2.2.8

.test/makefile

@@ -24,38 +24,32 @@ all: report.txt
 
 
 dag.png:
-	mamba activate test-snakemake-wrappers && \
 	snakemake -s ../workflow/Snakefile \
 		--rulegraph --forceall | dot -Tpng > dag.png && \
 	cp --verbose dag.png ../dag.png
 
 
 report.txt: pipeline.txt
-	mamba activate test-snakemake-wrappers && \
 	snakemake -s ../workflow/Snakefile --profile local \
 		--report report.zip 2>&1 | tee report.txt
 
 
 pipeline.txt: linter.txt
-	mamba activate test-snakemake-wrappers && \
 	snakemake -s ../workflow/Snakefile \
 		--cores 2 \
 		--profile local \
 		2>&1 | tee pipeline.txt
 
 
 linter.txt: format.txt black.txt
-	mamba activate test-snakemake-wrappers && \
 	snakemake -s ../workflow/Snakefile \
 		--lint 2>&1 | tee linter.txt
 
 
 format.txt:
-	mamba activate test-snakemake-wrappers && \
 	snakefmt $(snakefiles) 2>&1 | tee format.txt
 
 black.txt:
-	mamba activate test-snakemake-wrappers && \
 	black $(python_scripts) 2>&1 | tee black.txt
 
 

CHANGELOG.md

@@ -1,3 +1,11 @@
+# 2.2.8
+
+## Features
+
+* Update snakemake wrappers to 3.10.2
+* Report update
+* More readable tmp and logs
+
 # 2.2.7
 
 ## Fix

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/v3.7.0/wrappers/fastq_screen.html
+.. _FastqScreen: https://snakemake-wrappers.readthedocs.io/en/v3.10.2/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/v3.7.0/wrappers/fastqc.html
+.. _FastQC: https://snakemake-wrappers.readthedocs.io/en/v3.10.2/wrappers/fastqc.html

workflow/report/material_methods.rst

@@ -13,12 +13,12 @@ whole pipeline was powered by Snakemake_ [#snakemakepaper]_.
 .. [#snakemakepaper] Köster, Johannes, and Sven Rahmann. "Snakemake—a scalable bioinformatics workflow engine." Bioinformatics 28.19 (2012): 2520-2522.
 
 
-.. _MultiQC: https://snakemake-wrappers.readthedocs.io/en/v3.7.0/wrappers/multiqc.html
+.. _MultiQC: https://snakemake-wrappers.readthedocs.io/en/v3.10.2/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/v3.7.0/wrappers/fastqc.html
-.. _FastqScreen: https://snakemake-wrappers.readthedocs.io/en/v3.7.0/wrappers/fastq_screen.html
+.. _FastQC: https://snakemake-wrappers.readthedocs.io/en/v3.10.2/wrappers/fastqc.html
+.. _FastqScreen: https://snakemake-wrappers.readthedocs.io/en/v3.10.2/wrappers/fastq_screen.html
 
 
 :Authors:

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/v3.7.0/wrappers/fastqc.html
+.. _FastQC: https://snakemake-wrappers.readthedocs.io/en/v3.10.2/wrappers/fastqc.html
 .. _`web-browser`: https://en.wikipedia.org/wiki/Firefox

workflow/rules/common.smk

@@ -68,7 +68,7 @@ snakemake.utils.validate(genomes, "../schemas/genomes.schema.yaml")
 report: "../report/workflows.rst"
 
 
-snakemake_wrappers_prefix: str = "v3.7.0"
+snakemake_wrappers_prefix: str = "v3.10.2"
 stream_list: list[str] = ["1", "2"]
 tmp: str = f"{os.getcwd()}/tmp"
 

workflow/rules/fastq_screen.smk

@@ -1,47 +1,47 @@
 rule fair_fastqc_multiqc_fastq_screen_single_ended:
     input:
-        sample="tmp/fair_fastqc_multiqc/link_or_concat_single_ended_input/{sample}.fastq.gz",
+        sample="tmp/fair_fastqc_multiqc_link_or_concat_single_ended_input/{sample}.fastq.gz",
     output:
         txt=temp(
-            "tmp/fair_fastqc_multiqc/fastq_screen_single_ended/{sample}.fastq_screen.txt"
+            "tmp/fair_fastqc_multiqc_fastq_screen_single_ended/{sample}.fastq_screen.txt"
         ),
         tmp="results/QC/fastq_screen/{sample}.fastq_screen.png",
     threads: 20
     resources:
-        mem_mb=lambda wildcards, attempt: attempt * 512,
+        mem_mb=lambda wildcards, attempt: attempt * 500,
         runtime=lambda wildcards, input, attempt: attempt
         * 15
         * max(1, int(input.size_mb / 1024)),
         tmpdir=tmp,
     log:
-        "logs/fair_fastqc_multiqc/fastq_screen_single_ended/{sample}.log",
+        "logs/fair_fastqc_multiqc_fastq_screen_single_ended/{sample}.log",
     benchmark:
-        "benchmark/fair_fastqc_multiqc/fastq_screen_single_ended/{sample}.tsv"
+        "benchmark/fair_fastqc_multiqc_fastq_screen_single_ended/{sample}.tsv"
     params:
         subset=lookup_config(
-            dpath="params/fair_fastqc_multiqc/fastq_screen/subset",
+            dpath="params/fair_fastqc_multiqc_fastq_screen/subset",
             default=10000,
         ),
         aligner=lookup_config(
-            dpath="params/fair_fastqc_multiqc/fastq_screen/aligner",
+            dpath="params/fair_fastqc_multiqc_fastq_screen/aligner",
             default="bowtie2",
         ),
         fastq_screen_config=lookup_config(
-            dpath="params/fair_fastqc_multiqc/fastq_screen/fastq_screen_config",
+            dpath="params/fair_fastqc_multiqc_fastq_screen/fastq_screen_config",
         ),
     wrapper:
         f"{snakemake_wrappers_prefix}/bio/fastq_screen"
 
 
 use rule fair_fastqc_multiqc_fastq_screen_single_ended as fair_fastqc_multiqc_fastq_screen_pair_ended with:
     input:
-        sample="tmp/fair_fastqc_multiqc/link_or_concat_pair_ended_input/{sample}.{stream}.fastq.gz",
+        sample="tmp/fair_fastqc_multiqc_link_or_concat_pair_ended_input/{sample}.{stream}.fastq.gz",
     output:
         txt=temp(
-            "tmp/fair_fastqc_multiqc/fastq_screen_pair_ended/{sample}.{stream}.fastq_screen.txt"
+            "tmp/fair_fastqc_multiqc_fastq_screen_pair_ended/{sample}.{stream}.fastq_screen.txt"
         ),
         tmp="results/QC/fastq_screen/{sample}.{stream}.fastq_screen.png",
     log:
-        "logs/fair_fastqc_multiqc/fastq_screen_pair_ended/{sample}.{stream}.log",
+        "logs/fair_fastqc_multiqc_fastq_screen_pair_ended/{sample}.{stream}.log",
     benchmark:
-        "benchmark/fair_fastqc_multiqc/fastq_screen_pair_ended/{sample}.{stream}.tsv"
+        "benchmark/fair_fastqc_multiqc_fastq_screen_pair_ended/{sample}.{stream}.tsv"

workflow/rules/fastqc.smk

@@ -1,6 +1,6 @@
 rule fair_fastqc_multiqc_fastqc_pair_ended:
     input:
-        sample="tmp/fair_fastqc_multiqc/link_or_concat_pair_ended_input/{sample}.{stream}.fastq.gz",
+        sample="tmp/fair_fastqc_multiqc_link_or_concat_pair_ended_input/{sample}.{stream}.fastq.gz",
     output:
         html=report(
             "results/QC/report_pe/{sample}.{stream}.html",
@@ -22,18 +22,18 @@ rule fair_fastqc_multiqc_fastqc_pair_ended:
         * max(1, int(input.size_mb / 1024)),
         tmpdir=tmp,
     log:
-        "logs/fair_fastqc_multiqc/fastqc_pair_ended/{sample}.{stream}.log",
+        "logs/fair_fastqc_multiqc_fastqc_pair_ended/{sample}.{stream}.log",
     benchmark:
-        "benchmark/fair_fastqc_multiqc/fastqc_pair_ended/{sample}.{stream}.tsv"
+        "benchmark/fair_fastqc_multiqc_fastqc_pair_ended/{sample}.{stream}.tsv"
     params:
-        extra=lookup_config(dpath="params/fair_fastqc_multiqc/fastqc", default=""),
+        extra=lookup_config(dpath="params/fair_fastqc_multiqc_fastqc", default=""),
     wrapper:
         f"{snakemake_wrappers_prefix}/bio/fastqc"
 
 
 use rule fair_fastqc_multiqc_fastqc_pair_ended as fair_fastqc_multiqc_fastqc_single_ended with:
     input:
-        sample="tmp/fair_fastqc_multiqc/link_or_concat_single_ended_input/{sample}.fastq.gz",
+        sample="tmp/fair_fastqc_multiqc_link_or_concat_single_ended_input/{sample}.fastq.gz",
     output:
         html=report(
             "results/QC/report_pe/{sample}.html",
@@ -48,6 +48,6 @@ use rule fair_fastqc_multiqc_fastqc_pair_ended as fair_fastqc_multiqc_fastqc_sin
         ),
         zip="results/QC/report_pe/{sample}_fastqc.zip",
     log:
-        "logs/fair_fastqc_multiqc/fastqc_single_ended/{sample}.log",
+        "logs/fair_fastqc_multiqc_fastqc_single_ended/{sample}.log",
     benchmark:
-        "benchmark/fair_fastqc_multiqc/fastqc_single_ended/{sample}.tsv"
+        "benchmark/fair_fastqc_multiqc_fastqc_single_ended/{sample}.tsv"

workflow/rules/multiqc.smk

@@ -1,19 +1,19 @@
 rule fair_fastqc_multiqc_bigr_logo:
     output:
-        "tmp/fair_fastqc_multiqc/bigr_logo.png",
+        "tmp/fair_fastqc_multiqc_bigr_logo.png",
     threads: 1
     resources:
         mem_mb=lambda wildcards, attempt: attempt * 512,
         runtime=lambda wildcards, attempt: attempt * 10,
         tmpdir=tmp,
     localrule: True
     log:
-        "logs/fair_fastqc_multiqc/bigr_logo.log",
+        "logs/fair_fastqc_multiqc_bigr_logo/bigr_logo.log",
     benchmark:
-        "benchmark/fair_fastqc_multiqc/bigr_logo.tsv"
+        "benchmark/fair_fastqc_multiqc_bigr_logo/bigr_logo.tsv"
     params:
         extra=lookup_config(
-            dpath="params/fair_fastqc_multiqc/wget", default="--verbose"
+            dpath="params/fair_genome_indexer_wget", default="--verbose"
         ),
         address="https://raw.githubusercontent.com/tdayris/fair_fastqc_multiqc/main/images/bigr_logo.png",
     conda:
@@ -24,22 +24,22 @@ rule fair_fastqc_multiqc_bigr_logo:
 
 rule fair_fastqc_multiqc_multiqc_config:
     input:
-        "tmp/fair_fastqc_multiqc/bigr_logo.png",
+        "tmp/fair_fastqc_multiqc_bigr_logo.png",
     output:
-        temp("tmp/fair_fastqc_multiqc/multiqc_config.yaml"),
+        temp("tmp/fair_fastqc_multiqc_multiqc_config.yaml"),
     threads: 1
     resources:
         mem_mb=lambda wildcards, attempt: attempt * 512,
         runtime=lambda wildcards, attempt: attempt * 5,
         tmpdir=tmp,
     localrule: True
     log:
-        "logs/fair_fastqc_multiqc/multiqc_config.log",
+        "logs/fair_fastqc_multiqc_multiqc_config.log",
     benchmark:
-        "benchmark/fair_fastqc_multiqc/multiqc_config.tsv"
+        "benchmark/fair_fastqc_multiqc_multiqc_config.tsv"
     params:
         extra=lambda wildcards, input: lookup_config(
-            dpath="params/fair_fastqc_multiqc/multiqc/config",
+            dpath="params/fair_fastqc_multiqc_multiqc_config",
             default={
                 "title": "Raw quality control report",
                 "subtitle": "Produced on raw fastq recieved from sequencer",
@@ -67,12 +67,14 @@ rule fair_fastqc_multiqc_multiqc_config:
                     "Quality controls": {
                         "fastqc": "1.12.1",
                         "fastq_screen": "0.15.3",
-                        "bowtie2": "1.3.1",
-                        "multiqc": "1.20.0",
+                        "bowtie2": "2.5.3",
+                        "bowtie1": "1.3.1",
+                        "multiqc": "1.21.0",
                     },
                     "Pipeline": {
                         "snakemake": "8.5.3",
-                        "fair_fastqc_multiqc": "2.1.0",
+                        "snakemake-wrappers-utils": "0.6.2",
+                        "fair_fastqc_multiqc": "2.2.8",
                     },
                 },
                 "disable_version_detection": True,
@@ -82,8 +84,8 @@ rule fair_fastqc_multiqc_multiqc_config:
                 ],
                 "report_section_order": {
                     "fastqc": {"order": 1000},
-                    "fastq_screen": {"before": "fastqc"},
-                    "software_versions": {"before": "fastq_screen"},
+                    "fastq_screen": {"order": "900"},
+                    "software_versions": {"order": "800"},
                 },
             },
         ),
@@ -106,7 +108,7 @@ rule fair_fastqc_multiqc_multiqc_report:
         ),
         fastq_screen_single_ended=branch(
             lookup_config(
-                dpath="params/fair_fastqc_multiqc/fastq_screen/fastq_screen_config"
+                dpath="params/fair_fastqc_multiqc_fastq_screen/fastq_screen_config"
             ),
             then=collect(
                 "tmp/fair_fastqc_multiqc/fastq_screen_single_ended/{single_ended_data.sample_id}.fastq_screen.txt",
@@ -116,17 +118,17 @@ rule fair_fastqc_multiqc_multiqc_report:
         ),
         fastq_screen_pair_ended=branch(
             lookup_config(
-                dpath="params/fair_fastqc_multiqc/fastq_screen/fastq_screen_config"
+                dpath="params/fair_fastqc_multiqc_fastq_screen/fastq_screen_config"
             ),
             then=collect(
-                "tmp/fair_fastqc_multiqc/fastq_screen_pair_ended/{pair_ended_data.sample_id}.{stream}.fastq_screen.txt",
+                "tmp/fair_fastqc_multiqc_fastq_screen_pair_ended/{pair_ended_data.sample_id}.{stream}.fastq_screen.txt",
                 pair_ended_data=get_pair_ended_samples(),
                 stream=stream_list,
             ),
             otherwise=[],
         ),
-        config="tmp/fair_fastqc_multiqc/multiqc_config.yaml",
-        logo="tmp/fair_fastqc_multiqc/bigr_logo.png",
+        config="tmp/fair_fastqc_multiqc_multiqc_config.yaml",
+        logo="tmp/fair_fastqc_multiqc_bigr_logo.png",
     output:
         report(
             "results/QC/MultiQC_FastQC.html",
@@ -148,16 +150,16 @@ rule fair_fastqc_multiqc_multiqc_report:
         tmpdir=tmp,
     params:
         extra=lookup_config(
-            dpath="params/fair_fastqc_multiqc/multiqc/extra",
+            dpath="params/fair_fastqc_multiqc_multiqc/extra",
             default="--verbose --no-megaqc-upload --no-ansi --force",
         ),
         use_input_files_only=lookup_config(
-            dpath="params/fair_fastqc_multiqc/multiqc/use_input_file_only",
+            dpath="params/fair_fastqc_multiqc_multiqc/use_input_file_only",
             default=True,
         ),
     log:
-        "logs/fair_fastqc_multiqc/multiqc_report.log",
+        "logs/fair_fastqc_multiqc_multiqc_report.log",
     benchmark:
-        "benchmark/fair_fastqc_multiqc/multiqc_report.tsv"
+        "benchmark/fair_fastqc_multiqc_multiqc_report.tsv"
     wrapper:
         f"{snakemake_wrappers_prefix}/bio/multiqc"

workflow/rules/prepare_input.smk

@@ -1,7 +1,7 @@
 rule fair_fastqc_multiqc_link_or_concat_single_ended_input:
     output:
         temp(
-            "tmp/fair_fastqc_multiqc/link_or_concat_single_ended_input/{sample}.fastq.gz"
+            "tmp/fair_fastqc_multiqc_link_or_concat_single_ended_input/{sample}.fastq.gz"
         ),
     threads: 1
     resources:
@@ -11,9 +11,9 @@ rule fair_fastqc_multiqc_link_or_concat_single_ended_input:
         * 15,
         tmpdir=tmp,
     log:
-        "logs/fair_fastqc_multiqc/link_or_concat_single_ended_input/{sample}.log",
+        "logs/fair_fastqc_multiqc_link_or_concat_single_ended_input/{sample}.log",
     benchmark:
-        "benchmark/fair_fastqc_multiqc/link_or_concat_single_ended_input/{sample}.tsv"
+        "benchmark/fair_fastqc_multiqc_link_or_concat_single_ended_input/{sample}.tsv"
     params:
         in_files=collect(
             "{sample.upstream_file}",
@@ -31,12 +31,12 @@ rule fair_fastqc_multiqc_link_or_concat_single_ended_input:
 use rule fair_fastqc_multiqc_link_or_concat_single_ended_input as fair_fastqc_multiqc_link_or_concat_pair_ended_input with:
     output:
         temp(
-            "tmp/fair_fastqc_multiqc/link_or_concat_pair_ended_input/{sample}.{stream}.fastq.gz"
+            "tmp/fair_fastqc_multiqc_link_or_concat_pair_ended_input/{sample}.{stream}.fastq.gz"
         ),
     log:
-        "logs/fair_fastqc_multiqc/link_or_concat_pair_ended_input/{sample}.{stream}.log",
+        "logs/fair_fastqc_multiqc_link_or_concat_pair_ended_input/{sample}.{stream}.log",
     benchmark:
-        "benchmark/fair_fastqc_multiqc/link_or_concat_pair_ended_input/{sample}.{stream}.tsv"
+        "benchmark/fair_fastqc_multiqc_link_or_concat_pair_ended_input/{sample}.{stream}.tsv"
     params:
         in_files=branch(
             evaluate("{stream} == '1'"),