2.4.3

.test/tasks.py

@@ -26,12 +26,21 @@ def get_latest_release(address: str) -> str:
     print("Searching fair-genome-indexer version on the web...")
     fair_genome_indexer_version = get_latest_release("tdayris/fair_genome_indexer")
 
-
 fair_fastqc_multiqc_version = os.environ.get("FAIR_FASTQC_MULTIQC_VERSION")
 if not fair_fastqc_multiqc_version:
-    print("Searching fair-fastqc-multi-qc version on the web...")
+    print("Searching fair-fastqc-multiqc version on the web...")
     fair_fastqc_multiqc_version = get_latest_release("tdayris/fair_fastqc_multiqc")
 
+fair_bowtie2_mapping_version = os.environ.get("FAIR_BOWTIE2_MAPPING_VERSION")
+if not fair_bowtie2_mapping_version:
+    print("Searching fair-bowtie2-mapping version on the web...")
+    fair_bowtie2_mapping_version = get_latest_release("tdayris/fair_bowtie2_mapping")
+
+fair_star_mapping_version = os.environ.get("FAIR_STAR_MAPPING_VERSION")
+if not fair_star_mapping_version:
+    print("Searching fair-star-mapping version on the web...")
+    fair_star_mapping_version = get_latest_release("tdayris/fair_star_mapping")
+
 locations = {
     "snakefile": "../workflow/Snakefile",
     "rules": "../workflow/rules/",
@@ -118,10 +127,10 @@ def update_docs_cff(
                 "orcid": "https://orcid.org/0009-0009-2758-8450",
             }
         ],
-        "title": "fair-fastqc-multiqc",
+        "title": "fair-star-mapping",
         "version": future_version,
         "date-released": today,
-        "url": "https://github.com/tdayris/fair_fastqc_multiqc",
+        "url": "https://github.com/tdayris/fair_star_mapping",
     }
     print(cff)
     with open(cff_path, "w") as yaml_cff_stream:
@@ -152,8 +161,11 @@ def update_docs_wrappers(c, to: str = snakemake_wrappers_version, future_version
         r's|fair-genome-indexer (Version v\?[0-9]\+\.[0-9]\+\.[0-9]\+)'
         f'|fair-genome-indexer (Version {fair_genome_indexer_version})|g;'
         r's|fair-fastqc-multiqc (Version v\?[0-9]\+\.[0-9]\+\.[0-9]\+)'
-        f'|fair-fastqc-multiqc (Version {future_version})|g'
-
+        f'|fair-fastqc-multiqc (Version {fair_fastqc_multiqc_version})|g;'
+        r's|fair-bowtie2-mapping (Version v\?[0-9]\+\.[0-9]\+\.[0-9]\+)'
+        f'|fair-bowtie2-mapping (Version {fair_bowtie2_mapping_version})|g;'
+        r's|fair-star-mapping (Version v\?[0-9]\+\.[0-9]\+\.[0-9]\+)'
+        f'|fair-star-mapping (Version {future_version})|g'
     )
     print("Updating '../workflow/report/material_methods.rst'...")
     c.run(f"sed -i '{regex}' '../workflow/report/material_methods.rst' >> update_docs.txt 2>&1")
@@ -183,7 +195,17 @@ def update_wrappers_rules(
     for root, dirs, files in os.walk(rules):
         for file in files:
             if file == "fair_genome_indexer.smk":
-                c.run(f"""sed -i 's|tag="[0-9]\+\.[0-9]\+\.[0-9]\+"|tag="{fair_genome_indexer_version}"|g' '{root}/{file}' >> wrappers_update.txt 2>&1""")
+                print("Updating fair_genome_indexer...")
+                c.run(fr"""sed -i 's|tag="[0-9]\+\.[0-9]\+\.[0-9]\+"|tag="{fair_genome_indexer_version}"|g' '{root}/{file}' >> wrappers_update.txt 2>&1""")
+            elif file == "fair_fastqc_multiqc.smk":
+                print("Updating fair_fastq_multiqc...")
+                c.run(fr"""sed -i 's|tag="[0-9]\+\.[0-9]\+\.[0-9]\+"|tag="{fair_fastqc_multiqc_version}"|g' '{root}/{file}' >> wrappers_update.txt 2>&1""")
+            elif file == "fair_bowtie2_mapping.smk":
+                print("Updating fair_bowtie2_mapping...")
+                c.run(fr"""sed -i 's|tag="[0-9]\+\.[0-9]\+\.[0-9]\+"|tag="{fair_bowtie2_mapping_version}"|g' '{root}/{file}' >> wrappers_update.txt 2>&1""")
+            elif file == "fair_star_mapping.smk":
+                print("Updating fair_star_mapping...")
+                c.run(fr"""sed -i 's|tag="[0-9]\+\.[0-9]\+\.[0-9]\+"|tag="{fair_star_mapping_version}"|g' '{root}/{file}' >> wrappers_update.txt 2>&1""")
             elif file.endswith(".smk"):
                 print(f"Updating '{root}/{file}'...")
                 c.run(

CHANGELOG.md

@@ -1,3 +1,10 @@
+# 2.4.3
+
+## Features
+
+* Snakemake-wrappers update to 5.5.0
+* Tasks update
+
 # 2.4.2
 
 ## Features:

CITATION.cff

@@ -3,8 +3,8 @@ authors:
   given-names: Thibault
   orcid: https://orcid.org/0009-0009-2758-8450
 cff-version: 1.2.0
-date-released: '2024-12-04'
+date-released: '2024-12-11'
 message: If you use this software, please cite it as below.
-title: fair-fastqc-multiqc
-url: https://github.com/tdayris/fair_fastqc_multiqc
-version: 2.4.2
+title: fair-star-mapping
+url: https://github.com/tdayris/fair_star_mapping
+version: 2.4.3

README.md

@@ -40,9 +40,9 @@ The tools used in this pipeline are described [here](https://github.com/tdayris/
 
 | Step        | Wrapper                                                                                         |
 | ----------- | ----------------------------------------------------------------------------------------------- |
-| FastQC      | [fastqc-wrapper](https://snakemake-wrappers.readthedocs.io/en/v5.3.0/wrappers/fastqc.html)     |
-| FastScreen  | [fastq-screen](https://snakemake-wrappers.readthedocs.io/en/v5.3.0/wrappers/fastq_screen.html) |
-| MultiQC     | [multiqc-wrapper](https://snakemake-wrappers.readthedocs.io/en/v5.3.0/wrappers/multiqc.html)   |
-| SeqKit      | [seqkit-wrapper](https://snakemake-wrappers.readthedocs.io/en/v5.3.0/wrappers/seqkit.html)     |
+| FastQC      | [fastqc-wrapper](https://snakemake-wrappers.readthedocs.io/en/v5.5.0/wrappers/fastqc.html)     |
+| FastScreen  | [fastq-screen](https://snakemake-wrappers.readthedocs.io/en/v5.5.0/wrappers/fastq_screen.html) |
+| MultiQC     | [multiqc-wrapper](https://snakemake-wrappers.readthedocs.io/en/v5.5.0/wrappers/multiqc.html)   |
+| SeqKit      | [seqkit-wrapper](https://snakemake-wrappers.readthedocs.io/en/v5.5.0/wrappers/seqkit.html)     |
 | fastq_utils | [fastq_utils](https://github.com/nunofonseca/fastq_utils)                                       |
 | fastqinfo   | [fastqinfo](https://github.com/raymondkiu/fastq-info)                                           |

workflow/report/fastq_screen.rst

@@ -2,4 +2,4 @@ This PNG_ image contains FastqScreen_ quality reports for sample {{ snakemake.wi
 It is a stand-alone file, and can be opened in your favorite web-browser.
 
 .. _PNG: https://en.wikipedia.org/wiki/PNG
-.. _FastqScreen: https://snakemake-wrappers.readthedocs.io/en/v5.3.0/wrappers/fastq_screen.html
+.. _FastqScreen: https://snakemake-wrappers.readthedocs.io/en/v5.5.0/wrappers/fastq_screen.html

workflow/report/fastqc.rst

@@ -2,4 +2,4 @@ This HTML_ file contains FastQC_ quality reports for sample {{ snakemake.wildcar
 It is a stand-alone file, and can be opened in your favorite web-browser.
 
 .. _HTML: https://en.wikipedia.org/wiki/HTML
-.. _FastQC: https://snakemake-wrappers.readthedocs.io/en/v5.3.0/wrappers/fastqc.html
+.. _FastQC: https://snakemake-wrappers.readthedocs.io/en/v5.5.0/wrappers/fastqc.html

workflow/report/material_methods.rst

@@ -23,12 +23,12 @@ and relies on fair_genome_indexer_ [#fair_genome_indexer_quote]_ pipeline.
 .. [#fair_genome_indexer_quote] Dayris, T. (2024). fair-genome-indexer (Version 3.9.3) [Computer software]. https://github.com/tdayris/fair_genome_indexer
 
 
-.. _MultiQC: https://snakemake-wrappers.readthedocs.io/en/v5.3.0/wrappers/multiqc.html
+.. _MultiQC: https://snakemake-wrappers.readthedocs.io/en/v5.5.0/wrappers/multiqc.html
 .. _Snakemake: https://snakemake.readthedocs.io
 .. _Github: https://github.com/tdayris/fair_fastqc_multiqc
 .. _`Snakemake workflow`: https://snakemake.github.io/snakemake-workflow-catalog?usage=tdayris/fair_fastqc_multiqc
-.. _FastQC: https://snakemake-wrappers.readthedocs.io/en/v5.3.0/wrappers/fastqc.html
-.. _FastqScreen: https://snakemake-wrappers.readthedocs.io/en/v5.3.0/wrappers/fastq_screen.html
+.. _FastQC: https://snakemake-wrappers.readthedocs.io/en/v5.5.0/wrappers/fastqc.html
+.. _FastqScreen: https://snakemake-wrappers.readthedocs.io/en/v5.5.0/wrappers/fastq_screen.html
 .. _Fastq_utils: https://github.com/nunofonseca/fastq_utils
 .. _Seqkit: https://bioinf.shenwei.me/seqkit/
 .. _Fastqinfo: https://github.com/raymondkiu/fastq-info
@@ -39,4 +39,4 @@ and relies on fair_genome_indexer_ [#fair_genome_indexer_quote]_ pipeline.
 :Authors:
     Thibault Dayris
 
-:Version: 2.4.2 of 2024-12-04
+:Version: 2.4.3 of 2024-12-11

workflow/report/multiqc.rst

@@ -2,5 +2,5 @@ This HTML_ file contains quality reports of FastQC_ for all samples.
 It is a stand-alone file, and can be opened in your favorite `web-browser`_.
 
 .. _HTML: https://en.wikipedia.org/wiki/HTML
-.. _FastQC: https://snakemake-wrappers.readthedocs.io/en/v5.3.0/wrappers/fastqc.html
+.. _FastQC: https://snakemake-wrappers.readthedocs.io/en/v5.5.0/wrappers/fastqc.html
 .. _`web-browser`: https://en.wikipedia.org/wiki/Firefox

workflow/rules/fastq_screen.smk

@@ -30,7 +30,7 @@ rule fair_fastqc_multiqc_fastq_screen_single_ended:
             dpath="params/fair_fastqc_multiqc_fastq_screen_config",
         ),
     wrapper:
-        "v5.3.0/bio/fastq_screen"
+        "v5.5.0/bio/fastq_screen"
 
 
 use rule fair_fastqc_multiqc_fastq_screen_single_ended as fair_fastqc_multiqc_fastq_screen_pair_ended with:

workflow/rules/fastqc.smk

@@ -28,7 +28,7 @@ rule fair_fastqc_multiqc_fastqc_pair_ended:
     params:
         extra=lookup_config(dpath="params/fair_fastqc_multiqc_fastqc", default=""),
     wrapper:
-        "v5.3.0/bio/fastqc"
+        "v5.5.0/bio/fastqc"
 
 
 use rule fair_fastqc_multiqc_fastqc_pair_ended as fair_fastqc_multiqc_fastqc_single_ended with:

workflow/rules/multiqc.smk

@@ -111,4 +111,4 @@ rule fair_fastqc_multiqc_multiqc_report:
     benchmark:
         "benchmark/fair_fastqc_multiqc_multiqc_report.tsv"
     wrapper:
-        "v5.3.0/bio/multiqc"
+        "v5.5.0/bio/multiqc"

workflow/rules/seqkit.smk

@@ -32,7 +32,7 @@ rule fair_fastqc_multiqc_seqkit_stats_pair_ended:
             default="",
         ),
     wrapper:
-        "v5.3.0/bio/seqkit"
+        "v5.5.0/bio/seqkit"
 
 
 use rule fair_fastqc_multiqc_seqkit_stats_pair_ended as fair_fastqc_multiqc_seqkit_stats_single_ended with: