Use paired_or_unpaired input, fix tests, update readme

workflows/paleogenomics/adna-analysis/README.md

@@ -7,10 +7,7 @@ The pipeline processes the sequencing-read input provided to the workflow togeth
 ## Required & Optional Inputs
 To run this workflow successfully, you need to provide the following input datasets and parameters:
 
-* **`Choose Read Type` :** Select whether your input is Single-End or Paired-End.
-* **`Input Single-end reads` :** Input single-end FASTQ reads (list collection) for the sample.
-* **`Input Paired-end Forward reads (R1)` :** Input paired-end forward FASTQ reads (list collection) for the sample.
-* **`Input Paired-end reverse reads (R2)` :** Input paired-end reverse FASTQ reads (list collection) for the sample.
+* **`Input FASTQ reads` :** Input FASTQ reads for the sample, as a list of paired or unpaired reads (a `list:paired_or_unpaired` collection). Each element of the list is either a pair of forward and reverse reads or a single unpaired dataset, so single-end and paired-end samples are given to the workflow the same way — and a single run may mix both. Galaxy routes each element down the appropriate trimming and mapping path automatically, so no read-type parameter is needed.
 * **`Reference genome` :** Reference genome sequence in FASTA format. This is essential for read mapping and variant calling.
 * **`Choose Mapper` :** Switch to select the alignment tool. Choose between BWA and Bowtie2.
 * **`HapMap chromosome X reference` :** Optional HapMap dataset used for X-chromosome contamination estimation in ANGSD (used only if provided).

workflows/paleogenomics/adna-analysis/adna-analysis-tests.yml

@@ -1,14 +1,17 @@
 - doc: Test outline for adna-analysis.ga (Single-End, BWA, No BED, HapMap Present)
   job:
-    Choose Read Type: Single-End
-    Input Single-end reads:
+    Input FASTQ reads:
       class: Collection
-      collection_type: list
+      collection_type: list:paired_or_unpaired
       elements:
-      - class: File
+      - class: Collection
         identifier: NIST7035
-        location: https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R1_001_10MB.fastq.gz
-        filetype: fastqsanger.gz
+        collection_type: paired_or_unpaired
+        elements:
+        - class: File
+          identifier: unpaired
+          location: https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R1_001_10MB.fastq.gz
+          filetype: fastqsanger.gz
     Reference genome:
       class: File
       location: https://github.com/nf-core/test-datasets/raw/eager/reference/Human/hs37d5_chr21-MT.fa.gz
@@ -54,7 +57,7 @@
     mapDamage Visualisation:
       element_tests:
         NIST7035:
-          element_tests:
+          elements:
             dnacomp:
               asserts:
                 has_text:
@@ -66,11 +69,9 @@
             has_text:
               text: "freeBayes"
     ANGSD report of nuclear contamination estimation:
-      element_tests:
-        NIST7035:
-          asserts:
-            has_text:
-              text: "Method1_MOM_estimate"
+      asserts:
+        has_text:
+          text: "Method1_MOM_estimate"
     Bcftools variant calling summary statistics report:
       element_tests:
         NIST7035:
@@ -92,23 +93,22 @@
 
 - doc: Test outline for adna-analysis.ga (Paired-End, Bowtie2, BED Present, No HapMap)
   job:
-    Choose Read Type: Paired-End
-    Input Paired-end Forward reads (R1):
-      class: Collection
-      collection_type: list
-      elements:
-      - class: File
-        identifier: NIST7035
-        location: https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R1_001_10MB.fastq.gz
-        filetype: fastqsanger.gz
-    Input Paired-end reverse reads (R2):
+    Input FASTQ reads:
       class: Collection
-      collection_type: list
+      collection_type: list:paired_or_unpaired
       elements:
-      - class: File
+      - class: Collection
         identifier: NIST7035
-        location: https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R2_001_10MB.fastq.gz
-        filetype: fastqsanger.gz
+        collection_type: paired_or_unpaired
+        elements:
+        - class: File
+          identifier: forward
+          location: https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R1_001_10MB.fastq.gz
+          filetype: fastqsanger.gz
+        - class: File
+          identifier: reverse
+          location: https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R2_001_10MB.fastq.gz
+          filetype: fastqsanger.gz
     Reference genome:
       class: File
       location: https://github.com/nf-core/test-datasets/raw/eager/reference/Human/hs37d5_chr21-MT.fa.gz
@@ -154,7 +154,7 @@
     mapDamage Visualisation:
       element_tests:
         NIST7035:
-          element_tests:
+          elements:
             dnacomp:
               asserts:
                 has_text: