[WIP] scRNA-seq Duboule lab workflows

workflows/scrna-seq/fastq-to-matrix-10x/.dockstore.yml

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+version: 1.2
+workflows:
+- name: scrna-seq-fastq-to-matrix-10x-cellplex
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /scrna-seq-fastq-to-matrix-10x-cellplex.ga
+  testParameterFiles:
+  - /scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml
+  authors:
+  - name: Lucille Delisle
+    orcid: 0000-0002-1964-4960
+  - name: Mehmet Tekman
+    orcid: 0000-0002-4181-2676
+  - name: Hans-Rudolf Hotz
+    orcid: 0000-0002-2799-424X
+  - name: Daniel Blankenberg
+    orcid: 0000-0002-6833-9049
+  - name: Wendi Bacon
+    orcid: 0000-0002-8170-8806
+- name: scrna-seq-fastq-to-matrix-10x-v3
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /scrna-seq-fastq-to-matrix-10x-v3.ga
+  testParameterFiles:
+  - /scrna-seq-fastq-to-matrix-10x-v3-tests.yml
+  authors:
+  - name: Lucille Delisle
+    orcid: 0000-0002-1964-4960
+  - name: Mehmet Tekman
+    orcid: 0000-0002-4181-2676
+  - name: Hans-Rudolf Hotz
+    orcid: 0000-0002-2799-424X
+  - name: Daniel Blankenberg
+    orcid: 0000-0002-6833-9049
+  - name: Wendi Bacon
+    orcid: 0000-0002-8170-8806

workflows/scrna-seq/fastq-to-matrix-10x/CHANGELOG.md

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+# Changelog
+
+## [0.1] 2023-12-01
+
+First release.

workflows/scrna-seq/fastq-to-matrix-10x/README.md

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+# Single-cell RNA-seq fastq to matrix for 10X data
+
+TODO

workflows/scrna-seq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml

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+- doc: Test outline for scrna-seq-fastq-to-matrix-10X-cellplex.ga
+  job:
+    fastq PE collection GEX:
+      class: Collection
+      collection_type: list:paired
+      elements:
+      - class: Collection
+        type: paired
+        identifier: subsample
+        elements:
+        - identifier: forward
+          class: File
+          location: https://zenodo.org/records/10229382/files/subSample_GEX_R1.fastq.gz
+          filetype: fastqsanger.gz
+        - identifier: reverse
+          class: File
+          location: https://zenodo.org/records/10229382/files/subSample_GEX_R2.fastq.gz
+          filetype: fastqsanger.gz
+    reference genome: mm10full # To test on usegalaxy.eu
+    gtf:
+      class: File
+      location: https://zenodo.org/records/10079673/files/mm10_custom102_allGastruloids_min10_extended.gtf.gz
+      decompress: true
+      filetype: gtf
+    cellranger_barcodes_3M-february-2018.txt:
+      class: File
+      location: https://zenodo.org/record/3457880/files/3M-february-2018.txt.gz
+      decompress: true
+      filetype: tabular
+    fastq PE collection CMO:
+      class: Collection
+      collection_type: list:paired
+      elements:
+      - class: Collection
+        type: paired
+        identifier: subsample
+        elements:
+        - identifier: forward
+          class: File
+          location: https://zenodo.org/records/10229382/files/subSample_CMO_R1.fastq.gz
+          filetype: fastqsanger.gz
+        - identifier: reverse
+          class: File
+          location: https://zenodo.org/records/10229382/files/subSample_CMO_R2.fastq.gz
+          filetype: fastqsanger.gz
+    sample name and CMO sequence collection:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: subsample
+        location: https://zenodo.org/records/10229382/files/CMO.csv
+        filetype: csv
+    Number of expected cells (used by CITE-seq-Count)): 1000
+  outputs:
+    MultiQC_STARsolo:
+      class: File
+      asserts:
+        - that: "has_text_matching"
+          expression: "<tbody><tr><th class=\"rowheader\" data-original-sn=\"subsample\">subsample</th><td class=\"data-coloured mqc-generalstats-star-uniquely_mapped_percent \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:7[0-9].[0-9]%; background-color:#bbd9c6;\"></span><span class=\"val\">7[0-9].[0-9]%</span></div></td><td class=\"data-coloured mqc-generalstats-star-uniquely_mapped \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:100.0%; background-color:#d1b3bc;\"></span><span class=\"val\">[0-9].[0-9]</span></div></td></tr></tbody>"
+    Seurat input for gene expression (filtered):
+      class: Collection
+      collection_type: list:list
+      elements:
+        class: Collection
+        collection_type: list
+        identifier: subsample
+        elements:
+        - class: File
+          identifier: matrix
+          asserts:
+            - has_line:
+              line: "55141 353 1026324"
+        - class: File
+          identifier: barcodes
+          asserts:
+            - has_line:
+              line: "AAACGAAAGCATGCAG"
+        - class: File
+          identifier: genes
+          asserts:
+            - has_line:
+              line: "ENSMUSG00000102693	4933401J01Rik"
+    CITE-seq-Count report:
+      class: Collection
+      collection_type: list
+      elements:
+        identifier: subsample
+        class: File
+        asserts:
+          - that: "has_line"
+            line: "CITE-seq-Count Version: 1.4.4"
+          - that: "has_line"
+            line: "Reads processed: 1171367"
+          - that: "has_line"
+            line: "Percentage mapped: 99"
+          - that: "has_line"
+            line: "Percentage unmapped: 1"
+    Seurat input for CMO (UMI):
+      class: Collection
+      collection_type: list:list
+      elements:
+        class: Collection
+        collection_type: list
+        identifier: subsample
+        elements:
+        - class: File
+          identifier: matrix
+          asserts:
+            - has_line:
+              line: "8 toto 220553"
+        - class: File
+          identifier: barcodes
+          asserts:
+            - has_line:
+              line: "CGGGTCAAGGATGGAG"
+        - class: File
+          identifier: genes
+          asserts:
+            - has_line:
+              line: "mESC.rep1-CGCGATATGGTCGGA"
+
+      class: Collection
+      collection_type: list:list