- name: salmon index command: nextflow run ./tests/software/salmon -profile docker -entry test_salmon_index -c tests/config/nextflow.config tags: - salmon - salmon_index files: - path: output/salmon/salmon/ref_indexing.log md5sum: 712121a1bc50e7ef3e0c0f115886be13 - 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: 542ae3f1088357c2f867fe56cc01ca5c - path: output/salmon/salmon/ctable.bin md5sum: 320ed80e82259e47bd178275889067c5 - 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: 23ba28cc5a2511cb1cd7ef6ed555d3f8 - path: output/salmon/salmon/seq.bin md5sum: 8750937e595a8e56e7bc9a9a7d600c44 - name: salmon quant paired end command: nextflow run ./tests/software/salmon -profile docker -entry test_salmon_quant_pe -c tests/config/nextflow.confi tags: - salmon - salmon_quant - salmon_quant_pe files: - 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 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 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 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 - name: salmon quant single-end command: nextflow run ./tests/software/salmon -profile docker -entry test_salmon_quant_se -c tests/config/nextflow.config tags: - salmon - 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 - 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