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Per-sample logging #13

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Commits on Jul 19, 2024

  1. Per-sample logging 

    .out and .err files output seperately for each sample
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Commits on Jul 25, 2024

  1. Create snakefile 

    Snakefile taking csv containing sample names (ID), and forward and reverse read paths as input
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  2. Create config.yaml

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Commits on Jul 30, 2024

  1. accept samples.csv file and output to HPC scratch space

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  2. Update config.yaml

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Commits on Jul 31, 2024

  1. Update config.yaml

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  2. Create BGE_test_amples.csv

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  3. Rename BGE_test_amples.csv to BGE_test_samples.csv

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  4. Create BOLD_output_mge_fetch_BGE_test_data.csv

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  5. Create config2.yaml

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  6. Delete snakemake/protein_reference_file: ". directory

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  7. Create config2.yaml

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  8. Update snakefile

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  9. Update snakefile

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  10. Create README.md

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  11. Create snakemake.sh

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  12. Update README.md

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  13. Update snakefile

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Commits on Aug 1, 2024

  1. Update snakefile 

    Working snakefile that takes a samples_file.csv as input, and outputs to a {gene} dir in the snakemake dir.
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  2. Create Snakefile2 

    Broken snakefile that is intended to take a samples_file.csv that also contains paths to specific references to run each sample against.
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  3. Update config2.yaml

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Commits on Aug 2, 2024

  1. Update README.md

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  2. Update README.md

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  3. Update README.md

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  4. Update Snakefile2

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  5. Update README.md

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  6. Create BGE_test_samples_all.csv

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  7. Rename config2.yaml to config3.yaml

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  8. Create config2.yaml

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  9. Create config2.yaml

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  10. Create snakemake2.sh

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  11. Create snakemake3.sh

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  12. Rename Snakefile2 to Snakefile3

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  13. Create Snakefile2

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  14. Create Snakefile2

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  15. Rename snakefile to Snakefile

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  16. Update Snakefile2

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  17. Update Snakefile

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  18. Update Snakefile

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Commits on Aug 7, 2024

  1. Create 1_gene_fetch.py

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  2. Update BGE_test_samples.csv

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  3. Update and rename BOLD_output_mge_fetch_BGE_test_data.csv to gene_fet… 

    …ch_BGE_test_data
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  4. Delete snakemake/BGE_test_samples_all.csv

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  5. Delete snakemake/snakemake3.sh

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  6. Delete snakemake/snakemake2.sh

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  7. Delete snakemake/Snakefile3

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  8. Delete snakemake/config3.yaml

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  9. Update config2.yaml

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  10. Update config.yaml

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  11. Update Snakefile

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  12. Update README.md

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  13. Update README.md

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  14. Update README.md

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  15. Update README.md

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  16. Update Snakefile

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  17. Update config.yaml

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  18. Update Snakefile2

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  19. Update README.md

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  20. Create insecta_cox1.fasta

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  21. Create BSNHM011-24.fasta

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  22. Add files via upload

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  23. Update gene_fetch_BGE_test_data

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  24. Update BGE_test_samples.csv

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  25. Create WK-3860-BGE-0001-A10_S87_L006_R1_001.fastq.gz

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  26. Delete snakemake/seq_data directory

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  27. Update README.md

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  28. Update README.md

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  29. Delete example-analysis-with-Snakemake-workflow-using-SRA-files-as-in… 

    …put directory
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  30. Add files via upload

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  31. Update README.md

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  32. Update README.md

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  33. Update 5_mge_stats-snakemake.py

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Commits on Aug 9, 2024

  1. Update 4_mge_tidy-snakemake.py 

    Rename sequence headers prior to concatenation.
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Commits on Aug 12, 2024

  1. Rename 4_mge_tidy-snakemake.py to 3_mge_tidy-snakemake.py

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  2. Rename 5_mge_stats-snakemake.py to 3_mge_stats-snakemake.py

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  3. Update and rename 3_mge_stats-snakemake.py to 4_mge_stats-snakemake.py

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  4. Update and rename Snakefile2 to 2_snakefile-genefetch

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  5. Update and rename config2.yaml to config-genefetch.yaml

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  6. Update and rename config.yaml to config-insecta.yaml

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  7. Update and rename Snakefile to 2_snakefile-insecta

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  8. Update 2_snakefile-genefetch

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  9. Update README.md

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  10. Rename gene_fetch_BGE_test_data to gene_fetch_BGE_test_data.csv

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  11. Update README.md

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  12. Update README.md

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  13. Update README.md

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  14. Update README.md

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  15. Update 2_snakefile-insecta

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  16. Merge pull request #1 from bge-barcoding/main 

    snakemake updates for BGE
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Commits on Aug 23, 2024

  1. Update 1_gene_fetch.py 

    Validates the taxonomy of returned protein sequence against BOLD taxonomic ranks
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Commits on Aug 27, 2024

  1. Update config-genefetch.yaml

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  2. Update 2_snakefile-genefetch

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  3. Delete Snakefile2

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  4. Delete config2.yaml

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Commits on Aug 28, 2024

  1. Update README.md

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  2. Create BOLD_output-test_data.csv

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  3. Update snakemake.sh

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  4. Create mge_env.yaml

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  5. Update README.md

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  6. Update 4_mge_stats-snakemake.py

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Commits on Aug 30, 2024

  1. Update and rename 2_snakefile-genefetch to snakefile-genefetch 

    Added mge_tidy and mge_stats functionality to snakefile
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  2. Update README.md

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  3. Update and rename 2_snakefile-insecta to snakefile_genefetch-fastpmerge

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  4. Update 4_mge_stats-snakemake.py 

    Removed slow biopython BLASTn functionality.
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  5. Update 1_gene_fetch.py 

    Added validation of taxonomy for returned protein reference sequence
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  6. Delete snakemake/protein_references directory

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  7. Rename BSNHM011-24.fasta to BSNHM011-24.fasta

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  8. Rename BSNHM038-24.fasta to BSNHM038-24.fasta

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  9. Rename BSNHM046-24.fasta to BSNHM046-24.fasta

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  10. Rename BSNHM050-24.fasta to BSNHM050-24.fasta

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  11. Rename BSNHM059-24.fasta to BSNHM059-24.fasta

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  15. Rename BSNHM133-24.fasta to BSNHM133-24.fasta

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  16. Rename BSNHM141-24.fasta to BSNHM141-24.fasta

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  17. Rename BSNHM154-24.fasta to BSNHM154-24.fasta

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  18. Rename BSNHM186-24.fasta to BSNHM186-24.fasta

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  19. Rename snakemake/gene_fetch_BGE_test_data.csv to snakemake/protein_re… 

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  24. Merge pull request #2 from bge-barcoding/main 

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  2. Merge pull request #3 from bge-barcoding/main 

    Updates to snakefile etc
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  1. Create Snakefile-contam_refs

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  13. Rename Snakefile-contam_refs to snakefile-contam_refs

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    SchistoDan authored Dec 3, 2024
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