From dc0969a7548dab91c81aee03af8885d88dd99238 Mon Sep 17 00:00:00 2001 From: Till Englert Date: Mon, 5 Aug 2024 07:08:53 +0200 Subject: [PATCH] testing branch commits --- bin/download_proteins_entrez.py | 4 ++-- bin/generate_peptides.py | 2 +- bin/generate_protein_and_entity_ids.py | 2 +- tests/pipeline/test.nf.test.snap | 16 ++++++++-------- tests/pipeline/test_all.nf.test.snap | 18 +++++++++--------- tests/pipeline/test_assembly_only.nf.test.snap | 14 +++++++------- tests/pipeline/test_bins_only.nf.test.snap | 14 +++++++------- tests/pipeline/test_coassembly.nf.test.snap | 18 +++++++++--------- tests/pipeline/test_mhcflurry.nf.test.snap | 14 +++++++------- tests/pipeline/test_mhcnuggets_1.nf.test.snap | 14 +++++++------- tests/pipeline/test_mhcnuggets_2.nf.test.snap | 14 +++++++------- tests/pipeline/test_mouse.nf.test.snap | 18 +++++++++--------- .../test_mouse_all_pep_lengths.nf.test.snap | 14 +++++++------- tests/pipeline/test_taxa_only.nf.test.snap | 16 ++++++++-------- .../test_taxa_specific_assembly.nf.test.snap | 16 ++++++++-------- 15 files changed, 97 insertions(+), 97 deletions(-) diff --git a/bin/download_proteins_entrez.py b/bin/download_proteins_entrez.py index b19d9482..741355cf 100755 --- a/bin/download_proteins_entrez.py +++ b/bin/download_proteins_entrez.py @@ -307,7 +307,7 @@ def main(args=None): # some proteins, such as 487413233, occur within multiple sequences of the assembly! # -> assembly only listed once! - proteinIds = list(dict_proteinId_assemblyIds.keys()) + proteinIds = sorted(list(dict_proteinId_assemblyIds.keys())) print("# proteins (unique): ", len(proteinIds)) # -> # proteins with refseq source (<= # IPG proteins) @@ -394,7 +394,7 @@ def main(args=None): for proteinId in proteinIds: accVersion = dict_protein_uid_acc[proteinId] # write out protein_tmp_id, entity_name (taxon_id) - for assemblyId in dict_proteinId_assemblyIds[proteinId]: + for assemblyId in sorted(dict_proteinId_assemblyIds[proteinId]): taxId = dict_assemblyId_taxId[assemblyId] print(accVersion, taxId, sep="\t", file=args.entities_proteins, flush=True) diff --git a/bin/generate_peptides.py b/bin/generate_peptides.py index c398844e..097f7c70 100755 --- a/bin/generate_peptides.py +++ b/bin/generate_peptides.py @@ -159,7 +159,7 @@ def main(args=None): results["count"] = pd.to_numeric(results["count"], downcast="unsigned") # prepare df for joining results.set_index("peptide_sequence", inplace=True) - results.sort_index(inplace=True) + results.sort_index(inplace=True, kind="stable") unique_peptides = pd.DataFrame(index=results.index.drop_duplicates()) unique_peptides["peptide_id"] = range(id_counter, id_counter + len(unique_peptides)) diff --git a/bin/generate_protein_and_entity_ids.py b/bin/generate_protein_and_entity_ids.py index d3122f6b..793fe1c3 100755 --- a/bin/generate_protein_and_entity_ids.py +++ b/bin/generate_protein_and_entity_ids.py @@ -150,7 +150,7 @@ def main(args=None): # (i.e. microbiome_bare_id) and assign the corresponding microbiome_id to the entities for microbiome_id in microbiomes.groupby("microbiome_bare_id").get_group(microbiome_bare_id)[ "microbiome_id" - ]: + ].sort_values(): entities = pd.DataFrame() entities = proteins[["entity_name"]].drop_duplicates() entities["entity_id"] = range(next_entity_id, next_entity_id + len(entities)) diff --git a/tests/pipeline/test.nf.test.snap b/tests/pipeline/test.nf.test.snap index f91ab948..277ec42c 100644 --- a/tests/pipeline/test.nf.test.snap +++ b/tests/pipeline/test.nf.test.snap @@ -4,23 +4,23 @@ "alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa", "conditions_alleles.tsv:md5,e865774e32935a69306461ff47428aa8", "conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c", - "entities_proteins.tsv:md5,40559463e23017a527de4a0d44029762", - "entities.tsv:md5,57b7ddd2bbc0ae2f577e53ebfee0bed9", + "entities_proteins.tsv:md5,fd4cbfeca8e8f176c9e2f7aff39921bf", + "entities.tsv:md5,beb0a0fca43b5511cdabaf24bcc9113a", "microbiomes_entities.no_weights.tsv:md5,4d45837586c7c6dc4a19b41735215b01", "microbiomes_entities.nucl.tsv:md5,f5a3ff3cc1f8100f56238b9fab405e66", - "microbiomes_entities.tsv:md5,f8d9569231eeee796b23e250b37ea2ff", + "microbiomes_entities.tsv:md5,ea5c9629387ee19ccc485af0157a922c", "microbiomes.tsv:md5,20f141ba0c97325e9d99a9c0765f9a37", - "proteins_peptides.tsv:md5,40b02b3372c1cbfe7197f5440e724a24", - "peptides.tsv.gz:md5,b776a0ad7d110f8984dc43f74f2f5f2a", - "proteins.tsv.gz:md5,2a3e88df7aaa7c92c043671d4c823b75", - "predictions.tsv.gz:md5,3c86baab1aa53a295c9fe14f65aa1259", + "proteins_peptides.tsv:md5,e4d6b0199769075ff20c8eeca1485852", + "peptides.tsv.gz:md5,66f6ceef1d5212d061b46c90703282d9", + "proteins.tsv.gz:md5,3b397fc51074066efe2d31a5aff2abe3", + "predictions.tsv.gz:md5,a50679d98e43e09858bf5f29ed222cd2", "stats.txt:md5,83204291158696ce5d19c4e976f38efe" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-18T11:22:51.147921797" + "timestamp": "2024-08-02T07:24:38.491278622" }, "logs": { "content": [ diff --git a/tests/pipeline/test_all.nf.test.snap b/tests/pipeline/test_all.nf.test.snap index 11141483..53b0815f 100644 --- a/tests/pipeline/test_all.nf.test.snap +++ b/tests/pipeline/test_all.nf.test.snap @@ -14,23 +14,23 @@ "alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa", "conditions_alleles.tsv:md5,0e992c19471bb56c9b6e6a6f71302742", "conditions.tsv:md5,87707cd0dee14b0ca4face090ba9dce9", - "entities_proteins.tsv:md5,6eb14bc6f5a22a56244897e3c37f7698", - "entities.tsv:md5,243f199fd2cb7d9ff8e0c416865f8334", - "microbiomes_entities.no_weights.tsv:md5,b62d2213adce7c6111056d8181fe6b2c", + "entities_proteins.tsv:md5,57a704e833a65a1809c369452864e241", + "entities.tsv:md5,b7d3d019c258859c93bbc15095d304f1", + "microbiomes_entities.no_weights.tsv:md5,977da228f562b386b0f84fc718cc22e9", "microbiomes_entities.nucl.tsv:md5,aa0d4cc3546508c8e5b81bc9b4b16e39", - "microbiomes_entities.tsv:md5,64b5e7a2c23009f9ab54b5667cd45efb", + "microbiomes_entities.tsv:md5,03309271d7a983c7b4a5c73418676bbc", "microbiomes.tsv:md5,70871c8b3023f5a8412c05f4a69dda2f", - "proteins_peptides.tsv:md5,37a4c26c385c2189457aa37430c15eb4", - "peptides.tsv.gz:md5,2956eeef0ce98f2af1e94ec3f48caccf", - "proteins.tsv.gz:md5,5628f70522e8696a90d49ccf989e0d1b", - "predictions.tsv.gz:md5,024939bcd5a845c02d28b27668e69c91", + "proteins_peptides.tsv:md5,aff145bbff9f962891db2c2a540242c4", + "peptides.tsv.gz:md5,36aba6d50b1aad95859a547b06d04fc5", + "proteins.tsv.gz:md5,027823577635c591b58326410b039b32", + "predictions.tsv.gz:md5,d3b36995f3b4027d1a14e726a0acc6c2", "stats.txt:md5,896155e0f043f30bd71c38c8ee7b466c" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-18T14:41:01.231189333" + "timestamp": "2024-08-02T07:59:44.990798256" }, "logs": { "content": [ diff --git a/tests/pipeline/test_assembly_only.nf.test.snap b/tests/pipeline/test_assembly_only.nf.test.snap index 06b985db..010f0d24 100644 --- a/tests/pipeline/test_assembly_only.nf.test.snap +++ b/tests/pipeline/test_assembly_only.nf.test.snap @@ -4,23 +4,23 @@ "alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa", "conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f", "conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c", - "entities_proteins.tsv:md5,20fa4e2263edf5875a55f668bfd54255", - "entities.tsv:md5,03eb30795257d5e6a0a52bdfc09481fd", + "entities_proteins.tsv:md5,2ba821a04755841dc6f116965f853f40", + "entities.tsv:md5,61f364c97c883f45663ae27d115b229f", "microbiomes_entities.no_weights.tsv:md5,bd449dafeb86c374552f2e22a9780b19", "microbiomes_entities.nucl.tsv:md5,3888070b634251c0ae3e9fd4857140d7", - "microbiomes_entities.tsv:md5,f93b40a413fde8dd0a10712270c1a5f0", + "microbiomes_entities.tsv:md5,6cef150e7f5fc2f3320d9a93da00f5de", "microbiomes.tsv:md5,3d597aec25752f7ca83436b31bfaa128", - "proteins_peptides.tsv:md5,d3643f39837bc11a4984fa5260c2820f", - "peptides.tsv.gz:md5,afb2ba3ea67d4affb72d6e7f6451d45c", + "proteins_peptides.tsv:md5,c2a16b2d30c9cf5ea52207dd799b4603", + "peptides.tsv.gz:md5,dd0f94bea5079df8ef06895de255038b", "proteins.tsv.gz:md5,104b786dfa89e183a46e29f1f37f17de", - "predictions.tsv.gz:md5,bfff151d9a6dc15006a91c8fd7feddcc", + "predictions.tsv.gz:md5,98eeb5672f338ad5e8de7e2047261037", "stats.txt:md5,d138e30d814db5203a789b7eddd04732" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-18T08:16:13.284036932" + "timestamp": "2024-08-01T12:28:55.298980309" }, "logs": { "content": [ diff --git a/tests/pipeline/test_bins_only.nf.test.snap b/tests/pipeline/test_bins_only.nf.test.snap index 825ff822..a58860c8 100644 --- a/tests/pipeline/test_bins_only.nf.test.snap +++ b/tests/pipeline/test_bins_only.nf.test.snap @@ -4,23 +4,23 @@ "alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa", "conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f", "conditions.tsv:md5,5b04349198a406fc16760c7e8808bb23", - "entities_proteins.tsv:md5,58c51a20d57c93252d1bdf1469916a6d", - "entities.tsv:md5,4a739da6f90ba23b83f37e655147569e", + "entities_proteins.tsv:md5,20e495ff06ccacb0f81dbd65e556fc83", + "entities.tsv:md5,7a472316b8e96e9b12d7ca3ff6a88d39", "microbiomes_entities.no_weights.tsv:md5,bf3ff9d0390b49c6ecafd89c93909b67", "microbiomes_entities.nucl.tsv:md5,84b6b907695caaddc959682504749832", "microbiomes_entities.tsv:md5,2f40573eb52f3d823aad2f09a639eee2", "microbiomes.tsv:md5,3f58c3029d21a59316861c28af4361d1", - "proteins_peptides.tsv:md5,1efa2eb7dcf90e4b6496d83543f86ecc", - "peptides.tsv.gz:md5,eb5ce3f59f7536ad1ecc96b136d0a10f", - "proteins.tsv.gz:md5,3771dbafc5d6dffa6381ec8dc5b2f69e", - "predictions.tsv.gz:md5,d15c308bf9783a3008a2cc4125665dd3", + "proteins_peptides.tsv:md5,50df6a9278679870190795d7b7968113", + "peptides.tsv.gz:md5,34497a1a57af3c3e48fceb762cf94f75", + "proteins.tsv.gz:md5,1ae4d6be0e8bc4beb3d225aed3379d1c", + "predictions.tsv.gz:md5,1dd8ab58446c326432beadb44a0b327a", "stats.txt:md5,62d598a845aff61f2be843daa250f485" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-18T11:59:48.935446889" + "timestamp": "2024-08-01T13:39:59.996820893" }, "logs": { "content": [ diff --git a/tests/pipeline/test_coassembly.nf.test.snap b/tests/pipeline/test_coassembly.nf.test.snap index ac9d7708..78b2790d 100644 --- a/tests/pipeline/test_coassembly.nf.test.snap +++ b/tests/pipeline/test_coassembly.nf.test.snap @@ -4,23 +4,23 @@ "alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa", "conditions_alleles.tsv:md5,ad6438cc0e62033f39629d7d002169b5", "conditions.tsv:md5,092aba068d94feb11b61a22d694359d7", - "entities_proteins.tsv:md5,40559463e23017a527de4a0d44029762", - "entities.tsv:md5,57b7ddd2bbc0ae2f577e53ebfee0bed9", - "microbiomes_entities.no_weights.tsv:md5,4f01d93b99cae67bc21a646ea4ee0a06", + "entities_proteins.tsv:md5,522e78ac27cbbc30e0a40fa316ee93c5", + "entities.tsv:md5,a3a3d919964f1dec57abbae3c74fb8f7", + "microbiomes_entities.no_weights.tsv:md5,45512c04e01b2f652b60c5438377411e", "microbiomes_entities.nucl.tsv:md5,2f884256b54995a265af83b2eb68e773", - "microbiomes_entities.tsv:md5,6e0af270f7dc6a245eb7f75f6cd475f5", + "microbiomes_entities.tsv:md5,134661aa3d07b62ccd0cd242c4e8fe6b", "microbiomes.tsv:md5,b89503022fcbd9b7d7f9eefe7cbccf0f", - "proteins_peptides.tsv:md5,40b02b3372c1cbfe7197f5440e724a24", - "peptides.tsv.gz:md5,b776a0ad7d110f8984dc43f74f2f5f2a", - "proteins.tsv.gz:md5,2a3e88df7aaa7c92c043671d4c823b75", - "predictions.tsv.gz:md5,227c6c6dd1b92e40757e1f12bd60512b", + "proteins_peptides.tsv:md5,ce3ba728c26a7a6866ecbfc11946c1cc", + "peptides.tsv.gz:md5,66f6ceef1d5212d061b46c90703282d9", + "proteins.tsv.gz:md5,e8a2211019ca7b516ccfa5313cb3d2de", + "predictions.tsv.gz:md5,bf3a26621094771540cd9b4642eb2f81", "stats.txt:md5,f2957aced6994532212f0d25b3efba98" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-18T14:04:13.49212786" + "timestamp": "2024-08-02T10:23:41.546325795" }, "logs": { "content": [ diff --git a/tests/pipeline/test_mhcflurry.nf.test.snap b/tests/pipeline/test_mhcflurry.nf.test.snap index 67120f10..6d914bea 100644 --- a/tests/pipeline/test_mhcflurry.nf.test.snap +++ b/tests/pipeline/test_mhcflurry.nf.test.snap @@ -4,23 +4,23 @@ "alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa", "conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f", "conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c", - "entities_proteins.tsv:md5,20fa4e2263edf5875a55f668bfd54255", - "entities.tsv:md5,03eb30795257d5e6a0a52bdfc09481fd", + "entities_proteins.tsv:md5,2ba821a04755841dc6f116965f853f40", + "entities.tsv:md5,61f364c97c883f45663ae27d115b229f", "microbiomes_entities.no_weights.tsv:md5,bd449dafeb86c374552f2e22a9780b19", "microbiomes_entities.nucl.tsv:md5,3888070b634251c0ae3e9fd4857140d7", - "microbiomes_entities.tsv:md5,f93b40a413fde8dd0a10712270c1a5f0", + "microbiomes_entities.tsv:md5,6cef150e7f5fc2f3320d9a93da00f5de", "microbiomes.tsv:md5,3d597aec25752f7ca83436b31bfaa128", - "proteins_peptides.tsv:md5,d3643f39837bc11a4984fa5260c2820f", - "peptides.tsv.gz:md5,afb2ba3ea67d4affb72d6e7f6451d45c", + "proteins_peptides.tsv:md5,c2a16b2d30c9cf5ea52207dd799b4603", + "peptides.tsv.gz:md5,dd0f94bea5079df8ef06895de255038b", "proteins.tsv.gz:md5,104b786dfa89e183a46e29f1f37f17de", - "predictions.tsv.gz:md5,14e08243d25907c53182bfeff23361f1", + "predictions.tsv.gz:md5,ac12cfb575078de97c490487d86813ef", "stats.txt:md5,d138e30d814db5203a789b7eddd04732" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-18T08:42:10.642128393" + "timestamp": "2024-08-01T13:55:42.000764934" }, "logs": { "content": [ diff --git a/tests/pipeline/test_mhcnuggets_1.nf.test.snap b/tests/pipeline/test_mhcnuggets_1.nf.test.snap index 8fff9d5f..37453864 100644 --- a/tests/pipeline/test_mhcnuggets_1.nf.test.snap +++ b/tests/pipeline/test_mhcnuggets_1.nf.test.snap @@ -4,23 +4,23 @@ "alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa", "conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f", "conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c", - "entities_proteins.tsv:md5,20fa4e2263edf5875a55f668bfd54255", - "entities.tsv:md5,03eb30795257d5e6a0a52bdfc09481fd", + "entities_proteins.tsv:md5,2ba821a04755841dc6f116965f853f40", + "entities.tsv:md5,61f364c97c883f45663ae27d115b229f", "microbiomes_entities.no_weights.tsv:md5,bd449dafeb86c374552f2e22a9780b19", "microbiomes_entities.nucl.tsv:md5,3888070b634251c0ae3e9fd4857140d7", - "microbiomes_entities.tsv:md5,f93b40a413fde8dd0a10712270c1a5f0", + "microbiomes_entities.tsv:md5,6cef150e7f5fc2f3320d9a93da00f5de", "microbiomes.tsv:md5,3d597aec25752f7ca83436b31bfaa128", - "proteins_peptides.tsv:md5,d3643f39837bc11a4984fa5260c2820f", - "peptides.tsv.gz:md5,afb2ba3ea67d4affb72d6e7f6451d45c", + "proteins_peptides.tsv:md5,c2a16b2d30c9cf5ea52207dd799b4603", + "peptides.tsv.gz:md5,dd0f94bea5079df8ef06895de255038b", "proteins.tsv.gz:md5,104b786dfa89e183a46e29f1f37f17de", - "predictions.tsv.gz:md5,29f3565a2c200753d0d890009ea68c8e", + "predictions.tsv.gz:md5,956fd0987dd9132a01559cc9c89ff4ca", "stats.txt:md5,d138e30d814db5203a789b7eddd04732" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-18T08:43:42.547130099" + "timestamp": "2024-08-01T13:57:14.849262708" }, "logs": { "content": [ diff --git a/tests/pipeline/test_mhcnuggets_2.nf.test.snap b/tests/pipeline/test_mhcnuggets_2.nf.test.snap index 52d30f44..5639403b 100644 --- a/tests/pipeline/test_mhcnuggets_2.nf.test.snap +++ b/tests/pipeline/test_mhcnuggets_2.nf.test.snap @@ -4,23 +4,23 @@ "alleles.tsv:md5,ab0e4dbbb55b8154d37256018c19d67c", "conditions_alleles.tsv:md5,769c299e94c7df654a5a14da2771c95d", "conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c", - "entities_proteins.tsv:md5,20fa4e2263edf5875a55f668bfd54255", - "entities.tsv:md5,03eb30795257d5e6a0a52bdfc09481fd", + "entities_proteins.tsv:md5,2ba821a04755841dc6f116965f853f40", + "entities.tsv:md5,61f364c97c883f45663ae27d115b229f", "microbiomes_entities.no_weights.tsv:md5,bd449dafeb86c374552f2e22a9780b19", "microbiomes_entities.nucl.tsv:md5,3888070b634251c0ae3e9fd4857140d7", - "microbiomes_entities.tsv:md5,f93b40a413fde8dd0a10712270c1a5f0", + "microbiomes_entities.tsv:md5,6cef150e7f5fc2f3320d9a93da00f5de", "microbiomes.tsv:md5,3d597aec25752f7ca83436b31bfaa128", - "proteins_peptides.tsv:md5,d3643f39837bc11a4984fa5260c2820f", - "peptides.tsv.gz:md5,afb2ba3ea67d4affb72d6e7f6451d45c", + "proteins_peptides.tsv:md5,c2a16b2d30c9cf5ea52207dd799b4603", + "peptides.tsv.gz:md5,dd0f94bea5079df8ef06895de255038b", "proteins.tsv.gz:md5,104b786dfa89e183a46e29f1f37f17de", - "predictions.tsv.gz:md5,409c7af0f77acb5f57d26ec985d6753f", + "predictions.tsv.gz:md5,d88dfc746b74451b1cd00eb06ea834bb", "stats.txt:md5,d138e30d814db5203a789b7eddd04732" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-18T08:45:26.411151617" + "timestamp": "2024-08-01T13:58:50.730628977" }, "logs": { "content": [ diff --git a/tests/pipeline/test_mouse.nf.test.snap b/tests/pipeline/test_mouse.nf.test.snap index 3fcb155a..50b5264f 100644 --- a/tests/pipeline/test_mouse.nf.test.snap +++ b/tests/pipeline/test_mouse.nf.test.snap @@ -14,23 +14,23 @@ "alleles.tsv:md5,314847ac5a69fe93ce75c6db0c2496d8", "conditions_alleles.tsv:md5,e865774e32935a69306461ff47428aa8", "conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c", - "entities_proteins.tsv:md5,490726a86418ba9eb6d248d439c690df", - "entities.tsv:md5,8c4aea9d11b4e00b539098743a70686c", - "microbiomes_entities.no_weights.tsv:md5,4d45837586c7c6dc4a19b41735215b01", + "entities_proteins.tsv:md5,72713ba58d4c87e54b015afdb2e4c856", + "entities.tsv:md5,02424da04f3ca8ddd587f63d2202acf6", + "microbiomes_entities.no_weights.tsv:md5,55eae24113e41d074d4b2e91912d7be6", "microbiomes_entities.nucl.tsv:md5,f5a3ff3cc1f8100f56238b9fab405e66", - "microbiomes_entities.tsv:md5,f8d9569231eeee796b23e250b37ea2ff", + "microbiomes_entities.tsv:md5,c8e318f1ff72f1469a1359085ff7bbef", "microbiomes.tsv:md5,2130005595bdc7ffc770d8304fd9a936", - "proteins_peptides.tsv:md5,033de254de014518dc3954700bf45979", - "peptides.tsv.gz:md5,1669dfbfd06c54ea2595934268698d0e", - "proteins.tsv.gz:md5,10935afd27899a048eed2c374ef52ccd", - "predictions.tsv.gz:md5,02f424dcbef3bbda87dfe15f82cacf01", + "proteins_peptides.tsv:md5,4179b229762eac3862de4d407db105a8", + "peptides.tsv.gz:md5,260d711f2ea11fb3327f3eff6b6a7516", + "proteins.tsv.gz:md5,3314974c69464fd88fb4a7de16811436", + "predictions.tsv.gz:md5,b9edf43eb41ac84bf129001fdc70b852", "stats.txt:md5,6e5ecca241fb1cd3fea7ea66c4b81e2a" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-18T14:43:57.443165259" + "timestamp": "2024-08-02T11:37:25.76942764" }, "logs": { "content": [ diff --git a/tests/pipeline/test_mouse_all_pep_lengths.nf.test.snap b/tests/pipeline/test_mouse_all_pep_lengths.nf.test.snap index aebe3932..e82a0ab2 100644 --- a/tests/pipeline/test_mouse_all_pep_lengths.nf.test.snap +++ b/tests/pipeline/test_mouse_all_pep_lengths.nf.test.snap @@ -4,23 +4,23 @@ "alleles.tsv:md5,314847ac5a69fe93ce75c6db0c2496d8", "conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f", "conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c", - "entities_proteins.tsv:md5,20fa4e2263edf5875a55f668bfd54255", - "entities.tsv:md5,03eb30795257d5e6a0a52bdfc09481fd", + "entities_proteins.tsv:md5,2ba821a04755841dc6f116965f853f40", + "entities.tsv:md5,61f364c97c883f45663ae27d115b229f", "microbiomes_entities.no_weights.tsv:md5,bd449dafeb86c374552f2e22a9780b19", "microbiomes_entities.nucl.tsv:md5,3888070b634251c0ae3e9fd4857140d7", - "microbiomes_entities.tsv:md5,f93b40a413fde8dd0a10712270c1a5f0", + "microbiomes_entities.tsv:md5,6cef150e7f5fc2f3320d9a93da00f5de", "microbiomes.tsv:md5,3d597aec25752f7ca83436b31bfaa128", - "proteins_peptides.tsv:md5,a36f320c292c459266d487c09527369c", - "peptides.tsv.gz:md5,4c05dc85b7de0a165f0c6745aaaeb60b", + "proteins_peptides.tsv:md5,101da74f4d060728f471d130490c1e83", + "peptides.tsv.gz:md5,d3120ff2e6c4599883e958605ea7089a", "proteins.tsv.gz:md5,104b786dfa89e183a46e29f1f37f17de", - "predictions.tsv.gz:md5,e9030a6180bc8492ba989e361b6f48d9", + "predictions.tsv.gz:md5,84ef89b536bae027616716ff387ac395", "stats.txt:md5,2675aa8f40b92d9df9c1537d77e8ade1" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-18T07:19:25.909691429" + "timestamp": "2024-08-01T13:02:54.575826204" }, "logs": { "content": [ diff --git a/tests/pipeline/test_taxa_only.nf.test.snap b/tests/pipeline/test_taxa_only.nf.test.snap index 87825762..88e60291 100644 --- a/tests/pipeline/test_taxa_only.nf.test.snap +++ b/tests/pipeline/test_taxa_only.nf.test.snap @@ -14,23 +14,23 @@ "alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa", "conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f", "conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c", - "entities_proteins.tsv:md5,ca52fb4e86fc2bf79ac6196f16b20b39", + "entities_proteins.tsv:md5,25ca7e495a9b98a194ce71384820803f", "entities.tsv:md5,c766a12bbb1d4ef4707be7077f774191", - "microbiomes_entities.no_weights.tsv:md5,bf602ff424a227edcf8b0b51e33c3af5", + "microbiomes_entities.no_weights.tsv:md5,2d18c7210b304eb7593106073bc3686f", "microbiomes_entities.nucl.tsv:md5,84b6b907695caaddc959682504749832", "microbiomes_entities.tsv:md5,9fc7c15404073c65179dd908dc9fde78", "microbiomes.tsv:md5,05bafa72c953e6cb0bd72c296d6fe707", - "proteins_peptides.tsv:md5,4b388b4c053192bcc6b95e54cf1d8bd0", - "peptides.tsv.gz:md5,70d25f2b10438f46431995a18f23bdf2", - "proteins.tsv.gz:md5,6f8d47a842ce55855f0075fd48455397", - "predictions.tsv.gz:md5,a1747e6748fed828131ad44ce88bb424", - "stats.txt:md5,0c00426cf413b8bd729a9ce723211e39" + "proteins_peptides.tsv:md5,3cc6b7bdc6b91016cce5a94ff4a0fa6e", + "peptides.tsv.gz:md5,0e3c1e87feb2aac34de1ba3b246f27ca", + "proteins.tsv.gz:md5,e51aef45c63fd5047e8d21eab26038a5", + "predictions.tsv.gz:md5,6a931de30c25a2d984193d2586a7eb4b", + "stats.txt:md5,c10c27a1ba080ff59dcb5b62467129b2" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-18T14:49:36.279842816" + "timestamp": "2024-08-02T06:34:04.10122" }, "logs": { "content": [ diff --git a/tests/pipeline/test_taxa_specific_assembly.nf.test.snap b/tests/pipeline/test_taxa_specific_assembly.nf.test.snap index 19c05ab7..fe8ec9f7 100644 --- a/tests/pipeline/test_taxa_specific_assembly.nf.test.snap +++ b/tests/pipeline/test_taxa_specific_assembly.nf.test.snap @@ -14,23 +14,23 @@ "alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa", "conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f", "conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c", - "entities_proteins.tsv:md5,ca52fb4e86fc2bf79ac6196f16b20b39", + "entities_proteins.tsv:md5,25ca7e495a9b98a194ce71384820803f", "entities.tsv:md5,c766a12bbb1d4ef4707be7077f774191", - "microbiomes_entities.no_weights.tsv:md5,bf602ff424a227edcf8b0b51e33c3af5", + "microbiomes_entities.no_weights.tsv:md5,2d18c7210b304eb7593106073bc3686f", "microbiomes_entities.nucl.tsv:md5,84b6b907695caaddc959682504749832", "microbiomes_entities.tsv:md5,9fc7c15404073c65179dd908dc9fde78", "microbiomes.tsv:md5,02bf660f1c06ace8993249ef6b527385", - "proteins_peptides.tsv:md5,4b388b4c053192bcc6b95e54cf1d8bd0", - "peptides.tsv.gz:md5,70d25f2b10438f46431995a18f23bdf2", - "proteins.tsv.gz:md5,6f8d47a842ce55855f0075fd48455397", - "predictions.tsv.gz:md5,a1747e6748fed828131ad44ce88bb424", - "stats.txt:md5,0c00426cf413b8bd729a9ce723211e39" + "proteins_peptides.tsv:md5,3cc6b7bdc6b91016cce5a94ff4a0fa6e", + "peptides.tsv.gz:md5,0e3c1e87feb2aac34de1ba3b246f27ca", + "proteins.tsv.gz:md5,e51aef45c63fd5047e8d21eab26038a5", + "predictions.tsv.gz:md5,6a931de30c25a2d984193d2586a7eb4b", + "stats.txt:md5,c10c27a1ba080ff59dcb5b62467129b2" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.3" }, - 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