Add workflow Metadata and Sequences from BioProjectIDs

workflows/data-fetching/metadata-and-sequences-from-BioProjectIDs/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /metadata-and-sequences-from-bioproject-ids.ga
+  testParameterFiles:
+  - /metadata-and-sequences-from-bioproject-ids-tests.yml
+  authors:
+  - name: Giuseppe Defazio
+    orcid: 0000-0002-9356-5224

workflows/data-fetching/metadata-and-sequences-from-BioProjectIDs/.workflowhub.yml

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+version: '0.1'
+registries:
+- url: https://workflowhub.eu
+  project: iwc
+  workflow: metadata-and-sequences-from-bioprojects-ids/main

workflows/data-fetching/metadata-and-sequences-from-BioProjectIDs/CHANGELOG.md

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+# Changelog
+
+## [0.1] - 2026-03-23
+
+- Added workflow

workflows/data-fetching/metadata-and-sequences-from-BioProjectIDs/README.md

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+# Metadata and Sequences from BioProject IDs
+
+This workflow takes BioProject IDs as input and is able to retrieve SRA tables and FASTQ files from IDs using pysradb and SRA fetching.
+The workflow may be very useful in Meta-analysis and reanalysis scenarios, giving the possibility to collect metadata and data from BioProject IDs of studies with the same design.
+
+## Input
+
+The workflow needs a single txt input file, without header, with the first column reporting one or more BioProject IDs as follows:
+
+````
+PRJNA1425250
+PRJNA1417619
+PRJNA1425251
+PRJNA1417617
+PRJNA1425252
+PRJEB1417616
+````
+
+
+## Outputs
+
+There are 3 main outputs:
+
+- Data collection for SRA manifest of input BioProject ID(s)
+- Data collection for Paired End FASTQ files
+- Data collection for Single End FASTQ files

workflows/data-fetching/metadata-and-sequences-from-BioProjectIDs/metadata-and-sequences-from-bioproject-ids-tests.yml

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+- doc: Test 1 for Metadata-and-Sequences-from-BioProjectIDs
+  job:
+    BioProject IDs:
+      class: File
+      path: test-data/test1_single_prj_pe.txt
+      filetype: txt
+    assay (metadata download): false
+    desc (metadata download): false
+    detailed (metadata download): true
+    expand (metadata download): false
+    Group by Experiments (fastq download): false
+    Group by Sample (fastq download): false
+  outputs:
+    Metadata file ( SRA table ):
+      element_tests:
+        PRJNA1417618:
+          path: test-data/test1_metadata_file_split_file_000000.txt.tsv
+    Paired End Reads:
+      element_tests:
+        SRR37073390:
+          forward:
+            path: test-data/test1_paired_end_collection_forward.fastq
+            decompress: true
+            compare: contains
+          reverse:
+            path: test-data/test1_paired_end_collection_reverse.fastq
+            decompress: true
+            compare: contains
+
+- doc: Test 2 for Metadata-and-Sequences-from-BioProjectIDs
+  job:
+    BioProject IDs:
+      class: File
+      path: test-data/test2_multiple_prj_mixed.txt
+      filetype: txt
+    assay (metadata download): false
+    desc (metadata download): false
+    detailed (metadata download): true
+    expand (metadata download): false
+    Group by Experiments (fastq download): false
+    Group by Sample (fastq download): false
+  outputs:
+    Metadata file ( SRA table ):
+      element_tests:
+        PRJNA1425250:
+          path: test-data/test2_metadata_file_split_file_000000.txt.tsv
+          compare: contains
+        PRJNA1417618:
+          path: test-data/test2_metadata_file_split_file_000001.txt.tsv
+          compare: contains
+    Paired End Reads:
+      element_tests:
+        SRR37273408:
+          forward:
+            path: test-data/test2_SRR37273408_forward.fastq
+            decompress: true
+            compare: contains
+          reverse:
+            path: test-data/test2_SRR37273408_reverse.fastq
+            decompress: true
+            compare: contains
+        SRR37073390:
+          forward:
+            path: test-data/test2_SRR37073390_forward.fastq
+            decompress: true
+            compare: contains
+          reverse:
+            path: test-data/test2_SRR37073390_reverse.fastq
+            decompress: true
+            compare: contains
+    Single End Reads:
+      element_tests:
+        SRR37273407:
+          path: test-data/test2_SRR37273407_forward.fastq
+          decompress: true
+          compare: contains