feat!: refactoring of workflow to make it more flexible, remove hardcoded options

.github/workflows/conventional-prs.yml

@@ -1,4 +1,5 @@
-name: Lint PR
+name: Conventional PRs
+
 on:
   pull_request_target:
     types:
@@ -11,10 +12,5 @@ permissions:
   pull-requests: read
 
 jobs:
-  main:
-    name: Validate PR title
-    runs-on: ubuntu-latest
-    steps:
-      - uses: amannn/action-semantic-pull-request@v5
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  conventional-prs:
+    uses: MPUSP/mpusp-github-actions/.github/workflows/conventional-prs.yml@main

.github/workflows/deploy-apptainer.yml

@@ -0,0 +1,17 @@
+name: Deploy Apptainer
+
+on:
+  workflow_run:
+    workflows: ["Release Please"]
+    types:
+      - completed
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  packages: write
+
+jobs:
+  deploy-apptainer:
+    if: ${{ github.event_name == 'workflow_dispatch' || github.event.workflow_run.conclusion == 'success' }}
+    uses: MPUSP/mpusp-github-actions/.github/workflows/deploy-apptainer.yml@main

.github/workflows/release-please.yml

@@ -1,19 +1,14 @@
+name: Release Please
+
 on:
   push:
-    branches:
-      - main
+    branches: [main]
 
 permissions:
   contents: write
   pull-requests: write
-
-name: release-please
+  issues: write
 
 jobs:
   release-please:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: googleapis/release-please-action@v4
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-          release-type: simple
+    uses: MPUSP/mpusp-github-actions/.github/workflows/release-please.yml@main

.github/workflows/snakemake-tests.yml

@@ -0,0 +1,12 @@
+name: Snakemake Tests
+
+on:
+  pull_request:
+    branches: [main]
+
+jobs:
+  snakemake-tests:
+    uses: MPUSP/mpusp-github-actions/.github/workflows/snakemake-tests.yml@main
+    with:
+      cores: 2
+      dryrun: false

.snakemake-workflow-catalog.yml

@@ -1,6 +1,11 @@
+# configuration of display in snakemake workflow catalog: https://snakemake.github.io/snakemake-workflow-catalog
+
 usage:
-  software-stack-deployment: # definition of software deployment method (at least one of conda, singularity, or singularity+conda)
-    conda: true # whether pipeline works with --use-conda
-    singularity: false # whether pipeline works with --use-singularity
-    singularity+conda: false # whether pipeline works with --use-singularity --use-conda
-  report: true # add this to confirm that the workflow allows to use 'snakemake --report report.zip' to generate a report containing all results and explanations
+  mandatory-flags:
+    desc: # describe your flags here in a few sentences
+    flags: # put your flags here
+  software-stack-deployment:
+    conda: true # whether pipeline works with '--sdm conda'
+    apptainer: false # whether pipeline works with '--sdm apptainer/singularity'
+    apptainer+conda: true # whether pipeline works with '--sdm conda apptainer/singularity'
+    report: true # whether creation of reports using 'snakemake --report report.zip' is supported

.test/config/config.yml

@@ -1,5 +1,5 @@
-samplesheet: "config/samplesheet/samples_mpusp_custom.tsv"
-libtype: "sense"
+samplesheet: "config/samplesheet/samples_neb_umi.tsv"
+libtype: "antisense"
 
 get_genome:
   database: "ncbi"
@@ -11,48 +11,34 @@ get_genome:
       "RefSeq": "gene",
       "RefSeq": "pseudogene",
       "RefSeq": "CDS",
-      "Protein Homology": "CDS"
+      "Protein Homology": "CDS",
     ]
 
 extract_features:
   biotypes: ["protein_coding", "pseudogene", "ncRNA", "rRNA", "tRNA"]
 
 umi_extraction:
-  method: "string"
-  pattern: "--bc-pattern=NNNCCCNNNCCCNNNC"
+  method: "none"
+  pattern: ""
 umi_dedup: "--edit-distance-threshold=0"
 
-cutadapt:
-  read1_adapter: "TACACGACGCTCTTCCGATCT"
-  read2_adapter: "AGATCGGAAGAGCGTCGTGTA"
-  default:
-    [
-      "-q 10 ",
-      "-m 18 ",
-      "--overlap=3"
-    ]
+fastp:
+  extra: "-M 10 -l 18 --adapter_sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"
 
 star:
-  index: Null
-  genomeSAindexNbases: 9
-  multi: 10
-  sam_multi: 1
-  intron_max: 1
-  default:
+  index: "--genomeSAindexNbases 9"
+  extra:
     [
-      "--readFilesCommand zcat ",
-      "--outSAMstrandField None ",
-      "--outSAMattributes All ",
-      "--outSAMattrIHstart 0 ",
-      "--outFilterType Normal ",
-      "--outFilterMultimapScoreRange 1 ",
-      "-o STARmappings ",
-      "--outSAMtype BAM Unsorted ",
-      "--outStd BAM_Unsorted ",
-      "--outMultimapperOrder Random ",
-      "--alignEndsType EndToEnd",
+      "--outFilterMultimapNmax 10",
+      "--outSAMmultNmax 1",
+      "--outMultimapperOrder Random",
+      "--alignIntronMax 1",
     ]
 
+samtools:
+  sort: ""
+  index: ""
+
 feature_counts:
   defaults:
     [
@@ -61,18 +47,16 @@ feature_counts:
       "-g locus_tag",
       "-M",
       "--fracOverlap 0.2",
-      "--largestOverlap"
+      "--largestOverlap",
     ]
 
 deeptools:
-  bin_size: 1
-  normalize: "CPM"
-  defaults: "--exactScaling"
-  paired_end: "--extendReads"
+  genome_size: 2000000
+  extra: "--binSize 1 --normalizeUsing CPM --exactScaling --extendReads"
+
+fastqc:
+  extra: "--quiet --nogroup"
 
 multiqc:
-    config: "config/multiqc_config.yml"
-    defaults: ["--dirs-depth 2 ",
-        "--exclude general_stats ",
-        "--force ",
-        "--dirs"]
+  config: "config/multiqc_config.yml"
+  extra: "--dirs"

.test/config/multiqc_config.yml

@@ -1,4 +1,5 @@
 report_header_info:
+  - Snakemake workflow: https://github.com/MPUSP/snakemake-bacterial-rnaseq-processing
   - Contact E-mail: "bioinformatics@mpusp.mpg.de"
   - Application Type: "Bacterial RNAseq"
   - Sequencing Platform: "Illumina"
@@ -15,7 +16,7 @@ custom_logo_url: "https://www.mpusp.mpg.de/"
 custom_logo_title: "Max Planck Unit for the Science of Pathogens"
 
 skip_versions_section: false
-disable_version_detection: true
+disable_version_detection: false
 versions_table_group_header: "Workflow Analysis Steps"
 
 skip_generalstats: true
@@ -24,21 +25,10 @@ remove_sections:
   - samtools-stats
 
 module_order:
+  - fastqc
+  - fastp
   - star
-  - cutadapt
-  - fastqc:
-      name: "FastQC (trimmed)"
-      anchor: "fastqc_trimmed"
-      info: "This section of the report shows FastQC results after adapter trimming."
-      target: ""
-      path_filters:
-        - "*/clipped_reads/*_fastqc.zip"
-  - fastqc:
-      name: "FastQC (raw)"
-      anchor: "fastqc_raw"
-      path_filters:
-        - "*/raw_reads/*_fastqc.zip"
-
-report_section_order:
-  fastqc_raw:
-    before: fastqc_trimmed
+  - umitools
+  - featurecounts
+  - samtools
+  - biotype_dist

.test/config/samplesheet/samples_mpusp_custom.tsv

@@ -1,3 +1,3 @@
-sample	condition	replicate	experiment	data_folder	fq1	fq2	fq_umi
-RNA-1	RNA	1	rnaseq_mpusp_custom	data/rnaseq_mpusp_custom	RNA-1_R1.fastq.gz	RNA-1_R2.fastq.gz	-
-RNA-2	RNA	2	rnaseq_mpusp_custom	data/rnaseq_mpusp_custom	RNA-2_R1.fastq.gz	RNA-2_R2.fastq.gz	-
+sample	condition	replicate	read1	read2	readumi
+RNA-1	RNA	1	data/rnaseq_mpusp_custom/RNA-1_R1.fastq.gz	data/rnaseq_mpusp_custom/RNA-1_R2.fastq.gz	-
+RNA-2	RNA	2	data/rnaseq_mpusp_custom/RNA-2_R1.fastq.gz	data/rnaseq_mpusp_custom/RNA-2_R2.fastq.gz	-

.test/config/samplesheet/samples_neb_umi.tsv

@@ -1,3 +1,3 @@
-sample	condition	replicate	experiment	data_folder	fq1	fq2	fq_umi
-RNA-1	RNA	1	rnaseq_neb_umi	data/rnaseq_neb_umi	RNA-1_R1.fastq.gz	RNA-1_R2.fastq.gz	RNA-1_UMI.fastq.gz
-RNA-2	RNA	2	rnaseq_neb_umi	data/rnaseq_neb_umi	RNA-2_R1.fastq.gz	RNA-2_R2.fastq.gz	RNA-2_UMI.fastq.gz
+sample	condition	replicate	read1	read2	readumi
+RNA-1	RNA	1	data/rnaseq_neb_umi/RNA-1_R1.fastq.gz	data/rnaseq_neb_umi/RNA-1_R2.fastq.gz	data/rnaseq_neb_umi/RNA-1_UMI.fastq.gz
+RNA-2	RNA	2	data/rnaseq_neb_umi/RNA-2_R1.fastq.gz	data/rnaseq_neb_umi/RNA-2_R2.fastq.gz	data/rnaseq_neb_umi/RNA-2_UMI.fastq.gz

.test/config/samplesheet/samples_nextflex.tsv

@@ -1,3 +1,3 @@
-sample	condition	replicate	experiment	data_folder	fq1	fq2	fq_umi
-RNA-1	RNA	1	rnaseq_nextflex	data/rnaseq_nextflex	RNA-1_R1.fastq.gz	RNA-1_R2.fastq.gz	-
-RNA-2	RNA	2	rnaseq_nextflex	data/rnaseq_nextflex	RNA-2_R1.fastq.gz	RNA-2_R2.fastq.gz	-
+sample	condition	replicate	read1	read2	readumi
+RNA-1	RNA	1	data/rnaseq_nextflex/RNA-1_R1.fastq.gz	data/rnaseq_nextflex/RNA-1_R2.fastq.gz	-
+RNA-2	RNA	2	data/rnaseq_nextflex/RNA-2_R1.fastq.gz	data/rnaseq_nextflex/RNA-2_R2.fastq.gz	-