Merge branch 'container_update_CW-5998' into 'dev'

Container update CW-5998

See merge request epi2melabs/workflows/wf-transcriptomes!215

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.

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'})
         )
 

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
     """
 }
 

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,