update for tests

.github/workflows/release-please.yml

@@ -10,8 +10,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
 
-      - uses: GoogleCloudPlatform/release-please-action@v2
+      - uses: google-github-actions/release-please-action@v3
         id: release
         with:
-          release-type: go # just keep a changelog, no version anywhere outside of git tags
-          package-name: <repo>
+          release-type: simple
+          package-name: release-please-action

.gitignore

@@ -1,6 +1,8 @@
 *
 !.github
 !.github/**
+!.tests
+!.tests/**
 !config
 !config/REAMDE.md
 !config/config.yaml

.tests/config/config.yaml

@@ -0,0 +1,18 @@
+pepfile: config/pep/config.yaml
+
+run-date: "test"
+
+adapter-seqs: "-a GCGAATTTCGACGATCGTTGCATTAACTCGCGAA -g AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"
+
+data-handling:
+  # path to store data within the workflow
+  data: "data/"
+  resources: "resources/"
+
+quality-criteria:
+  # minimal length of acceptable reads
+  min-length-reads: 15
+  # average quality of acceptable reads (PHRED)
+  min-PHRED: 20
+
+human-ref: "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.29_GRCh38.p14/GCA_000001405.29_GRCh38.p14_genomic.fna.gz"

.tests/config/multiqc_config.yaml

@@ -0,0 +1,52 @@
+show_analysis_time: True
+
+# order of report
+module_order:
+  - fastqc:
+      name: "Reads Quality Control"
+      target: "FastQC"
+  - fastp:
+      name: "Reads Preprocessing"
+      target: "fastp"
+
+report_section_order:
+  fastqc_sequence_length_distribution: remove
+  fastqc_per_sequence_gc_content: remove
+  fastqc_per_base_n_content: remove
+  fastqc_per_base_sequence_content: remove
+  fastqc_sequence_duplication_levels: remove
+  fastqc_per_base_sequence_quality: remove
+  fastqc_status_checks:
+    before: "fastqc_sequence_counts"
+
+# sample name cleaning
+fn_clean_exts:
+  - ".fastp"
+  - ".trimmed"
+  - ".fastq"
+  - ".gz"
+  - "_L001_R1_001"
+  - "_L001_R2_001"
+  - "_L002_R1_001"
+  - "_L002_R2_001"
+  - "_R1"
+  - "_S"
+  - ".1"
+  - ".2"
+
+# customising general Statistics
+table_columns_visible:
+  Reads Quality Control:
+    percent_duplicates: False
+    percent_gc: False
+    avg_sequence_length: False
+    median_sequence_length: False
+    percent_fails: False
+    total_sequences: False
+  Reads Preprocessing:
+    pct_duplication: False
+    after_filtering_q30_rate: True
+    after_filtering_q30_bases: False
+    after_filtering_gc_content: False
+    pct_surviving: True
+    pct_adapter: False

.tests/config/pep/config.yaml

@@ -0,0 +1,2 @@
+pep_version: 2.0.0
+sample_table: "samples.csv"

.tests/config/pep/samples.csv

@@ -0,0 +1,2 @@
+sample_name,fq1,fq2
+115_L001,/groups/ds/resistance_cefiderocol/data/illumina/115_L001_R1.fastq.gz,/groups/ds/resistance_cefiderocol/data/illumina/115_L001_R2.fastq.gz