ME Labs" to match current branding. This has no effect on the workflow outputs. - pre-commit configuration to resolve an internal dependency problem with flake8. This has no effect on the workflow. - + - Stringtie updated to v2.2.3, which fixes stalling at transcriptome assembly step. + - Gffcompare updated to v0.12.6, which fixes issue where ref_gene_id was assigned an nan value. ### Fixed - Updated to wf-template v5.6.1, fixing: - dacite.exceptions.WrongTypeError during report generation when barcode is null. diff --git a/bin/workflow_glue/parse_gffcompare.py b/bin/workflow_glue/parse_gffcompare.py index 20ed5b2..a71630a 100644 --- a/bin/workflow_glue/parse_gffcompare.py +++ b/bin/workflow_glue/parse_gffcompare.py @@ -197,6 +197,8 @@ def tracking_summary(tracking_file, output_dir, annotations=None): df = ( pd.DataFrame(tracking['class'].value_counts()) .reset_index() + # Reminder when updating pandas > 2 + # .rename(columns={'count': 'Count'}) .rename(columns={'index': 'class', 'class': 'Count'}) ) diff --git a/main.nf b/main.nf index 8debb9e..4c17c95 100644 --- a/main.nf +++ b/main.nf @@ -25,17 +25,17 @@ process getVersions { script: """ python -c "import pysam; print(f'pysam,{pysam.__version__}')" >> versions.txt + python -c "import pychopper; print(f'pychopper,{pychopper.__version__}')" >> versions.txt python -c "import pandas; print(f'pandas,{pandas.__version__}')" >> versions.txt python -c "import sklearn; print(f'scikit-learn,{sklearn.__version__}')" >> versions.txt - fastcat --version | sed 's/^/fastcat,/' >> versions.txt minimap2 --version | sed 's/^/minimap2,/' >> versions.txt samtools --version | head -n 1 | sed 's/ /,/' >> versions.txt bedtools --version | head -n 1 | sed 's/ /,/' >> versions.txt - python -c "import pychopper; print(f'pychopper,{pychopper.__version__}')" >> versions.txt gffread --version | sed 's/^/gffread,/' >> versions.txt seqkit version | head -n 1 | sed 's/ /,/' >> versions.txt stringtie --version | sed 's/^/stringtie,/' >> versions.txt gffcompare --version | head -n 1 | sed 's/ /,/' >> versions.txt + python -c "import gffutils; print(f'gffutils,{gffutils.__version__}')" >> versions.txt """ } diff --git a/nextflow.config b/nextflow.config index 5e62528..357d8bd 100644 --- a/nextflow.config +++ b/nextflow.config @@ -95,7 +95,7 @@ params { "--sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv'", ] agent = null - container_sha = "shac733d952a14257cf3c5c5d5d44c6aed84d5fe5a1" + container_sha = "shaaaf20a5a0e76f9e18bad21af639a6b69e4a31a2f" common_sha = "sha1c69fd30053aad5d516e9567b3944384325a0fee" } } @@ -111,7 +111,7 @@ manifest { } epi2melabs { - tags = "wf-transcriptomes,isoforms,transcriptomics,denovo,human,mouse,plant" + tags = "wf-transcriptomes,isoforms,transcriptomics,human,mouse,plant" } // used by default for "standard" (docker) and singularity profiles,