added quant test workflow

2024-11-13 05:13:09 +00:00 · 2021-01-26 15:58:22 +01:00 · 2021-01-26 15:58:22 +01:00 · 431a2eb73b
commit 431a2eb73b
parent 915e0574a2
2 changed files with 98 additions and 574 deletions
--- a/.github/workflows/salmon_quant.yml
+++ b/.github/workflows/salmon_quant.yml
@ -0,0 +1,40 @@
+name: salmon_quant
+on:
+  push:
+    paths:
+      - software/salmon/quant/**
+      - .github/workflows/salmon_quant.yml
+      - tests/software/salmon/**
+  pull_request:
+    paths:
+      - software/salmon/quant/**
+      - .github/workflows/salmon_quant.yml
+      - tests/software/salmon/**
+
+jobs:
+  ci_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_version: [20.11.0-edge]
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          NXF_VER: ${{ matrix.nxf_version }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+
+      # Test the module
+      - run: pytest --tag salmon_quant --symlink --wt 2
--- a/tests/software/salmon/test.yml
+++ b/tests/software/salmon/test.yml
@ -26,308 +26,50 @@
      md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71

 - name: salmon quant paired end
-  command: nextflow run ./tests/software/salmon -profile docker -entry test_salmon_quant_pe -c tests/config/nextflow.confi
+  command: nextflow run ./tests/software/salmon -profile docker -entry test_salmon_quant_pe -c tests/config/nextflow.config
  tags:
    - salmon
    - salmon_quant
    - salmon_quant_pe
  files:
-    - path: output/salmon/test/cmd_info.json
+    - path: ./output/salmon/test/cmd_info.json
      md5sum: 007676e4d79de0809a03e0ea045ed4a1
-    - path: output/salmon/test/quant.sf
-      md5sum: addb78e233f248b8f62cae3e217bf689
-    - path: output/salmon/test/lib_format_counts.json
-      md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea
-    - path: output/salmon/test/logs/salmon_quant.log
-      md5sum: f7fe6e71b4ad4232e217db300c29202b
-    - path: output/salmon/test/cmd_info.json
-      md5sum: 007676e4d79de0809a03e0ea045ed4a1
-    - path: output/salmon/test/quant.sf
-      md5sum: addb78e233f248b8f62cae3e217bf689
-    - path: output/salmon/test/lib_format_counts.json
-      md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea
-    - path: output/salmon/test/logs/salmon_quant.log
-      md5sum: f7fe6e71b4ad4232e217db300c29202b
-    - path: output/salmon/test/aux_info/expected_bias.gz
-      md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
-    - path: output/salmon/test/aux_info/observed_bias_3p.gz
-      md5sum: ef13c06a538e9c34ca9f84212c82f44e
-    - path: output/salmon/test/aux_info/meta_info.json
-      md5sum: f82491a19755bb1c32d49e9f0e12eebd
-    - path: output/salmon/test/aux_info/fld.gz
-      md5sum: 7f342560fea53327f0532623e53052f7
-    - path: output/salmon/test/aux_info/ambig_info.tsv
-      md5sum: 950001575c24fb6bc2c7a6848043b126
-    - path: output/salmon/test/aux_info/observed_bias.gz
-      md5sum: ef13c06a538e9c34ca9f84212c82f44e
-    - path: output/salmon/test/cmd_info.json
-      md5sum: 007676e4d79de0809a03e0ea045ed4a1
-    - path: output/salmon/test/quant.sf
-      md5sum: addb78e233f248b8f62cae3e217bf689
-    - path: output/salmon/test/lib_format_counts.json
-      md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea
-    - path: output/salmon/test/logs/salmon_quant.log
-      md5sum: f7fe6e71b4ad4232e217db300c29202b
-    - path: output/salmon/test/cmd_info.json
-      md5sum: 007676e4d79de0809a03e0ea045ed4a1
-    - path: output/salmon/test/quant.sf
-      md5sum: addb78e233f248b8f62cae3e217bf689
-    - path: output/salmon/test/lib_format_counts.json
-      md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea
-    - path: output/salmon/test/logs/salmon_quant.log
-      md5sum: f7fe6e71b4ad4232e217db300c29202b
-    - path: output/salmon/test/aux_info/expected_bias.gz
-      md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
-    - path: output/salmon/test/aux_info/observed_bias_3p.gz
-      md5sum: ef13c06a538e9c34ca9f84212c82f44e
-    - path: output/salmon/test/aux_info/meta_info.json
-      md5sum: f82491a19755bb1c32d49e9f0e12eebd
-    - path: output/salmon/test/aux_info/fld.gz
-      md5sum: 7f342560fea53327f0532623e53052f7
-    - path: output/salmon/test/aux_info/ambig_info.tsv
-      md5sum: 950001575c24fb6bc2c7a6848043b126
-    - path: output/salmon/test/aux_info/observed_bias.gz
-      md5sum: ef13c06a538e9c34ca9f84212c82f44e
-    - path: output/salmon/test/libParams/flenDist.txt
-      md5sum: f90c7256c9b18d4131f4d4ecb69d0f55
-    - path: output/salmon/test/cmd_info.json
-      md5sum: 007676e4d79de0809a03e0ea045ed4a1
-    - path: output/salmon/test/quant.sf
-      md5sum: addb78e233f248b8f62cae3e217bf689
-    - path: output/salmon/test/lib_format_counts.json
-      md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea
-    - path: output/salmon/test/logs/salmon_quant.log
-      md5sum: f7fe6e71b4ad4232e217db300c29202b
-    - path: output/salmon/test/cmd_info.json
-      md5sum: 007676e4d79de0809a03e0ea045ed4a1
-    - path: output/salmon/test/quant.sf
-      md5sum: addb78e233f248b8f62cae3e217bf689
-    - path: output/salmon/test/lib_format_counts.json
-      md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea
-    - path: output/salmon/test/logs/salmon_quant.log
-      md5sum: f7fe6e71b4ad4232e217db300c29202b
-    - path: output/salmon/test/aux_info/expected_bias.gz
-      md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
-    - path: output/salmon/test/aux_info/observed_bias_3p.gz
-      md5sum: ef13c06a538e9c34ca9f84212c82f44e
-    - path: output/salmon/test/aux_info/meta_info.json
-      md5sum: f82491a19755bb1c32d49e9f0e12eebd
-    - path: output/salmon/test/aux_info/fld.gz
-      md5sum: 7f342560fea53327f0532623e53052f7
-    - path: output/salmon/test/aux_info/ambig_info.tsv
-      md5sum: 950001575c24fb6bc2c7a6848043b126
-    - path: output/salmon/test/aux_info/observed_bias.gz
-      md5sum: ef13c06a538e9c34ca9f84212c82f44e
-    - path: output/salmon/test/cmd_info.json
-      md5sum: 007676e4d79de0809a03e0ea045ed4a1
-    - path: output/salmon/test/quant.sf
-      md5sum: addb78e233f248b8f62cae3e217bf689
-    - path: output/salmon/test/lib_format_counts.json
-      md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea
-    - path: output/salmon/test/logs/salmon_quant.log
-      md5sum: f7fe6e71b4ad4232e217db300c29202b
-    - path: output/salmon/test/cmd_info.json
-      md5sum: 007676e4d79de0809a03e0ea045ed4a1
-    - path: output/salmon/test/quant.sf
-      md5sum: addb78e233f248b8f62cae3e217bf689
-    - path: output/salmon/test/lib_format_counts.json
-      md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea
-    - path: output/salmon/test/logs/salmon_quant.log
-      md5sum: f7fe6e71b4ad4232e217db300c29202b
-    - path: output/salmon/test/aux_info/expected_bias.gz
-      md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
-    - path: output/salmon/test/aux_info/observed_bias_3p.gz
-      md5sum: ef13c06a538e9c34ca9f84212c82f44e
-    - path: output/salmon/test/aux_info/meta_info.json
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-    - path: output/salmon/test/aux_info/fld.gz
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-    - path: output/salmon/test/aux_info/ambig_info.tsv
-      md5sum: 950001575c24fb6bc2c7a6848043b126
-    - path: output/salmon/test/aux_info/observed_bias.gz
-      md5sum: ef13c06a538e9c34ca9f84212c82f44e
-    - path: output/salmon/test/libParams/flenDist.txt
-      md5sum: f90c7256c9b18d4131f4d4ecb69d0f55
-    - path: output/salmon/test/quant.genes.sf
-      md5sum: eb3e7b44801a0b3af07c25963927e20d
-    - path: output/salmon/salmon/ref_indexing.log
-      md5sum: 1f824b721361da702b5b1b1c3b02be49
-    - path: output/salmon/salmon/refseq.bin
-      md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
-    - path: output/salmon/salmon/versionInfo.json
-      md5sum: 204865f645102587c4953fccb256797c
-    - path: output/salmon/salmon/complete_ref_lens.bin
-      md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: output/salmon/salmon/mphf.bin
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-    - path: output/salmon/salmon/pre_indexing.log
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-    - path: output/salmon/salmon/ctable.bin
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-    - path: output/salmon/salmon/duplicate_clusters.tsv
-      md5sum: 51b5292e3a874119c0e1aa566e95d70c
-    - path: output/salmon/salmon/reflengths.bin
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-    - path: output/salmon/salmon/info.json
-      md5sum: 61ff4d3471134c280668355ddd39e99f
-    - path: output/salmon/salmon/refAccumLengths.bin
+    - path: ./output/salmon/salmon/refAccumLengths.bin
      md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
-    - path: output/salmon/salmon/ctg_offsets.bin
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-    - path: output/salmon/salmon/rank.bin
-      md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
-    - path: output/salmon/salmon/pos.bin
-      md5sum: 3b2d741929d6842e7818fcaa16f01bdc
-    - path: output/salmon/salmon/seq.bin
-      md5sum: 196b06f78c8aa6aa960eb5921288d0f4
-    - path: output/salmon/test/cmd_info.json
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-    - path: output/salmon/test/quant.sf
-      md5sum: addb78e233f248b8f62cae3e217bf689
-    - path: output/salmon/test/lib_format_counts.json
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-    - path: output/salmon/test/logs/salmon_quant.log
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-    - path: output/salmon/test/cmd_info.json
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-    - path: output/salmon/test/quant.sf
-      md5sum: addb78e233f248b8f62cae3e217bf689
-    - path: output/salmon/test/lib_format_counts.json
-      md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea
-    - path: output/salmon/test/logs/salmon_quant.log
-      md5sum: f7fe6e71b4ad4232e217db300c29202b
-    - path: output/salmon/test/aux_info/expected_bias.gz
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-    - path: output/salmon/test/aux_info/observed_bias_3p.gz
-      md5sum: ef13c06a538e9c34ca9f84212c82f44e
-    - path: output/salmon/test/aux_info/meta_info.json
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-    - path: output/salmon/test/aux_info/fld.gz
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-    - path: output/salmon/test/aux_info/ambig_info.tsv
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-    - path: output/salmon/test/aux_info/observed_bias.gz
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-    - path: output/salmon/test/cmd_info.json
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-      md5sum: addb78e233f248b8f62cae3e217bf689
-    - path: output/salmon/test/lib_format_counts.json
-      md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea
-    - path: output/salmon/test/logs/salmon_quant.log
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-    - path: output/salmon/test/cmd_info.json
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-    - path: output/salmon/test/quant.sf
-      md5sum: addb78e233f248b8f62cae3e217bf689
-    - path: output/salmon/test/lib_format_counts.json
-      md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea
-    - path: output/salmon/test/logs/salmon_quant.log
-      md5sum: f7fe6e71b4ad4232e217db300c29202b
-    - path: output/salmon/test/aux_info/expected_bias.gz
-      md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
-    - path: output/salmon/test/aux_info/observed_bias_3p.gz
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-    - path: output/salmon/test/aux_info/meta_info.json
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-    - path: output/salmon/test/aux_info/ambig_info.tsv
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-    - path: output/salmon/test/aux_info/observed_bias.gz
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-    - path: output/salmon/test/libParams/flenDist.txt
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-    - path: output/salmon/test/quant.sf
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-    - path: output/salmon/test/lib_format_counts.json
-      md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea
-    - path: output/salmon/test/logs/salmon_quant.log
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-    - path: output/salmon/test/cmd_info.json
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-    - path: output/salmon/test/quant.sf
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-    - path: output/salmon/test/logs/salmon_quant.log
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-    - path: output/salmon/test/aux_info/expected_bias.gz
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-    - path: output/salmon/test/aux_info/ambig_info.tsv
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-    - path: output/salmon/test/aux_info/observed_bias.gz
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-    - path: output/salmon/test/cmd_info.json
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-    - path: output/salmon/test/quant.sf
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-    - path: output/salmon/test/logs/salmon_quant.log
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-    - path: output/salmon/test/aux_info/expected_bias.gz
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-    - path: output/salmon/test/aux_info/observed_bias_3p.gz
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-    - path: output/salmon/test/aux_info/meta_info.json
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-    - path: output/salmon/test/aux_info/ambig_info.tsv
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-    - path: output/salmon/test/aux_info/observed_bias.gz
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-    - path: output/salmon/test/libParams/flenDist.txt
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-    - path: output/salmon/test/quant.genes.sf
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-    - path: output/salmon/salmon/versionInfo.json
-      md5sum: 204865f645102587c4953fccb256797c
-    - path: output/salmon/salmon/complete_ref_lens.bin
+    - path: ./output/salmon/salmon/complete_ref_lens.bin
      md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: output/salmon/salmon/mphf.bin
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-    - path: output/salmon/salmon/pre_indexing.log
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-    - path: output/salmon/salmon/ctable.bin
-      md5sum: 79c06180158c7ee44fab6672c2b27fbb
-    - path: output/salmon/salmon/duplicate_clusters.tsv
+    - path: ./output/salmon/test/aux_info/expected_bias.gz
+      md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
+    - path: ./output/salmon/salmon/duplicate_clusters.tsv
      md5sum: 51b5292e3a874119c0e1aa566e95d70c
-    - path: output/salmon/salmon/reflengths.bin
-      md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: output/salmon/salmon/info.json
+    - path: ./output/salmon/test/aux_info/observed_bias_3p.gz
+      md5sum: ef13c06a538e9c34ca9f84212c82f44e
+    - path: ./output/salmon/salmon/versionInfo.json
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+    - path: ./output/salmon/test/aux_info/observed_bias.gz
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      md5sum: 61ff4d3471134c280668355ddd39e99f
-    - path: output/salmon/salmon/refAccumLengths.bin
-      md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
-    - path: output/salmon/salmon/ctg_offsets.bin
+    - path: ./output/salmon/salmon/mphf.bin
+      md5sum: 53669a47610e33e031faafd32703b714
+    - path: ./output/salmon/test/aux_info/ambig_info.tsv
+      md5sum: 950001575c24fb6bc2c7a6848043b126
+    - path: ./output/salmon/test/lib_format_counts.json
+      md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea
+    - path: ./output/salmon/salmon/ctg_offsets.bin
      md5sum: 27a76542337df436436e66017f66dd25
-    - path: output/salmon/salmon/rank.bin
+    - path: ./output/salmon/salmon/reflengths.bin
+      md5sum: f57562f1fca3ae7b133f895ae13c3d08
+    - path: ./output/salmon/test/quant.sf
+      md5sum: addb78e233f248b8f62cae3e217bf689
+    - path: ./output/salmon/test/libParams/flenDist.txt
+      md5sum: f90c7256c9b18d4131f4d4ecb69d0f55
+    - path: ./output/salmon/salmon/refseq.bin
+      md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
+    - path: ./output/salmon/salmon/rank.bin
      md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
-    - path: output/salmon/salmon/pos.bin
-      md5sum: 3b2d741929d6842e7818fcaa16f01bdc
-    - path: output/salmon/salmon/seq.bin
-      md5sum: 196b06f78c8aa6aa960eb5921288d0f4

 - name: salmon quant single-end
  command: nextflow run ./tests/software/salmon -profile docker -entry test_salmon_quant_se -c tests/config/nextflow.config
@ -336,299 +78,41 @@
    - salmon_quant
    - salmon_quant_se
  files:
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    - path: ./output/salmon/salmon/duplicate_clusters.tsv
      md5sum: 51b5292e3a874119c0e1aa566e95d70c
+    - path: ./output/salmon/test/quant.genes.sf
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    - path: ./output/salmon/salmon/reflengths.bin
      md5sum: f57562f1fca3ae7b133f895ae13c3d08
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-    - path: ./output/salmon/salmon/ctable.bin
-      md5sum: fa76c33c22592a201cbcae299dbf2de6
-    - path: ./output/salmon/salmon/duplicate_clusters.tsv
-      md5sum: 51b5292e3a874119c0e1aa566e95d70c
-    - path: ./output/salmon/salmon/reflengths.bin
-      md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: ./output/salmon/salmon/info.json
-      md5sum: 61ff4d3471134c280668355ddd39e99f
-    - path: ./output/salmon/salmon/refAccumLengths.bin
-      md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
    - path: ./output/salmon/salmon/ctg_offsets.bin
      md5sum: 27a76542337df436436e66017f66dd25
-    - path: ./output/salmon/salmon/rank.bin
-      md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
-    - path: ./output/salmon/salmon/pos.bin
-      md5sum: f8e96e67430eac6945ecdecf73d0c025
-    - path: ./output/salmon/salmon/seq.bin
-      md5sum: a64df36de51fc94ab8f707be98c91062
+    - path: ./output/salmon/test/quant.sf
+      md5sum: b08095ac70f89efc3146cdf488d0eb73