From 431a2eb73b9e7d4c21cd83fa3c65f4713bc34037 Mon Sep 17 00:00:00 2001 From: kevinmenden Date: Tue, 26 Jan 2021 15:58:22 +0100 Subject: [PATCH] added quant test workflow --- .github/workflows/salmon_quant.yml | 40 ++ tests/software/salmon/test.yml | 632 +++-------------------------- 2 files changed, 98 insertions(+), 574 deletions(-) create mode 100644 .github/workflows/salmon_quant.yml diff --git a/.github/workflows/salmon_quant.yml b/.github/workflows/salmon_quant.yml new file mode 100644 index 00000000..16a6bf9c --- /dev/null +++ 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 diff --git a/tests/software/salmon/test.yml b/tests/software/salmon/test.yml index ec8ef998..f49ace38 100644 --- 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 - 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/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 - md5sum: 53669a47610e33e031faafd32703b714 - - path: output/salmon/salmon/pre_indexing.log - md5sum: 68f309b5557feb35829b9715b0afad39 - - path: output/salmon/salmon/ctable.bin - md5sum: 79c06180158c7ee44fab6672c2b27fbb - - 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 + - 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: 3b2d741929d6842e7818fcaa16f01bdc - - path: output/salmon/salmon/seq.bin - md5sum: 196b06f78c8aa6aa960eb5921288d0f4 - - 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 - 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/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 + - path: ./output/salmon/salmon/complete_ref_lens.bin md5sum: f57562f1fca3ae7b133f895ae13c3d08 - - path: output/salmon/salmon/mphf.bin - md5sum: 53669a47610e33e031faafd32703b714 - - path: output/salmon/salmon/pre_indexing.log - md5sum: 68f309b5557feb35829b9715b0afad39 - - 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 + md5sum: 204865f645102587c4953fccb256797c + - path: ./output/salmon/test/aux_info/observed_bias.gz + md5sum: ef13c06a538e9c34ca9f84212c82f44e + - path: ./output/salmon/test/quant.genes.sf + md5sum: eb3e7b44801a0b3af07c25963927e20d + - path: ./output/salmon/salmon/info.json 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: - - path: ./output/salmon/test/cmd_info.json - md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a - - path: ./output/salmon/test/quant.sf - md5sum: b08095ac70f89efc3146cdf488d0eb73 - - path: ./output/salmon/test/lib_format_counts.json - md5sum: aca0a40187eb407b1b8fc85c01284583 - - path: ./output/salmon/test/logs/salmon_quant.log - md5sum: 7a41329e3b6cd24d86b8fe13a420d9e8 - - path: ./output/salmon/test/cmd_info.json - md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a - - path: ./output/salmon/test/quant.sf - md5sum: b08095ac70f89efc3146cdf488d0eb73 - - path: ./output/salmon/test/lib_format_counts.json - md5sum: aca0a40187eb407b1b8fc85c01284583 - - path: ./output/salmon/test/logs/salmon_quant.log - md5sum: 7a41329e3b6cd24d86b8fe13a420d9e8 - - 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: 73264fdcfdf915a539c308bc68eaf243 - - path: ./output/salmon/test/aux_info/fld.gz - md5sum: b3f48b080ee24668b94a92a9793d766e - - path: ./output/salmon/test/aux_info/ambig_info.tsv - md5sum: c3306d26186ffe018ad4f19d52256180 - - path: ./output/salmon/test/aux_info/observed_bias.gz - md5sum: ef13c06a538e9c34ca9f84212c82f44e - - path: ./output/salmon/test/cmd_info.json - md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a - - path: ./output/salmon/test/quant.sf - md5sum: b08095ac70f89efc3146cdf488d0eb73 - - path: ./output/salmon/test/lib_format_counts.json - md5sum: aca0a40187eb407b1b8fc85c01284583 - - path: ./output/salmon/test/logs/salmon_quant.log - md5sum: 7a41329e3b6cd24d86b8fe13a420d9e8 - - path: ./output/salmon/test/cmd_info.json - md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a - - path: ./output/salmon/test/quant.sf - md5sum: b08095ac70f89efc3146cdf488d0eb73 - - path: ./output/salmon/test/lib_format_counts.json - md5sum: aca0a40187eb407b1b8fc85c01284583 - - path: ./output/salmon/test/logs/salmon_quant.log - md5sum: 7a41329e3b6cd24d86b8fe13a420d9e8 - - 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: 73264fdcfdf915a539c308bc68eaf243 - - path: ./output/salmon/test/aux_info/fld.gz - md5sum: b3f48b080ee24668b94a92a9793d766e - - path: ./output/salmon/test/aux_info/ambig_info.tsv - md5sum: c3306d26186ffe018ad4f19d52256180 - - path: ./output/salmon/test/aux_info/observed_bias.gz - md5sum: ef13c06a538e9c34ca9f84212c82f44e - - path: ./output/salmon/test/libParams/flenDist.txt - md5sum: 2de170bdc9f6fd237d286429b292bb28 - - path: ./output/salmon/test/cmd_info.json - md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a - - path: ./output/salmon/test/quant.sf - md5sum: b08095ac70f89efc3146cdf488d0eb73 - - path: ./output/salmon/test/lib_format_counts.json - md5sum: aca0a40187eb407b1b8fc85c01284583 - - path: ./output/salmon/test/logs/salmon_quant.log - md5sum: 7a41329e3b6cd24d86b8fe13a420d9e8 - - path: ./output/salmon/test/cmd_info.json - md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a - - path: ./output/salmon/test/quant.sf - md5sum: b08095ac70f89efc3146cdf488d0eb73 - - path: ./output/salmon/test/lib_format_counts.json - md5sum: aca0a40187eb407b1b8fc85c01284583 - - path: ./output/salmon/test/logs/salmon_quant.log - md5sum: 7a41329e3b6cd24d86b8fe13a420d9e8 - - 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: 73264fdcfdf915a539c308bc68eaf243 - - path: ./output/salmon/test/aux_info/fld.gz - md5sum: b3f48b080ee24668b94a92a9793d766e - - path: ./output/salmon/test/aux_info/ambig_info.tsv - md5sum: c3306d26186ffe018ad4f19d52256180 - - path: ./output/salmon/test/aux_info/observed_bias.gz - md5sum: ef13c06a538e9c34ca9f84212c82f44e - - path: ./output/salmon/test/cmd_info.json - md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a - - path: ./output/salmon/test/quant.sf - md5sum: b08095ac70f89efc3146cdf488d0eb73 - - path: ./output/salmon/test/lib_format_counts.json - md5sum: aca0a40187eb407b1b8fc85c01284583 - - path: ./output/salmon/test/logs/salmon_quant.log - md5sum: 7a41329e3b6cd24d86b8fe13a420d9e8 - - path: ./output/salmon/test/cmd_info.json - md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a - - path: ./output/salmon/test/quant.sf - md5sum: b08095ac70f89efc3146cdf488d0eb73 - - path: ./output/salmon/test/lib_format_counts.json - md5sum: aca0a40187eb407b1b8fc85c01284583 - - path: ./output/salmon/test/logs/salmon_quant.log - md5sum: 7a41329e3b6cd24d86b8fe13a420d9e8 - - 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: 73264fdcfdf915a539c308bc68eaf243 - - path: ./output/salmon/test/aux_info/fld.gz - md5sum: b3f48b080ee24668b94a92a9793d766e - - path: ./output/salmon/test/aux_info/ambig_info.tsv - md5sum: c3306d26186ffe018ad4f19d52256180 - - path: ./output/salmon/test/aux_info/observed_bias.gz - md5sum: ef13c06a538e9c34ca9f84212c82f44e - - path: ./output/salmon/test/libParams/flenDist.txt - md5sum: 2de170bdc9f6fd237d286429b292bb28 - - path: ./output/salmon/test/quant.genes.sf - md5sum: 5b39785b4d8da533c08ee4a6c8bc1211 - - path: ./output/salmon/salmon/ref_indexing.log - md5sum: 09c472422bd4e77a8a03b5296d947f9c - - 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 - md5sum: 53669a47610e33e031faafd32703b714 - - path: ./output/salmon/salmon/pre_indexing.log - md5sum: ea891a7a435745ebcc540740e8cb2f56 - - path: ./output/salmon/salmon/ctable.bin - md5sum: fa76c33c22592a201cbcae299dbf2de6 - path: ./output/salmon/salmon/duplicate_clusters.tsv md5sum: 51b5292e3a874119c0e1aa566e95d70c + - path: ./output/salmon/test/quant.genes.sf + md5sum: 5b39785b4d8da533c08ee4a6c8bc1211 + - path: ./output/salmon/test/aux_info/observed_bias_3p.gz + md5sum: ef13c06a538e9c34ca9f84212c82f44e + - path: ./output/salmon/salmon/refseq.bin + md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7 + - path: ./output/salmon/salmon/complete_ref_lens.bin + md5sum: f57562f1fca3ae7b133f895ae13c3d08 + - path: ./output/salmon/test/lib_format_counts.json + md5sum: aca0a40187eb407b1b8fc85c01284583 + - path: ./output/salmon/test/libParams/flenDist.txt + md5sum: 2de170bdc9f6fd237d286429b292bb28 + - path: ./output/salmon/test/aux_info/expected_bias.gz + md5sum: 24ee10af39b41ecf4f4e08faaaf537ee + - path: ./output/salmon/salmon/rank.bin + md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71 + - path: ./output/salmon/test/aux_info/observed_bias.gz + md5sum: ef13c06a538e9c34ca9f84212c82f44e + - path: ./output/salmon/test/cmd_info.json + md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a + - path: ./output/salmon/salmon/refAccumLengths.bin + md5sum: 8d1970505b2b08ca0eb5ff7722b48cde + - path: ./output/salmon/test/aux_info/ambig_info.tsv + md5sum: c3306d26186ffe018ad4f19d52256180 - 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/cmd_info.json - md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a - - path: ./output/salmon/test/quant.sf - md5sum: b08095ac70f89efc3146cdf488d0eb73 - - path: ./output/salmon/test/lib_format_counts.json - md5sum: aca0a40187eb407b1b8fc85c01284583 - - path: ./output/salmon/test/logs/salmon_quant.log - md5sum: 7a41329e3b6cd24d86b8fe13a420d9e8 - - path: ./output/salmon/test/cmd_info.json - md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a - - path: ./output/salmon/test/quant.sf - md5sum: b08095ac70f89efc3146cdf488d0eb73 - - path: ./output/salmon/test/lib_format_counts.json - md5sum: aca0a40187eb407b1b8fc85c01284583 - - path: ./output/salmon/test/logs/salmon_quant.log - md5sum: 7a41329e3b6cd24d86b8fe13a420d9e8 - - 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: 73264fdcfdf915a539c308bc68eaf243 - - path: ./output/salmon/test/aux_info/fld.gz - md5sum: b3f48b080ee24668b94a92a9793d766e - - path: ./output/salmon/test/aux_info/ambig_info.tsv - md5sum: c3306d26186ffe018ad4f19d52256180 - - path: ./output/salmon/test/aux_info/observed_bias.gz - md5sum: ef13c06a538e9c34ca9f84212c82f44e - - path: ./output/salmon/test/cmd_info.json - md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a - - path: ./output/salmon/test/quant.sf - md5sum: b08095ac70f89efc3146cdf488d0eb73 - - path: ./output/salmon/test/lib_format_counts.json - md5sum: aca0a40187eb407b1b8fc85c01284583 - - path: ./output/salmon/test/logs/salmon_quant.log - md5sum: 7a41329e3b6cd24d86b8fe13a420d9e8 - - path: ./output/salmon/test/cmd_info.json - md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a - - path: ./output/salmon/test/quant.sf - md5sum: b08095ac70f89efc3146cdf488d0eb73 - - path: ./output/salmon/test/lib_format_counts.json - md5sum: aca0a40187eb407b1b8fc85c01284583 - - path: ./output/salmon/test/logs/salmon_quant.log - md5sum: 7a41329e3b6cd24d86b8fe13a420d9e8 - - 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: 73264fdcfdf915a539c308bc68eaf243 - - path: ./output/salmon/test/aux_info/fld.gz - md5sum: b3f48b080ee24668b94a92a9793d766e - - path: ./output/salmon/test/aux_info/ambig_info.tsv - md5sum: c3306d26186ffe018ad4f19d52256180 - - path: ./output/salmon/test/aux_info/observed_bias.gz - md5sum: ef13c06a538e9c34ca9f84212c82f44e - - path: ./output/salmon/test/libParams/flenDist.txt - md5sum: 2de170bdc9f6fd237d286429b292bb28 - - path: ./output/salmon/test/cmd_info.json - md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a - - path: ./output/salmon/test/quant.sf - md5sum: b08095ac70f89efc3146cdf488d0eb73 - - path: ./output/salmon/test/lib_format_counts.json - md5sum: aca0a40187eb407b1b8fc85c01284583 - - path: ./output/salmon/test/logs/salmon_quant.log - md5sum: 7a41329e3b6cd24d86b8fe13a420d9e8 - - path: ./output/salmon/test/cmd_info.json - md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a - - path: ./output/salmon/test/quant.sf - md5sum: b08095ac70f89efc3146cdf488d0eb73 - - path: ./output/salmon/test/lib_format_counts.json - md5sum: aca0a40187eb407b1b8fc85c01284583 - - path: ./output/salmon/test/logs/salmon_quant.log - md5sum: 7a41329e3b6cd24d86b8fe13a420d9e8 - - 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: 73264fdcfdf915a539c308bc68eaf243 - - path: ./output/salmon/test/aux_info/fld.gz - md5sum: b3f48b080ee24668b94a92a9793d766e - - path: ./output/salmon/test/aux_info/ambig_info.tsv - md5sum: c3306d26186ffe018ad4f19d52256180 - - path: ./output/salmon/test/aux_info/observed_bias.gz - md5sum: ef13c06a538e9c34ca9f84212c82f44e - - path: ./output/salmon/test/cmd_info.json - md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a - - path: ./output/salmon/test/quant.sf - md5sum: b08095ac70f89efc3146cdf488d0eb73 - - path: ./output/salmon/test/lib_format_counts.json - md5sum: aca0a40187eb407b1b8fc85c01284583 - - path: ./output/salmon/test/logs/salmon_quant.log - md5sum: 7a41329e3b6cd24d86b8fe13a420d9e8 - - path: ./output/salmon/test/cmd_info.json - md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a - - path: ./output/salmon/test/quant.sf - md5sum: b08095ac70f89efc3146cdf488d0eb73 - - path: ./output/salmon/test/lib_format_counts.json - md5sum: aca0a40187eb407b1b8fc85c01284583 - - path: ./output/salmon/test/logs/salmon_quant.log - md5sum: 7a41329e3b6cd24d86b8fe13a420d9e8 - - 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: 73264fdcfdf915a539c308bc68eaf243 - - path: ./output/salmon/test/aux_info/fld.gz - md5sum: b3f48b080ee24668b94a92a9793d766e - - path: ./output/salmon/test/aux_info/ambig_info.tsv - md5sum: c3306d26186ffe018ad4f19d52256180 - - path: ./output/salmon/test/aux_info/observed_bias.gz - md5sum: ef13c06a538e9c34ca9f84212c82f44e - - path: ./output/salmon/test/libParams/flenDist.txt - md5sum: 2de170bdc9f6fd237d286429b292bb28 - - path: ./output/salmon/test/quant.genes.sf - md5sum: 5b39785b4d8da533c08ee4a6c8bc1211 - - path: ./output/salmon/salmon/ref_indexing.log - md5sum: 09c472422bd4e77a8a03b5296d947f9c - - 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 md5sum: 53669a47610e33e031faafd32703b714 - - path: ./output/salmon/salmon/pre_indexing.log - md5sum: ea891a7a435745ebcc540740e8cb2f56 - - 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