diff --git a/CHANGELOG.md b/CHANGELOG.md index 68623b759d1166b3addaf58d1624142230e0ee40..4a27c94cc997964d4cd17377c39d032a75b60825 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ * Use CI staging RIDs for CI unit tests: getBag, uploadInputBag, uploadExecutionRun, uploadQC, uploadProcessedFiles, uploadOutputBag (#133) * Add `-u "F"` to CI unit test uploadOutputBag `upload_output_bag.py` * Remove "fail" integration CI tests (#133 addendum) +* Add licence header to nf file, R and python scriptsand pytest scripts +* Stop using RCB and RMB (default) with deriva.core insert calls to match server update (#134) # v2.0.0 **User Facing** diff --git a/rna-seq.nf b/rna-seq.nf index 6073019182b2cb7f6ad5c6dd82fca011c58a0d95..604fdaf1358ece0c51ab6f3f7313a180ead74638 100644 --- a/rna-seq.nf +++ b/rna-seq.nf @@ -1,4 +1,10 @@ #!/usr/bin/env nextflow +//rna-seq.nf +//* +//* -------------------------------------------------------------------------- +//* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +//* -------------------------------------------------------------------------- +//* // ######## #### ###### ######## // ## ## ## ## ## ## diff --git a/workflow/scripts/calculateTPM.R b/workflow/scripts/calculateTPM.R index a26bf943dce7d082ed03b77939390abb022bba82..0127baa1f0a9e81f355ee8112020411d014ecde5 100644 --- a/workflow/scripts/calculateTPM.R +++ b/workflow/scripts/calculateTPM.R @@ -1,3 +1,11 @@ +#!/usr/bin/env R +#calculateTPM.R +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* + gc() library(optparse) diff --git a/workflow/scripts/convertGeneSymbols.R b/workflow/scripts/convertGeneSymbols.R index 6cc5c0a1089881ae1dfd32e248a1ffbcbcd7b24a..17551d35ae74cd32d02ac33f8a491fdf1270af22 100644 --- a/workflow/scripts/convertGeneSymbols.R +++ b/workflow/scripts/convertGeneSymbols.R @@ -1,3 +1,11 @@ +#!/usr/bin/env R +#convertGeneSymbols.R +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* + gc() library(optparse) diff --git a/workflow/scripts/delete_entry.py b/workflow/scripts/delete_entry.py index 1b26509a8c1541f65a39e660ec7e6ec158194ef1..77207e810e518ceca3888be8f14793f9891317db 100644 --- a/workflow/scripts/delete_entry.py +++ b/workflow/scripts/delete_entry.py @@ -1,3 +1,11 @@ +#!/usr/bin/env python3 +#delete_entry.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* + import argparse from deriva.core import ErmrestCatalog, get_credential, BaseCLI import sys @@ -34,4 +42,4 @@ if __name__ == '__main__': cli.remove_options(["--config-file"]) host = args.host credentials = {"cookie": args.cookie} - main(host, 2, credentials) \ No newline at end of file + main(host, 2, credentials) diff --git a/workflow/scripts/extract_ref_data.py b/workflow/scripts/extract_ref_data.py index bf06c95696354e6fe5d445718fbfb0769df4182d..87fc1e06ba0e50cac61ade8232d3330998ac9d42 100644 --- a/workflow/scripts/extract_ref_data.py +++ b/workflow/scripts/extract_ref_data.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#extract_ref_data.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import argparse import pandas as pd diff --git a/workflow/scripts/generate_references.py b/workflow/scripts/generate_references.py index 8e809f1e4471d3393ec4960778d2a210d54c11d1..d72b3522aa1963475b103d32a4087052402edca8 100644 --- a/workflow/scripts/generate_references.py +++ b/workflow/scripts/generate_references.py @@ -2,7 +2,7 @@ #generate_references.py #* #* -------------------------------------------------------------------------- -#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE) +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) #* -------------------------------------------------------------------------- #* diff --git a/workflow/scripts/generate_versions.py b/workflow/scripts/generate_versions.py index 2ff498659cc9acbf989ec45e61e8b755b9cc3a66..1ee16837731d88654be0f099a6a4aca9e3264c09 100644 --- a/workflow/scripts/generate_versions.py +++ b/workflow/scripts/generate_versions.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# -*- coding: utf-8 -*- - -# -# * -------------------------------------------------------------------------- -# * Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/master/LICENSE) -# * -------------------------------------------------------------------------- -# +#generate_versions.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* '''Make YAML of software versions.''' diff --git a/workflow/scripts/parse_meta.py b/workflow/scripts/parse_meta.py index 52f0f18200525f776fe73fcf2f4cd5be8db35045..64f9e559d6768127889055d59b23cc303fcb4e92 100644 --- a/workflow/scripts/parse_meta.py +++ b/workflow/scripts/parse_meta.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#parse_meta.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import argparse import pandas as pd diff --git a/workflow/scripts/tin_hist.py b/workflow/scripts/tin_hist.py index ee36bb6447dfe0adcdaab60e1224cca5b5a6e246..599f285120911770332034e5ace1dd211c51ecd4 100644 --- a/workflow/scripts/tin_hist.py +++ b/workflow/scripts/tin_hist.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#tin_hist.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import argparse import pandas as pd diff --git a/workflow/scripts/upload_execution_run.py b/workflow/scripts/upload_execution_run.py index 405c81aa9c2aa31c500157bee3db39413789a7fa..ec5270dc0ef47d73d044953c500769e9d5f401f2 100644 --- a/workflow/scripts/upload_execution_run.py +++ b/workflow/scripts/upload_execution_run.py @@ -1,3 +1,11 @@ +#!/usr/bin/env python3 +#upload_execution_run.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* + import argparse from deriva.core import ErmrestCatalog, get_credential, BaseCLI import sys @@ -33,7 +41,7 @@ def main(hostname, catalog_number, credential): "Execution_Status": args.status, "Execution_Status_Detail": args.statusDetail.replace('\\n','\n') } - entities = run_table.insert([run_data]) + entities = run_table.insert([run_data], add_system_defaults=False, defaults={"RID", "RCT", "RMT"}) rid = entities[0]["RID"] else: run_data = { @@ -58,4 +66,4 @@ if __name__ == '__main__': cli.remove_options(["--config-file"]) host = args.host credentials = {"cookie": args.cookie} - main(host, 2, credentials) \ No newline at end of file + main(host, 2, credentials) diff --git a/workflow/scripts/upload_input_bag.py b/workflow/scripts/upload_input_bag.py index ab4d338074ffec3098667dcf2817041e01ded8bd..ee10cbff8595f8ec5cbe975c133d70a71f4c4897 100644 --- a/workflow/scripts/upload_input_bag.py +++ b/workflow/scripts/upload_input_bag.py @@ -1,3 +1,11 @@ +#!/usr/bin/env python3 +#upload_input_bag.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* + import argparse from deriva.core import ErmrestCatalog, get_credential, BaseCLI import sys @@ -31,7 +39,7 @@ def main(hostname, catalog_number, credential): "Bag_Type": "Replicate_Input_Seq" } - entities = inputBag_table.insert([inputBag_data]) + entities = inputBag_table.insert([inputBag_data], add_system_defaults=False, defaults={"RID", "RCT", "RMT"}) rid = entities[0]["RID"] print(rid) @@ -43,4 +51,4 @@ if __name__ == '__main__': cli.remove_options(["--config-file"]) host = args.host credential = {"cookie": args.cookie} - main(host, 2, credential) \ No newline at end of file + main(host, 2, credential) diff --git a/workflow/scripts/upload_output_bag.py b/workflow/scripts/upload_output_bag.py index e1e1fc1a7fc59e2b003f3c6602f06182c9a3b054..7bd785d3d9ef188b3f4ad05fbf7a03764eb868df 100644 --- a/workflow/scripts/upload_output_bag.py +++ b/workflow/scripts/upload_output_bag.py @@ -1,3 +1,11 @@ +#!/usr/bin/env python3 +#upload_output_bag.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* + import argparse from deriva.core import ErmrestCatalog, get_credential, BaseCLI import sys @@ -34,7 +42,7 @@ def main(hostname, catalog_number, credential): "Notes": args.notes, "Bag_Type": "mRNA_Replicate_Analysis" } - entities = outputBag_table.insert([outputBag_data]) + entities = outputBag_table.insert([outputBag_data], add_system_defaults=False, defaults={"RID", "RCT", "RMT"}) rid = entities[0]["RID"] else: @@ -42,7 +50,7 @@ def main(hostname, catalog_number, credential): "RID": args.update, "Execution_Run": args.executionRunRID } - entities = outputBag_table.insert([outputBag_data]) + entities = outputBag_table.insert([outputBag_data], add_system_defaults=False, defaults={"RID", "RCT", "RMT"}) rid = entities[0]["RID"] print(rid) @@ -54,4 +62,4 @@ if __name__ == '__main__': cli.remove_options(["--config-file"]) host = args.host credential = {"cookie": args.cookie} - main(host, 2, credential) \ No newline at end of file + main(host, 2, credential) diff --git a/workflow/scripts/upload_qc.py b/workflow/scripts/upload_qc.py index 29fac063d9812ad05877d3e8f8f0d865d52eca14..e48d770ea28ebf333b5721676a097b83eabeb492 100644 --- a/workflow/scripts/upload_qc.py +++ b/workflow/scripts/upload_qc.py @@ -1,3 +1,11 @@ +#!/usr/bin/env python3 +#upload_qc.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* + import argparse from deriva.core import ErmrestCatalog, get_credential, BaseCLI import sys @@ -37,14 +45,14 @@ def main(hostname, catalog_number, credential): "Median_TIN": args.tin, "Notes": args.notes } - entities = run_table.insert([run_data]) + entities = run_table.insert([run_data], add_system_defaults=False, defaults={"RID", "RCT", "RMT"}) rid = entities[0]["RID"] elif args.update == "E": run_data = { "Execution_Run": args.executionRunRID, "Replicate": args.repRID } - entities = run_table.insert([run_data]) + entities = run_table.insert([run_data], add_system_defaults=False, defaults={"RID", "RCT", "RMT"}) rid = entities[0]["RID"] else: run_data = { @@ -72,4 +80,4 @@ if __name__ == '__main__': cli.remove_options(["--config-file"]) host = args.host credentials = {"cookie": args.cookie} - main(host, 2, credentials) \ No newline at end of file + main(host, 2, credentials) diff --git a/workflow/scripts/utils.py b/workflow/scripts/utils.py index 548b84c0642ee1479c1ac2e968ba1cd1aa9ed660..dc49b345661edf88964a3c3eb491e3f9e17feed9 100644 --- a/workflow/scripts/utils.py +++ b/workflow/scripts/utils.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#utils.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import shlex import logging diff --git a/workflow/tests/test_alignReads.py b/workflow/tests/test_alignReads.py index 06429a5b8c11daa539499fe1460ef34085031793..4e0b81c0814d2f14ab0ea612b66de544ae2dcec3 100644 --- a/workflow/tests/test_alignReads.py +++ b/workflow/tests/test_alignReads.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#test_alignReads.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import pytest import pandas as pd diff --git a/workflow/tests/test_completion.py b/workflow/tests/test_completion.py index 25a9941de634d36b84ad750c5968fa75009dfd27..fefa9b9a435f705a81729eb4ff18178461dd430b 100644 --- a/workflow/tests/test_completion.py +++ b/workflow/tests/test_completion.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#test_completion.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import pytest import pandas as pd @@ -12,4 +18,4 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ @pytest.mark.completionMultiqc def test_multiqcExist(filename): assert os.path.exists(os.path.join( - test_output_path, filename)) \ No newline at end of file + test_output_path, filename)) diff --git a/workflow/tests/test_consistency.py b/workflow/tests/test_consistency.py index aa04f19bd23e3749532b87b598179b8f98b2218b..568589f68b857aa9c71606a74601e0ec5690a863 100644 --- a/workflow/tests/test_consistency.py +++ b/workflow/tests/test_consistency.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#test_consistency.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import pytest import pandas as pd diff --git a/workflow/tests/test_dataQC.py b/workflow/tests/test_dataQC.py index 55df66deaeda6dac18ea26455dd1e3948ceb28ba..ec4409a4333b78cb9d68f1f1cf0be7bcb36a14b7 100644 --- a/workflow/tests/test_dataQC.py +++ b/workflow/tests/test_dataQC.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#test_dataQC.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import pytest import pandas as pd diff --git a/workflow/tests/test_dedupReads.py b/workflow/tests/test_dedupReads.py index 15e227d4586334721257bc6382d60cf0709bac62..ca299cdcc2bd1c335b26dfaca796047dc80e3e2e 100644 --- a/workflow/tests/test_dedupReads.py +++ b/workflow/tests/test_dedupReads.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#test_dedupReads.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import pytest import pandas as pd diff --git a/workflow/tests/test_downsampleData.py b/workflow/tests/test_downsampleData.py index 6d98ad656b0bcb0a3e8aee5507149cdcf3cec5f0..1fc9f17a0c9f5084f7d7b35b98ecdb1b8b76e46a 100644 --- a/workflow/tests/test_downsampleData.py +++ b/workflow/tests/test_downsampleData.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#test_downsampleData.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import pytest import pandas as pd diff --git a/workflow/tests/test_fastqc.py b/workflow/tests/test_fastqc.py index 07e76108fbfc92f945060d8e5d1e1ea8f74e6a4a..86ae3ce5cd56aacb38b62bf547125e6f61fb20ba 100644 --- a/workflow/tests/test_fastqc.py +++ b/workflow/tests/test_fastqc.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#test_fastqc.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import pytest import pandas as pd diff --git a/workflow/tests/test_getBag.py b/workflow/tests/test_getBag.py index 23bfc0ea50c260a2f5c4cbf62321c066b5743ac2..76f4c6ab1285bfad5ff8da590bbd8bc3c49b8566 100644 --- a/workflow/tests/test_getBag.py +++ b/workflow/tests/test_getBag.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#test_getBag.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import pytest import pandas as pd diff --git a/workflow/tests/test_getData.py b/workflow/tests/test_getData.py index 596a120abe904eac8f3e0ad871c9f8c03a6cba5f..f89d9c97003aa278476ea536fa49c02d440bb2b5 100644 --- a/workflow/tests/test_getData.py +++ b/workflow/tests/test_getData.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#test_getData.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import pytest import pandas as pd diff --git a/workflow/tests/test_inferMetadata.py b/workflow/tests/test_inferMetadata.py index 7485163631e2604ac2d5477a5c27b2fc9b235b44..e10be1734129e592a9f7d6b23254ac0535106330 100644 --- a/workflow/tests/test_inferMetadata.py +++ b/workflow/tests/test_inferMetadata.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#test_inferMetadata.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import pytest import pandas as pd diff --git a/workflow/tests/test_makeBigWig.py b/workflow/tests/test_makeBigWig.py index 273b2cdbb892a464a26b152db2c5d5c0a46922bf..2b72fc53604b7b28b9239235f4b20b32d0ed0421 100644 --- a/workflow/tests/test_makeBigWig.py +++ b/workflow/tests/test_makeBigWig.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#test_makeBigWig.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import pytest import pandas as pd diff --git a/workflow/tests/test_makeFeatureCounts.py b/workflow/tests/test_makeFeatureCounts.py index 43e6810482d6131b064b3604c95e89e9296db603..2aa54b9d3742e18b074b84d7314f6938460f41c3 100644 --- a/workflow/tests/test_makeFeatureCounts.py +++ b/workflow/tests/test_makeFeatureCounts.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#test_makeFeatureCounts.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import pytest import pandas as pd diff --git a/workflow/tests/test_outputBag.py b/workflow/tests/test_outputBag.py index c73e6474efdb9093b0cc66c00b220426be707690..a633294aef9bbe96c48b734571775eee7e48bf37 100644 --- a/workflow/tests/test_outputBag.py +++ b/workflow/tests/test_outputBag.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#test_outputBag.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import pytest import pandas as pd diff --git a/workflow/tests/test_parseMetadata.py b/workflow/tests/test_parseMetadata.py index 738f5ec66ee4e08d4e64400da719b759a7876a37..1db3a3141683c28820e33731150ba6eb83a7f999 100644 --- a/workflow/tests/test_parseMetadata.py +++ b/workflow/tests/test_parseMetadata.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#test_parseMetadata.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import pytest import pandas as pd diff --git a/workflow/tests/test_seqwho.py b/workflow/tests/test_seqwho.py index 051cc4b379bc2378b2effff22f4737592d9b54cd..c35d119a541bd7a5d7777bc77e565bfcc1da59d9 100644 --- a/workflow/tests/test_seqwho.py +++ b/workflow/tests/test_seqwho.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#test_seqwho.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import pytest import pandas as pd diff --git a/workflow/tests/test_trimData.py b/workflow/tests/test_trimData.py index a0938e756715fb30254e5c72fee4cd38bffec330..fe7072a8039b6efb2291d23ebcb20b6444ecfb30 100644 --- a/workflow/tests/test_trimData.py +++ b/workflow/tests/test_trimData.py @@ -1,4 +1,10 @@ #!/usr/bin/env python3 +#test_trimData.py +#* +#* -------------------------------------------------------------------------- +#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE) +#* -------------------------------------------------------------------------- +#* import pytest import pandas as pd