From 130bf5af7d43e0ae057e27ab2ef2216d5e9e29bc Mon Sep 17 00:00:00 2001 From: Pablo Moreno Date: Mon, 4 Oct 2021 16:27:06 +0100 Subject: [PATCH 1/4] Expression Atlas smartseq plus tests --- .gitmodules | 3 +++ .../.ebi-gene-expression-group/scxa-workflows | 1 + .../SingleCellExpressionAtlas-smartseq-test.yml | 17 +++++++++++++++++ .../SingleCellExpressionAtlas-smartseq.ga | 1 + 4 files changed, 22 insertions(+) create mode 100644 .gitmodules create mode 160000 workflows/single-cell-RNAseq/.ebi-gene-expression-group/scxa-workflows create mode 100644 workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/SingleCellExpressionAtlas-smartseq-test.yml create mode 120000 workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/SingleCellExpressionAtlas-smartseq.ga diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000000..a15abe233c --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule "workflows/single-cell-RNAseq/.ebi-gene-expression-group/scxa-workflows"] + path = workflows/single-cell-RNAseq/.ebi-gene-expression-group/scxa-workflows + url = https://github.com/ebi-gene-expression-group/scxa-workflows diff --git a/workflows/single-cell-RNAseq/.ebi-gene-expression-group/scxa-workflows b/workflows/single-cell-RNAseq/.ebi-gene-expression-group/scxa-workflows new file mode 160000 index 0000000000..181064b47f --- /dev/null +++ b/workflows/single-cell-RNAseq/.ebi-gene-expression-group/scxa-workflows @@ -0,0 +1 @@ +Subproject commit 181064b47f02d7bb696e01f66e9d116af2836f60 diff --git a/workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/SingleCellExpressionAtlas-smartseq-test.yml b/workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/SingleCellExpressionAtlas-smartseq-test.yml new file mode 100644 index 0000000000..b89c1f701b --- /dev/null +++ b/workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/SingleCellExpressionAtlas-smartseq-test.yml @@ -0,0 +1,17 @@ +- doc: Test Single Cell Expression Atlas smartseq execution using E-MTAB-6077 + job: + genemeta: + class: File + location: http://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/E-MTAB-6077/Danio_rerio.GRCz11.99.gtf.gz + genes: + class: File + location: http://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/E-MTAB-6077/E-MTAB-6077.aggregated_counts.mtx_rows.gz + cellmeta: + class: File + location: http://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/E-MTAB-6077/E-MTAB-6077.cell_metadata.tsv + barcodes: + class: File + location: http://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/E-MTAB-6077/E-MTAB-6077.aggregated_counts.mtx_cols.gz + matrix: + class: File + location: http://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/E-MTAB-6077/E-MTAB-6077.aggregated_counts.mtx.gz diff --git a/workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/SingleCellExpressionAtlas-smartseq.ga b/workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/SingleCellExpressionAtlas-smartseq.ga new file mode 120000 index 0000000000..93dcd6df76 --- /dev/null +++ b/workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/SingleCellExpressionAtlas-smartseq.ga @@ -0,0 +1 @@ +../.ebi-gene-expression-group/scxa-workflows/w_smart-seq_clustering/scanpy_clustering_workflow.json \ No newline at end of file From 3bef62430cb9e98bc3a8ee5b48853e4db63c708f Mon Sep 17 00:00:00 2001 From: Pablo Moreno Date: Mon, 4 Oct 2021 16:59:59 +0100 Subject: [PATCH 2/4] Missing dockstore file --- .../SingleCellExpressionAtlas-downstream/.dockstore.yml | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/.dockstore.yml diff --git a/workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/.dockstore.yml b/workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/.dockstore.yml new file mode 100644 index 0000000000..0ba0b2c5aa --- /dev/null +++ b/workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/.dockstore.yml @@ -0,0 +1,7 @@ +version: 0.2.4 +workflows: +- name: 'SCXA prod v0.2.4, Scanpy 1.7.X' + primaryDescriptorPath: /SingleCellExpressionAtlas-smartseq.ga + subclass: Galaxy + testParameterFiles: + - /SingleCellExpressionAtlas-smartseq-test.yml From bbd97428fb7075680b62ddb86120e4966cac64d3 Mon Sep 17 00:00:00 2001 From: Pablo Moreno Date: Mon, 4 Oct 2021 17:08:15 +0100 Subject: [PATCH 3/4] Checkout with submodules --- .github/workflows/workflow_test.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/workflow_test.yml b/.github/workflows/workflow_test.yml index 9ae59945cb..9f07f7cbed 100644 --- a/.github/workflows/workflow_test.yml +++ b/.github/workflows/workflow_test.yml @@ -52,6 +52,7 @@ jobs: - uses: actions/checkout@v2 with: fetch-depth: 0 + submodules: true - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks uses: galaxyproject/planemo-ci-action@v1 id: discover @@ -76,6 +77,7 @@ jobs: - uses: actions/checkout@v2 with: fetch-depth: 1 + submodules: true - uses: actions/setup-python@v1 with: python-version: ${{ matrix.python-version }} @@ -117,6 +119,7 @@ jobs: - uses: actions/checkout@v2 with: fetch-depth: 1 + submodules: true - uses: actions/setup-python@v1 with: python-version: ${{ matrix.python-version }} @@ -193,6 +196,7 @@ jobs: - uses: actions/checkout@v2 with: fetch-depth: 1 + submodules: true - uses: actions/setup-python@v1 with: python-version: ${{ matrix.python-version }} From 47d6e85ced4fa1d8a762015727b7115bfb111815 Mon Sep 17 00:00:00 2001 From: Pablo Moreno Date: Wed, 13 Oct 2021 10:18:14 +0100 Subject: [PATCH 4/4] Point to wf with corrected param iterator and param box for batch correction --- .../.ebi-gene-expression-group/scxa-workflows | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/single-cell-RNAseq/.ebi-gene-expression-group/scxa-workflows b/workflows/single-cell-RNAseq/.ebi-gene-expression-group/scxa-workflows index 181064b47f..12596848f8 160000 --- a/workflows/single-cell-RNAseq/.ebi-gene-expression-group/scxa-workflows +++ b/workflows/single-cell-RNAseq/.ebi-gene-expression-group/scxa-workflows @@ -1 +1 @@ -Subproject commit 181064b47f02d7bb696e01f66e9d116af2836f60 +Subproject commit 12596848f8f89ff0d46fbf196211a869a1ad1016