Add short-read QC & trimming workflow

workflows/read_preprocessing/short-reads-qc-trimming/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /short-reads-quality-control-and-trimming.ga
+  testParameterFiles:
+  - /short-reads-quality-control-and-trimming-tests.yml
+  authors:
+  - name: "B\xE9r\xE9nice Batut"
+    orcid: 0000-0001-9852-1987
+  - name: Paul Zierep
+    orcid: 0000-0003-2982-388X

workflows/read_preprocessing/short-reads-qc-trimming/CHANGELOG.md

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+# Changelog
+
+## [0.1] 2025-10-07
+
+First release.

workflows/read_preprocessing/short-reads-qc-trimming/README.md

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+# Short-reads quality control and trimming
+
+Before starting any analysis, it is always a good idea to assess the quality of the input data and to discard poor-quality base content by trimming and filtering reads.
+
+This workflow takes paired-end Illumina (**short-reads**) fastq(.gz) files and executes the following steps:
+1. Quality control and trimming using **fastp**
+2. Aggregation of the quality control reports using **MultiQC**
+
+## Input Datasets
+
+- A list of paired datasets corresponding to paired-end raw reads in `fastqsanger` or `fastqsanger.gz` format.
+- Qualified quality score: The quality value that a base is qualified to have.
+- Minimal read length: Reads shorter than this value will be discarded.
+- Cutting mean quality: The bases in the sliding window with mean quality below this value will be cut.
+- [Optional] Adapter to remove on forward reads and reverse reads
+
+## Output Datasets
+
+- A list of paired datasets corresponding to paired-end **trimmed** reads in `fastqsanger` or `fastqsanger.gz`, ready for further analysis.
+- List of `JSON` reports of fastp for each sample that could be used as inputs for extra MultiQC
+- MultiQC report in HTML

workflows/read_preprocessing/short-reads-qc-trimming/short-reads-quality-control-and-trimming-tests.yml

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+- doc: Test outline for short-reads-quality-control-and-trimming
+  job:
+    Raw reads:
+      class: Collection
+      collection_type: list:paired
+      elements:
+      - class: Collection
+        type: paired
+        identifier: pair
+        elements:
+        - class: File
+          identifier: forward
+          location: https://zenodo.org/records/11484215/files/paired_r1.fastq.gz
+          filetype: fastqsanger.gz
+        - class: File
+          identifier: reverse
+          location: https://zenodo.org/records/11484215/files/paired_r2.fastq.gz
+          filetype: fastqsanger.gz
+    Adapter to remove on forward reads: null
+    Adapter to remove on reverse reads: null
+    Qualified quality score: '15'
+    Minimal read length: '15'
+    Cutting mean quality: '15'
+  outputs:
+    multiqc_html_report:
+      asserts:
+        has_text:
+          text: "Filtered Reads"
+        has_text:
+          text: "pair"
+    fastp_report_json:
+      element_tests:
+        pair:
+          asserts:
+            has_text:
+              text: "paired end (301 cycles + 301 cycles)"
+            has_text:
+              text: "300000"
+            has_text:
+              text: "295680"
+            has_text:
+              text: "59230948"