Update Snakemake to 8.24

CHANGELOG.rst

@@ -11,6 +11,7 @@ Changelog
 v2.3.1-dev
 **********
 * **Breaking change**: Update the json output format
+* **Breaking change**: Update snakemake to version 8.23
 * Fix a bug with the Java runtime environment for Picard
 
 **********

Snakefile

@@ -141,7 +141,7 @@ use rule normalized_coverage from expression as expression_normalized_coverage w
         counts=align.module_output.counts,
         gtf=config["expression"]["gtf"],
         bed=config["expression"].get("bed", []),
-        src=srcdir("includes/expression/scripts/coverage.py"),
+        src=workflow.source_path("includes/expression/scripts/coverage.py"),
 
 
 rule create_summary:
@@ -152,7 +152,7 @@ rule create_summary:
         snv_indels_json=align.module_output.json,
         itd_json=itd.module_output.json,
         expression_json=expression.module_output.json,
-        scr=srcdir("scripts/create_summary.py"),
+        scr=workflow.source_path("scripts/create_summary.py"),
     params:
         pipeline_ver=PIPELINE_VERSION,
     output:
@@ -178,11 +178,12 @@ rule generate_report:
     """Generates a PDF report of the essential results."""
     input:
         summary=rules.create_summary.output.js,
-        css=srcdir("report/assets/style.css"),
-        templates=srcdir("report/templates"),
-        imgs=srcdir("report/assets/img"),
-        toc=srcdir("report/assets/toc.xsl"),
-        scr=srcdir("scripts/generate_report.py"),
+        css=workflow.source_path("report/assets/style.css"),
+        toc=workflow.source_path("report/assets/toc.xsl"),
+        scr=workflow.source_path("scripts/generate_report.py"),
+    params:
+        templates="report/templates",
+        imgs="report/assets/img",
     output:
         "{sample}/hamlet_report.{sample}.pdf",
     log:
@@ -192,8 +193,8 @@ rule generate_report:
     shell:
         """
         python3 {input.scr} \
-            --templates-dir {input.templates} \
-            --imgs-dir {input.imgs} \
+            --templates-dir {params.templates} \
+            --imgs-dir {params.imgs} \
             --css-path {input.css} \
             --toc-path {input.toc} \
             {input.summary} \
@@ -205,11 +206,12 @@ rule generate_html_report:
     """Generates a HTML report of the essential results, used for testing only"""
     input:
         summary=rules.create_summary.output.js,
-        css=srcdir("report/assets/style.css"),
-        templates=srcdir("report/templates"),
-        imgs=srcdir("report/assets/img"),
-        toc=srcdir("report/assets/toc.xsl"),
-        scr=srcdir("scripts/generate_report.py"),
+        css=workflow.source_path("report/assets/style.css"),
+        toc=workflow.source_path("report/assets/toc.xsl"),
+        scr=workflow.source_path("scripts/generate_report.py"),
+    params:
+        templates="report/templates",
+        imgs="report/assets/img",
     output:
         "{sample}/hamlet_report.{sample}.html",
     log:
@@ -219,8 +221,8 @@ rule generate_html_report:
     shell:
         """
         python3 {input.scr} \
-            --templates-dir {input.templates} \
-            --imgs-dir {input.imgs} \
+            --templates-dir {params.templates} \
+            --imgs-dir {params.imgs} \
             --css-path {input.css} \
             --toc-path {input.toc} \
             {input.summary} \
@@ -233,7 +235,7 @@ rule multiqc:
         qc_stats=qc_seq.module_output.multiqc_files,
         snv_indel_stats=align.module_output.multiqc_files,
         expression_stats=expression.module_output.multiqc_files,
-        config=srcdir("cfg/multiqc.yml"),
+        config=workflow.source_path("cfg/multiqc.yml"),
     params:
         filelist="multiqc_filelist.txt",
         depth=2,

docs/source/CHANGELOG.rst

@@ -0,0 +1,183 @@
+#########
+Changelog
+#########
+
+.. Newest changes should be on top.
+
+..  This document is user facing. Please word the changes in such a way
+.. that users understand how the changes affect the new version.
+
+**********
+v2.3.1-dev
+**********
+* **Breaking change**: Update the json output format
+* **Breaking change**: Update snakemake to version 8.23
+* Fix a bug with the Java runtime environment for Picard
+
+**********
+v2.2.1
+**********
+
+Breaking changes
+================
+* The `bed_variant_call_regions` option has been removed, variants are now
+  called for all genes present in the `gtf` file.
+* Add graphviz/`dot` as a dependency (developer only).
+* Please create a new HAMLET configuration file with `create-config.py` script.
+* To use the latest hotspot regions and artifact blacklist, please recreate the
+  HAMLET reference data.
+
+Novel module
+============
+* Add novel module, **expression**, which analyzes gene expression.
+    * Add optional input `strandedness` to the sample configuration.
+    * Add json output file for the expression module.
+
+Bugfixes
+========
+* Fix a rare bug where different modules use the same MultiQC file list.
+* Fix a bug with filtering VEP records that contain multiple population.
+  frequency records for a single variant.
+
+Updates
+=======
+* Add ability to generate configurations for each module using the
+  `utilities/create-config.py` script.
+* Update the hotspot regions reference file.
+* Update the blacklist of known artifacts.
+* Remove various superfluous plots from the MultiQC report.
+
+**********
+v2.1.3
+**********
+* Add `pysam` to the conda environment (developer only)
+* Add exon number to variant table
+* Add chromosomes to fusion table
+
+**********
+v2.1.2
+**********
+* Set the maximum population frequency to 1%. This was accidentally set to 5% in v2.1.1
+
+**********
+v2.1.1
+**********
+
+Bugfixes
+========
+* Fix a bug where VEP removed rare variants
+
+**********
+v2.1.0
+**********
+
+Breaking changes
+================
+* Remove the JSON output for the qc-seq module (this has been replaced by a
+  MultiQC report)
+* Add sample name to STAR counts table
+
+Changes
+=======
+* Automatically remove _STAR temporary folders
+* Modified PDF formatting
+    * Change cover image
+    * Add bookmarks under chapter variant
+    * Sort the genes of interest alphabetically
+    * Remove the "Sequencing Results" section from the report (this has been replaced by a MultiQC report)
+* Replace FastQC with Sequali
+
+Bugfixes
+========
+* Fix a bug where the trimmed FastQ files are not removed when no longer needed
+
+Updates
+=======
+* Update Cutadapt to 4.6
+* Update MultiQC to 1.22
+* Update snakefmt to 0.10.0 (developer only)
+* Update black to 24.3.0 (developer only)
+
+
+**********
+v2.0.5
+**********
+* Increase space for the HGVS description in "Results Overview" table
+
+**********
+v2.0.4
+**********
+* Automatically check the release tag is set correctly
+
+**********
+v2.0.3
+**********
+
+Bugfixes
+========
+* Fix a bug where long HGVS descriptions make the "Results Overview" table overflow the page
+
+**********
+v2.0.2
+**********
+* Include the sample name in the final BAM file
+
+**********
+v2.0.1
+**********
+
+Bugfixes
+========
+* Update version number in HAMLET report
+
+**********
+v2.0.0
+**********
+
+Bugfixes
+========
+* Fix a bug with inconsistent config setting 'blacklist' in snv*indels
+* Fix a bug where unmapped reads are not included in STAR output file
+
+Tool changes
+============
+* Replace StarFusion and FusionCatcher with Arriba
+* Replace VarScan variant caller with VarDict
+* Replace GSNAP aligner with STAR
+
+Tool updates
+============
+* Update VEP to 108.2
+* Update Picard to 2.27.4
+* Update FastQC to 0.11.9
+* Update Cutadapt to 4.1
+
+Speed improvements
+==================
+* Use multiple threads for Cutadapt, and reduce the compression of output files
+
+Changes
+=======
+* Remove run name from the report
+* Deprecate option `fusion*partners`, in favour of `report_genes`, which points
+  to a list of fusion genes to report
+* Show allele frequency as a percentage in the pfd report
+* Add additional genes of interest
+    - SRSF2
+    - SF3B1
+    - U2AF1
+    - BCOR
+    - STAG2
+    - ZRSR2
+    - EZH2
+* Filter fusion results based on fusion partners
+* Add fusion plots from Arriba
+* Add default blacklist with common false*positive variants
+* Add support for variant blacklist in VEP hgvsc format
+* Add script to generate a configuration file
+* Add pipeline to generate reference files
+* Add per*module configuration options
+* Add support for PEP sample configuration
+* Add support for Snakemake 7.8.5
+* Remove variants plots
+* Use MANE select transcript for all genes

environment.yml

@@ -6,13 +6,13 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - bs4=4.11
-  - peppy>=0.35
-  - pytest-workflow>=1.6.0
-  - snakemake-minimal=7.32
-  - snakefmt=0.10.0
+  - bs4=4.12
+  - peppy=0.40.7
+  - pytest-workflow=2.1.0
+  - snakemake-minimal=8.24.1
+  - snakefmt=0.10.2
+  - sphinx=8.1.3
+  - sphinx-rtd-theme=3.0.0
   - black=24.3.0
-  - sphinx=7.1.2
-  - sphinx-rtd-theme
   - pysam=0.22
   - graphviz

includes/expression/Snakefile

@@ -14,7 +14,9 @@ rule normalized_coverage:
         counts=get_counts,
         gtf=config["gtf"],
         bed=config.get("bed", []),
-        src=srcdir("scripts/coverage.py"),
+        src=workflow.source_path("scripts/coverage.py"),
+        # Needed to localize the gtf script to the cache
+        utils=workflow.source_path("scripts/gtf.py"),
     params:
         housekeeping=config["housekeeping"],
         genes_of_interest=config["genes_of_interest"],
@@ -55,7 +57,7 @@ rule transform_counts:
     """Transform the counts table to use with seAMLess"""
     input:
         counts=get_counts,
-        src=srcdir("scripts/transform_counts.py"),
+        src=workflow.source_path("scripts/transform_counts.py"),
     output:
         tsv="{sample}/expression/seAMLess.tsv",
     params:
@@ -79,7 +81,7 @@ rule json_output:
     input:
         coverage=module_output.coverage,
         norm_coverage=module_output.normalized_expression,
-        src=srcdir("scripts/json-output.py"),
+        src=workflow.source_path("scripts/json-output.py"),
     params:
         strandedness=get_strand,
         genes=config["report"],
@@ -104,7 +106,7 @@ rule json_output:
 rule merge_samples:
     input:
         counts=[module_output.normalized_expression(sample) for sample in samples],
-        src=srcdir("scripts/multiqc.py"),
+        src=workflow.source_path("scripts/multiqc.py"),
     params:
         samples=[sample.sample for sample in samples],
         strandedness=[get_strand(sample) for sample in samples],
@@ -129,7 +131,7 @@ rule merge_samples:
 rule multiqc:
     input:
         stats=module_output.multiqc_files,
-        config=srcdir("../../cfg/multiqc.yml"),
+        config=workflow.source_path("../../cfg/multiqc.yml"),
     params:
         filelist="multiqc_filelist_expression.txt",
         depth=2,

includes/fusion/Snakefile

@@ -41,8 +41,8 @@ rule arriba:
 rule filter_fusions:
     input:
         fusions="{sample}/fusion/arriba/fusions.raw.tsv",
-        to_json=srcdir("scripts/arriba2json.py"),
-        to_tsv=srcdir("scripts/json2arriba.py"),
+        to_json=workflow.source_path("scripts/arriba2json.py"),
+        to_tsv=workflow.source_path("scripts/json2arriba.py"),
         report_genes=config["report_genes"],
     output:
         json="{sample}/fusion/arriba/fusions.json",
@@ -109,7 +109,7 @@ rule json_output:
     input:
         json="{sample}/fusion/arriba/fusions.json",
         plots="{sample}/fusion/arriba/plots",
-        src=srcdir("scripts/json-output.py"),
+        src=workflow.source_path("scripts/json-output.py"),
     output:
         json="{sample}/fusion/fusion-output.json",
     log:

includes/itd/Snakefile

@@ -153,7 +153,7 @@ rule json_output:
         flt3_plot="{sample}/itd/{sample}.flt3.png",
         kmt2a_csv="{sample}/itd/{sample}.kmt2a.csv",
         kmt2a_plot="{sample}/itd/{sample}.kmt2a.png",
-        src=srcdir("scripts/json-output.py"),
+        src=workflow.source_path("scripts/json-output.py"),
     output:
         "{sample}/itd/itd-output.json",
     log:

includes/qc-seq/Snakefile

@@ -71,7 +71,7 @@ rule sequali:
 rule multiqc:
     input:
         stats=module_output.multiqc_files,
-        config=srcdir("../../cfg/multiqc.yml"),
+        config=workflow.source_path("../../cfg/multiqc.yml"),
     params:
         filelist="multiqc_filelist_qc_seq.txt",
         depth=2,